Starting phenix.real_space_refine on Sat Feb 17 20:49:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzw_20538/02_2024/6pzw_20538.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzw_20538/02_2024/6pzw_20538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzw_20538/02_2024/6pzw_20538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzw_20538/02_2024/6pzw_20538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzw_20538/02_2024/6pzw_20538.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzw_20538/02_2024/6pzw_20538.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.143 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 124 5.16 5 C 12304 2.51 5 N 3379 2.21 5 O 3971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19778 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3054 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 366} Chain: "I" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "K" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 118} Chain: "D" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3054 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 366} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "F" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 118} Chain: "G" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "J" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 118} Chain: "C" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3054 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 366} Chain: "B" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3054 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 366} Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 118} 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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: "S" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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: "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: "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: "C" 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: "B" 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: 10.20, per 1000 atoms: 0.52 Number of scatterers: 19778 At special positions: 0 Unit cell: (167.89, 167.89, 88.58, 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 124 16.00 O 3971 8.00 N 3379 7.00 C 12304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.04 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=1.82 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.04 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=2.03 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.03 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=1.82 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=1.82 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.04 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.04 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=1.82 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 N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN P 4 " - " MAN P 5 " " MAN P 5 " - " MAN P 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " BMA P 3 " - " MAN P 4 " " MAN P 7 " - " MAN P 8 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA S 3 " - " MAN S 4 " " MAN S 7 " - " MAN S 8 " ALPHA1-6 " BMA N 3 " - " MAN N 7 " " MAN N 7 " - " MAN N 9 " " BMA P 3 " - " MAN P 7 " " MAN P 7 " - " MAN P 9 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 9 " " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 9 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG 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-ASN " NAG B1301 " - " ASN B 86 " " NAG C1301 " - " ASN C 86 " " NAG D1301 " - " ASN D 86 " " NAG M 1 " - " ASN A 146 " " NAG N 1 " - " ASN A 200 " " NAG O 1 " - " ASN D 146 " " NAG P 1 " - " ASN D 200 " " NAG Q 1 " - " ASN C 146 " " NAG R 1 " - " ASN C 200 " " NAG S 1 " - " ASN B 200 " " NAG T 1 " - " ASN B 146 " Time building additional restraints: 7.92 Conformation dependent library (CDL) restraints added in 3.2 seconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4496 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 52 sheets defined 6.0% alpha, 44.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 91 removed outlier: 6.905A pdb=" N GLY A 90 " --> pdb=" O TYR A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.713A pdb=" N SER A 445 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA A 420 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 125 removed outlier: 4.579A pdb=" N LEU A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR A 138 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 158 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 184 removed outlier: 5.645A pdb=" N TYR A 207 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 236 through 244 removed outlier: 7.492A pdb=" N THR A 252 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER A 267 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 254 " --> pdb=" O TRP A 265 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR A 256 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 283 removed outlier: 4.605A pdb=" N CYS A 278 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR A 290 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS A 280 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR A 288 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY A 282 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.894A pdb=" N SER A 372 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY I 13 " --> pdb=" O THR I 105 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP I 35 " --> pdb=" O MET I 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY I 13 " --> pdb=" O THR I 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR I 95A" --> pdb=" O THR I 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS K 92 " --> pdb=" O TRP