Starting phenix.real_space_refine on Wed Jun 18 08:22:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vi0_21208/06_2025/6vi0_21208.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vi0_21208/06_2025/6vi0_21208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vi0_21208/06_2025/6vi0_21208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vi0_21208/06_2025/6vi0_21208.map" model { file = "/net/cci-nas-00/data/ceres_data/6vi0_21208/06_2025/6vi0_21208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vi0_21208/06_2025/6vi0_21208.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 12987 2.51 5 N 3447 2.21 5 O 4251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20823 Number of models: 1 Model: "" Number of chains: 45 Chain: "B" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1044 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "G" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 744 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "H" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1039 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 9, 'TRANS': 119} Chain: "A" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1044 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "C" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 744 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "E" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1039 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 9, 'TRANS': 119} Chain: "F" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1044 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 744 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "K" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1039 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 9, 'TRANS': 119} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "f" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.82, per 1000 atoms: 0.66 Number of scatterers: 20823 At special positions: 0 Unit cell: (148.109, 143.816, 123.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 4251 8.00 N 3447 7.00 C 12987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.01 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.02 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 32 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 32 " - pdb=" SG CYS E 98 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.02 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.02 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 98 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN O 4 " - " MAN O 5 " " MAN P 4 " - " MAN P 5 " " MAN W 4 " - " MAN W 5 " " MAN X 4 " - " MAN X 5 " " MAN e 4 " - " MAN e 5 " " MAN f 4 " - " MAN f 5 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " MAN P 6 " - " MAN P 7 " " BMA R 3 " - " MAN R 6 " " MAN R 4 " - " MAN R 5 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " MAN X 6 " - " MAN X 7 " " BMA Z 3 " - " MAN Z 6 " " MAN Z 4 " - " MAN Z 5 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " " BMA h 3 " - " MAN h 6 " " MAN h 4 " - " MAN h 5 " ALPHA1-6 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 6 " " BMA P 3 " - " MAN P 6 " " MAN P 6 " - " MAN P 8 " " BMA R 3 " - " MAN R 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 6 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 8 " " BMA Z 3 " - " MAN Z 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 6 " " BMA f 3 " - " MAN f 6 " " MAN f 6 " - " MAN f 8 " " BMA h 3 " - " MAN h 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1611 " - " ASN A 611 " " NAG A1637 " - " ASN A 637 " " NAG B1611 " - " ASN B 611 " " NAG B1637 " - " ASN B 637 " " NAG C1088 " - " ASN C 88 " " NAG C1133 " - " ASN C 133 " " NAG C1156 " - " ASN C 156 " " NAG C1234 " - " ASN C 234 " " NAG C1301 " - " ASN C 301 " " NAG C1332 " - " ASN C 332 " " NAG C1339 " - " ASN C 339 " " NAG C1355 " - " ASN C 355 " " NAG C1392 " - " ASN C 392 " " NAG D1072 " - " ASN D 72 " " NAG F1611 " - " ASN F 611 " " NAG F1637 " - " ASN F 637 " " NAG G1088 " - " ASN G 88 " " NAG G1133 " - " ASN G 133 " " NAG G1156 " - " ASN G 156 " " NAG G1234 " - " ASN G 234 " " NAG G1301 " - " ASN G 301 " " NAG G1332 " - " ASN G 332 " " NAG G1339 " - " ASN G 339 " " NAG G1355 " - " ASN G 355 " " NAG G1392 " - " ASN G 392 " " NAG I1088 " - " ASN I 88 " " NAG I1133 " - " ASN I 133 " " NAG I1156 " - " ASN I 156 " " NAG I1234 " - " ASN I 234 " " NAG I1301 " - " ASN I 301 " " NAG I1332 " - " ASN I 332 " " NAG I1339 " - " ASN I 339 " " NAG I1355 " - " ASN I 355 " " NAG I1392 " - " ASN I 392 " " NAG J1072 " - " ASN J 72 " " NAG L1072 " - " ASN L 72 " " NAG M 1 " - " ASN G 160 " " NAG N 1 " - " ASN G 197 " " NAG O 1 " - " ASN G 262 " " NAG P 1 " - " ASN G 276 " " NAG Q 1 " - " ASN G 295 " " NAG R 1 " - " ASN G 363 " " NAG S 1 " - " ASN G 386 " " NAG T 1 " - " ASN G 448 " " NAG U 1 " - " ASN C 160 " " NAG V 1 " - " ASN C 197 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 276 " " NAG Y 1 " - " ASN C 295 " " NAG Z 1 " - " ASN C 363 " " NAG a 1 " - " ASN C 386 " " NAG b 1 " - " ASN C 448 " " NAG c 1 " - " ASN I 160 " " NAG d 1 " - " ASN I 197 " " NAG e 1 " - " ASN I 262 " " NAG f 1 " - " ASN I 276 " " NAG g 1 " - " ASN I 295 " " NAG h 1 " - " ASN I 363 " " NAG i 1 " - " ASN I 386 " " NAG j 1 " - " ASN I 448 " Time building additional restraints: 7.00 