K 103 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TRP K 103 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS K 94 " --> pdb=" O ASP K 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 90 through 91 removed outlier: 6.905A pdb=" N GLY D 90 " --> pdb=" O TYR D 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.713A pdb=" N SER D 445 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA D 420 " --> pdb=" O SER D 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 115 through 125 removed outlier: 4.579A pdb=" N LEU D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR D 138 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU D 158 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 179 through 184 removed outlier: 5.645A pdb=" N TYR D 207 " --> pdb=" O PRO D 211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 236 through 244 removed outlier: 7.492A pdb=" N THR D 252 " --> pdb=" O SER D 267 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER D 267 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE D 254 " --> pdb=" O TRP D 265 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP D 265 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR D 256 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 276 through 283 removed outlier: 4.605A pdb=" N CYS D 278 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR D 290 " --> pdb=" O CYS D 278 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS D 280 " --> pdb=" O THR D 288 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR D 288 " --> pdb=" O CYS D 280 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY D 282 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 353 through 354 removed outlier: 6.894A pdb=" N SER D 372 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU D 399 " --> pdb=" O SER D 372 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN D 393 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY E 13 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP E 35 " --> pdb=" O MET E 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY E 13 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR E 95A" --> pdb=" O THR E 92 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AC6, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY G 13 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP G 35 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY G 13 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR G 95A" --> pdb=" O THR G 92 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY J 33 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 90 through 91 removed outlier: 6.905A pdb=" N GLY C 90 " --> pdb=" O TYR C 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.713A pdb=" N SER C 445 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS C 102 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA C 420 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 115 through 125 removed outlier: 4.579A pdb=" N LEU C 115 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR C 138 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN C 136 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU C 158 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 179 through 184 removed outlier: 5.645A pdb=" N TYR C 207 " --> pdb=" O PRO C 211 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 236 through 244 removed outlier: 7.492A pdb=" N THR C 252 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER C 267 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE C 254 " --> pdb=" O TRP C 265 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP C 265 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR C 256 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 276 through 283 removed outlier: 4.605A pdb=" N CYS C 278 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR C 290 " --> pdb=" O CYS C 278 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS C 280 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 288 " --> pdb=" O CYS C 280 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY C 282 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 353 through 354 removed outlier: 6.894A pdb=" N SER C 372 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU C 399 " --> pdb=" O SER C 372 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 393 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 90 through 91 removed outlier: 6.905A pdb=" N GLY B 90 " --> pdb=" O TYR B 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.713A pdb=" N SER B 445 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA B 420 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 115 through 125 removed outlier: 4.579A pdb=" N LEU B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR B 138 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU B 158 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 179 through 184 removed outlier: 5.645A pdb=" N TYR B 207 " --> pdb=" O PRO B 211 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 236 through 244 removed outlier: 7.492A pdb=" N THR B 252 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER B 267 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 254 " --> pdb=" O TRP B 265 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR B 256 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 276 through 283 removed outlier: 4.605A pdb=" N CYS B 278 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR B 290 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS B 280 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR B 288 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY B 282 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.894A pdb=" N SER B 372 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU B 399 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 393 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY L 13 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY L 13 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR L 95A" --> pdb=" O THR L 92 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AF5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1620 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: 6.52 Time building geometry restraints manager: 8.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4736 1.32 - 1.46: 6456 1.46 - 1.59: 8906 1.59 - 1.73: 16 1.73 - 1.86: 144 Bond restraints: 20258 Sorted by residual: bond pdb=" C1 NAG D1301 " pdb=" O5 NAG D1301 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.542 -0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.542 -0.136 2.00e-02 2.50e+03 4.65e+01 ... (remaining 20253 not shown) Histogram of bond angle deviations from ideal: 95.18 - 103.01: 216 103.01 - 110.83: 7128 110.83 - 118.65: 8867 118.65 - 126.48: 10978 126.48 - 134.30: 368 Bond angle restraints: 27557 Sorted by residual: angle pdb=" C ASP D 330 " pdb=" N PRO D 331 " pdb=" CA PRO D 331 " ideal model delta sigma weight residual 120.52 128.51 -7.99 9.90e-01 1.02e+00 6.51e+01 angle pdb=" C ASP B 330 " pdb=" N PRO B 331 " pdb=" CA PRO B 331 " ideal model delta sigma weight residual 120.52 128.51 -7.99 9.90e-01 1.02e+00 6.51e+01 angle pdb=" C ASP C 330 " pdb=" N PRO C 331 " pdb=" CA PRO C 331 " ideal model delta sigma weight residual 120.52 128.51 -7.99 9.90e-01 1.02e+00 6.51e+01 angle pdb=" C ASP A 330 " pdb=" N PRO A 331 " pdb=" CA PRO A 331 " ideal model delta sigma weight residual 120.52 128.51 -7.99 9.90e-01 1.02e+00 6.51e+01 angle pdb=" N GLN A 226 " pdb=" CA GLN A 226 " pdb=" C GLN A 226 " ideal model delta sigma weight residual 111.82 121.15 -9.33 1.16e+00 7.43e-01 6.46e+01 ... (remaining 27552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.53: 12190 21.53 - 43.06: 291 43.06 - 64.59: 66 64.59 - 86.12: 32 86.12 - 107.65: 20 Dihedral angle restraints: 12599 sinusoidal: 5515 harmonic: 7084 Sorted by residual: dihedral pdb=" CB CYS D 318 " pdb=" SG CYS D 318 " pdb=" SG CYS D 337 " pdb=" CB CYS D 337 " ideal model delta sinusoidal sigma weight residual 93.00 130.37 -37.37 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 130.37 -37.37 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CB CYS B 318 " pdb=" SG CYS B 318 " pdb=" SG CYS B 337 " pdb=" CB CYS B 337 " ideal model delta sinusoidal sigma weight residual 93.00 130.37 -37.37 1 1.00e+01 1.00e-02 1.97e+01 ... (remaining 12596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2292 0.101 - 0.203: 648 0.203 - 0.304: 144 0.304 - 0.405: 15 0.405 - 0.507: 8 Chirality restraints: 3107 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 -2.54 0.14 2.00e-02 2.50e+03 5.05e+01 chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.05e+01 chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.05e+01 ... (remaining 3104 not shown) Planarity restraints: 3498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " -0.096 2.00e-02 2.50e+03 8.14e-02 8.28e+01 pdb=" C7 NAG T 2 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " 0.021 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " 0.130 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 456 " 0.070 2.00e-02 2.50e+03 3.45e-02 2.98e+01 pdb=" CG TRP A 456 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 456 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 456 " -0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP A 456 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 456 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP A 456 " -0.045 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 456 " 0.029 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 456 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 456 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 456 " -0.070 2.00e-02 2.50e+03 3.45e-02 2.98e+01 pdb=" CG TRP B 456 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 456 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B 456 " 0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP B 456 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 456 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP B 456 " 0.045 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 456 " -0.029 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 456 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 456 " -0.041 2.00e-02 2.50e+03 ... (remaining 3495 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 8545 2.90 - 3.40: 17140 3.40 - 3.90: 35063 3.90 - 4.40: 42355 4.40 - 4.90: 69527 Nonbonded interactions: 172630 Sorted by model distance: nonbonded pdb=" OH TYR A 354 " pdb=" O CYS A 421 " model vdw 2.401 2.440 nonbonded pdb=" OH TYR B 354 " pdb=" O CYS B 421 " model vdw 2.401 2.440 nonbonded pdb=" OH TYR D 354 " pdb=" O CYS D 421 " model vdw 2.401 2.440 nonbonded pdb=" OH TYR C 354 " pdb=" O CYS C 421 " model vdw 2.401 2.440 nonbonded pdb=" N ASP C 416 " pdb=" OD1 ASP C 416 " model vdw 2.450 2.520 ... (remaining 172625 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' and resid 82 through 468) selection = (chain 'C' and resid 82 through 468) selection = (chain 'D' and resid 82 through 468) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'S' } 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: 1.730 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: 8.190 Check model and map are aligned: 0.290 Set scattering table: 0.200 Process input model: 52.010 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 : 0.020 0.138 20258 Z= 1.348 Angle : 1.731 11.208 27557 Z= 1.144 Chirality : 0.100 0.507 3107 Planarity : 0.009 0.081 3487 Dihedral : 11.602 107.652 7971 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.12 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.16), residues: 2448 helix: -2.49 (0.45), residues: 48 sheet: 1.24 (0.17), residues: 852 loop : 0.70 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.009 TRP B 456 HIS 0.010 0.002 HIS A 274 PHE 0.036 0.008 PHE A 131 TYR 0.060 0.009 TYR B 155 ARG 0.010 0.001 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 2.527 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 outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 1.3291 time to fit residues: 522.9387 Evaluate side-chains 144 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN I 53 ASN I 79 GLN K 30 ASN K 81 GLN K 105 GLN D 83 ASN E 53 ASN E 79 GLN F 30 ASN F 81 GLN F 105 GLN G 53 ASN G 79 GLN J 30 ASN J 81 GLN J 105 GLN C 83 ASN B 83 ASN L 53 ASN L 79 GLN H 30 ASN H 81 GLN H 105 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20258 Z= 0.208 Angle : 0.608 7.986 27557 Z= 0.323 Chirality : 0.045 0.165 3107 Planarity : 0.004 0.034 3487 Dihedral : 9.539 79.928 3651 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.33 % Allowed : 1.47 % Favored : 98.20 % Rotamer: Outliers : 1.13 % Allowed : 8.08 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2448 helix: -4.37 (0.15), residues: 24 sheet: 0.93 (0.17), residues: 876 loop : 0.38 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 206 HIS 0.005 0.001 HIS F 35 PHE 0.011 0.002 PHE A 410 TYR 0.018 0.002 TYR B 121 ARG 0.003 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 236 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 79 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7941 (mm-40) REVERT: E 79 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7941 (mm-40) REVERT: G 79 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7943 (mm-40) REVERT: L 79 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7939 (mm-40) outliers start: 24 outliers final: 8 residues processed: 248 average time/residue: 1.1611 time to fit residues: 331.1113 Evaluate side-chains 180 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain H residue 105 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 148 optimal weight: 0.0170 chunk 60 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN K 76 ASN K 105 GLN D 441 ASN F 76 ASN F 105 GLN J 76 ASN J 105 GLN C 441 ASN B 441 ASN H 76 ASN H 105 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20258 Z= 0.209 Angle : 0.557 6.682 27557 Z= 0.296 Chirality : 0.043 0.166 3107 Planarity : 0.004 0.040 3487 Dihedral : 8.807 72.345 3651 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.78 % Favored : 96.90 % Rotamer: Outliers : 1.88 % Allowed : 11.09 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2448 helix: -4.24 (0.13), residues: 24 sheet: 0.82 (0.17), residues: 900 loop : 0.28 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 206 HIS 0.004 0.001 HIS J 35 PHE 0.011 0.002 PHE B 410 TYR 0.020 0.002 TYR B 121 ARG 0.004 0.000 ARG K 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 236 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8449 (ttm170) REVERT: A 385 ASP cc_start: 0.7522 (t0) cc_final: 0.7252 (t70) REVERT: D 292 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8450 (ttm170) REVERT: D 385 ASP cc_start: 0.7520 (t0) cc_final: 0.7251 (t70) REVERT: C 292 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8451 (ttm170) REVERT: C 385 ASP cc_start: 0.7517 (t0) cc_final: 0.7249 (t70) REVERT: B 292 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8450 (ttm170) REVERT: B 385 ASP cc_start: 0.7515 (t0) cc_final: 0.7247 (t70) outliers start: 40 outliers final: 20 residues processed: 256 average time/residue: 1.2061 time to fit residues: 355.1020 Evaluate side-chains 208 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 416 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN J 105 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20258 Z= 0.425 Angle : 0.670 6.836 27557 Z= 0.348 Chirality : 0.047 0.164 3107 Planarity : 0.005 0.046 3487 Dihedral : 9.086 71.734 3651 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.78 % Favored : 96.90 % Rotamer: Outliers : 4.14 % Allowed : 10.10 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2448 helix: -4.18 (0.13), residues: 24 sheet: 0.55 (0.16), residues: 924 loop : 0.15 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 456 HIS 0.010 0.003 HIS D 98 PHE 0.013 0.002 PHE A 410 TYR 0.027 0.002 TYR C 121 ARG 0.008 0.001 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 192 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8310 (ttm170) REVERT: A 385 ASP cc_start: 0.7646 (t0) cc_final: 0.7427 (t70) REVERT: I 79 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7311 (mm-40) REVERT: D 292 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8315 (ttm170) REVERT: D 385 ASP cc_start: 0.7646 (t0) cc_final: 0.7426 (t70) REVERT: E 79 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7311 (mm-40) REVERT: G 79 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7316 (mm-40) REVERT: C 292 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8213 (ttm170) REVERT: C 385 ASP cc_start: 0.7645 (t0) cc_final: 0.7427 (t70) REVERT: B 292 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8212 (ttm170) REVERT: B 385 ASP cc_start: 0.7641 (t0) cc_final: 0.7422 (t70) REVERT: L 79 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7317 (mm-40) outliers start: 88 outliers final: 52 residues processed: 244 average time/residue: 1.1783 time to fit residues: 330.5356 Evaluate side-chains 240 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 180 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 105 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 95 optimal weight: 0.0370 chunk 197 optimal weight: 0.8980 chunk 160 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 208 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN J 105 GLN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20258 Z= 0.172 Angle : 0.537 5.440 27557 Z= 0.280 Chirality : 0.043 0.163 3107 Planarity : 0.004 0.047 3487 Dihedral : 8.442 65.193 3651 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.29 % Favored : 97.39 % Rotamer: Outliers : 4.51 % Allowed : 10.71 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2448 helix: -4.07 (0.13), residues: 24 sheet: 0.78 (0.17), residues: 904 loop : 0.09 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 161 HIS 0.004 0.001 HIS F 35 PHE 0.010 0.001 PHE C 410 TYR 0.016 0.001 TYR B 121 ARG 0.004 0.000 ARG F 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 204 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8326 (ttm170) REVERT: A 385 ASP cc_start: 0.7542 (t0) cc_final: 0.7326 (t70) REVERT: I 27 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: D 292 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8331 (ttm170) REVERT: D 385 ASP cc_start: 0.7538 (t0) cc_final: 0.7323 (t70) REVERT: E 27 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7644 (m-30) REVERT: G 27 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: C 292 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8333 (ttm170) REVERT: C 385 ASP cc_start: 0.7539 (t0) cc_final: 0.7327 (t70) REVERT: B 292 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8332 (ttm170) REVERT: B 385 ASP cc_start: 0.7537 (t0) cc_final: 0.7324 (t70) REVERT: L 27 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7646 (m-30) outliers start: 96 outliers final: 64 residues processed: 264 average time/residue: 1.1196 time to fit residues: 341.5635 Evaluate side-chains 260 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 188 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 105 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 232 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 0.0770 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN K 105 GLN ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN F 105 GLN J 76 ASN J 105 GLN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 105 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20258 Z= 0.299 Angle : 0.568 5.502 27557 Z= 0.294 Chirality : 0.044 0.164 3107 Planarity : 0.004 0.049 3487 Dihedral : 8.511 65.984 3651 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.78 % Favored : 96.90 % Rotamer: Outliers : 4.14 % Allowed : 11.04 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2448 helix: -4.04 (0.14), residues: 24 sheet: 0.74 (0.17), residues: 904 loop : 0.06 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 161 HIS 0.006 0.002 HIS F 35 PHE 0.010 0.002 PHE C 410 TYR 0.020 0.002 TYR B 121 ARG 0.003 0.000 ARG J 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 188 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8283 (ttm170) REVERT: A 385 ASP cc_start: 0.7602 (t0) cc_final: 0.7349 (t70) REVERT: I 27 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: K 11 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8591 (t) REVERT: D 292 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8290 (ttm170) REVERT: D 385 ASP cc_start: 0.7603 (t0) cc_final: 0.7352 (t70) REVERT: E 27 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: F 11 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8590 (t) REVERT: G 27 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: J 11 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8589 (t) REVERT: C 292 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8290 (ttm170) REVERT: C 385 ASP cc_start: 0.7601 (t0) cc_final: 0.7348 (t70) REVERT: B 292 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8287 (ttm170) REVERT: B 385 ASP cc_start: 0.7600 (t0) cc_final: 0.7347 (t70) REVERT: L 27 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: H 11 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8594 (t) outliers start: 88 outliers final: 56 residues processed: 248 average time/residue: 1.1692 time to fit residues: 333.0935 Evaluate side-chains 245 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 177 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 92 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 chunk 144 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN J 105 GLN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20258 Z= 0.313 Angle : 0.581 5.368 27557 Z= 0.299 Chirality : 0.045 0.168 3107 Planarity : 0.004 0.049 3487 Dihedral : 8.549 66.193 3651 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.27 % Favored : 96.41 % Rotamer: Outliers : 4.32 % Allowed : 11.14 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2448 helix: -4.11 (0.12), residues: 24 sheet: 0.72 (0.17), residues: 908 loop : -0.03 (0.17), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 47 HIS 0.006 0.002 HIS F 35 PHE 0.011 0.002 PHE B 410 TYR 0.020 0.002 TYR A 121 ARG 0.004 0.000 ARG C 419 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 196 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8220 (ttm170) REVERT: A 385 ASP cc_start: 0.7556 (t0) cc_final: 0.7314 (t70) REVERT: I 27 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: K 11 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8603 (t) REVERT: D 292 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8239 (ttm170) REVERT: D 385 ASP cc_start: 0.7561 (t0) cc_final: 0.7316 (t70) REVERT: E 27 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: F 11 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8600 (t) REVERT: G 27 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: J 11 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8600 (t) REVERT: C 292 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8220 (ttm170) REVERT: C 385 ASP cc_start: 0.7557 (t0) cc_final: 0.7315 (t70) REVERT: B 292 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8219 (ttm170) REVERT: B 385 ASP cc_start: 0.7554 (t0) cc_final: 0.7313 (t70) REVERT: L 27 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7613 (m-30) REVERT: H 11 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8602 (t) outliers start: 92 outliers final: 60 residues processed: 256 average time/residue: 1.1581 time to fit residues: 340.8186 Evaluate side-chains 248 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 176 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20258 Z= 0.296 Angle : 0.581 9.712 27557 Z= 0.298 Chirality : 0.045 0.208 3107 Planarity : 0.004 0.050 3487 Dihedral : 8.582 65.659 3651 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.27 % Favored : 96.57 % Rotamer: Outliers : 4.14 % Allowed : 11.98 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2448 helix: -4.08 (0.13), residues: 24 sheet: 0.71 (0.17), residues: 908 loop : -0.08 (0.17), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 161 HIS 0.005 0.001 HIS K 35 PHE 0.012 0.002 PHE B 410 TYR 0.019 0.001 TYR D 121 ARG 0.003 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 189 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8180 (ttm170) REVERT: I 27 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7616 (m-30) REVERT: K 11 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8613 (t) REVERT: D 292 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8180 (ttm170) REVERT: E 27 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: F 11 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8612 (t) REVERT: G 27 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: J 11 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8611 (t) REVERT: C 292 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8180 (ttm170) REVERT: B 292 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8179 (ttm170) REVERT: L 27 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7616 (m-30) REVERT: H 11 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8612 (t) outliers start: 88 outliers final: 64 residues processed: 245 average time/residue: 1.1551 time to fit residues: 326.4266 Evaluate side-chains 255 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 179 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.6980 chunk 221 optimal weight: 3.9990 chunk 202 optimal weight: 0.0170 chunk 215 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN A 441 ASN ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 ASN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20258 Z= 0.155 Angle : 0.514 7.981 27557 Z= 0.265 Chirality : 0.043 0.169 3107 Planarity : 0.004 0.049 3487 Dihedral : 7.891 58.862 3651 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.22 % Rotamer: Outliers : 3.81 % Allowed : 12.55 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.17), residues: 2448 helix: -4.05 (0.13), residues: 24 sheet: 0.87 (0.17), residues: 916 loop : -0.06 (0.17), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 161 HIS 0.003 0.001 HIS J 35 PHE 0.013 0.001 PHE C 410 TYR 0.014 0.001 TYR D 121 ARG 0.002 0.000 ARG D 292 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 195 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8316 (ttm170) REVERT: K 11 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8602 (t) REVERT: D 292 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8319 (ttm170) REVERT: F 11 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8600 (t) REVERT: J 11 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8599 (t) REVERT: C 292 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8318 (ttm170) REVERT: B 292 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8345 (ttm170) REVERT: H 11 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8601 (t) outliers start: 81 outliers final: 49 residues processed: 248 average time/residue: 1.2165 time to fit residues: 345.1812 Evaluate side-chains 244 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 187 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 20258 Z= 0.476 Angle : 0.662 9.043 27557 Z= 0.339 Chirality : 0.048 0.197 3107 Planarity : 0.005 0.051 3487 Dihedral : 8.857 67.443 3651 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.00 % Favored : 95.67 % Rotamer: Outliers : 3.24 % Allowed : 13.44 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2448 helix: -4.07 (0.13), residues: 24 sheet: 0.60 (0.17), residues: 928 loop : -0.09 (0.17), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 456 HIS 0.009 0.002 HIS F 35 PHE 0.012 0.002 PHE A 410 TYR 0.022 0.002 TYR A 121 ARG 0.004 0.001 ARG D 419 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 180 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8091 (ttm170) REVERT: D 292 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8092 (ttm170) REVERT: C 292 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8116 (ttm170) REVERT: B 292 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8091 (ttm170) outliers start: 69 outliers final: 56 residues processed: 233 average time/residue: 1.2136 time to fit residues: 325.0785 Evaluate side-chains 232 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 172 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 195 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.087818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.072023 restraints weight = 27053.416| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 1.77 r_work: 0.2691 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20258 Z= 0.163 Angle : 0.537 7.512 27557 Z= 0.277 Chirality : 0.043 0.170 3107 Planarity : 0.004 0.049 3487 Dihedral : 8.197 60.343 3651 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.78 % Favored : 96.90 % Rotamer: Outliers : 3.05 % Allowed : 13.30 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2448 helix: -4.04 (0.13), residues: 24 sheet: 0.74 (0.17), residues: 912 loop : -0.09 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 161 HIS 0.003 0.001 HIS K 35 PHE 0.011 0.001 PHE B 410 TYR 0.015 0.001 TYR D 121 ARG 0.004 0.000 ARG H 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6391.55 seconds wall clock time: 115 minutes 11.19 seconds (6911.19 seconds total)