Conformation dependent library (CDL) restraints added in 3.0 seconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4470 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 48 sheets defined 18.2% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.255A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 593 removed outlier: 3.684A pdb=" N TRP B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 removed outlier: 4.032A pdb=" N GLY B 597 " --> pdb=" O GLY B 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 594 through 597' Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.597A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 639 removed outlier: 4.159A pdb=" N THR B 639 " --> pdb=" O SER B 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 636 through 639' Processing helix chain 'B' and resid 641 through 658 removed outlier: 4.293A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 63 Processing helix chain 'G' and resid 99 through 115 removed outlier: 3.597A pdb=" N THR G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.907A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 354 removed outlier: 3.701A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 482 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.865A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.733A pdb=" N GLN H 64 " --> pdb=" O ARG H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 4.254A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 593 removed outlier: 3.682A pdb=" N TRP A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 597 removed outlier: 4.032A pdb=" N GLY A 597 " --> pdb=" O GLY A 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 594 through 597' Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.597A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 639 removed outlier: 4.159A pdb=" N THR A 639 " --> pdb=" O SER A 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 636 through 639' Processing helix chain 'A' and resid 641 through 664 removed outlier: 4.293A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.597A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.907A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.699A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 482 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.865A pdb=" N ASP D 82 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 83' Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.732A pdb=" N GLN E 64 " --> pdb=" O ARG E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.256A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 593 removed outlier: 3.683A pdb=" N TRP F 571 " --> pdb=" O LYS F 567 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 597 removed outlier: 4.033A pdb=" N GLY F 597 " --> pdb=" O GLY F 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 594 through 597' Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.597A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 639 removed outlier: 4.159A pdb=" N THR F 639 " --> pdb=" O SER F 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 636 through 639' Processing helix chain 'F' and resid 641 through 658 removed outlier: 4.293A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 63 Processing helix chain 'I' and resid 99 through 115 removed outlier: 3.597A pdb=" N THR I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.907A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 354 removed outlier: 3.701A pdb=" N GLU I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 482 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.866A pdb=" N ASP J 82 " --> pdb=" O GLU J 79 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 79 through 83' Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.733A pdb=" N GLN K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 7.347A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.693A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.713A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'G' and resid 158 through 162 Processing sheet with id=AA8, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.586A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 271 through 273 removed outlier: 7.119A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.256A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.795A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU G 466 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 302 through 308 removed outlier: 6.643A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 423 through 424 removed outlier: 4.271A pdb=" N ILE G 424 " --> pdb=" O MET G 434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.635A pdb=" N TYR L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER L 65 " --> pdb=" O ASN L 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.811A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.572A pdb=" N GLN H 72 " --> pdb=" O THR H 77 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'H' and resid 49 through 52 removed outlier: 3.610A pdb=" N TRP H 50 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN H 58 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 603 through 609 removed outlier: 7.346A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.692A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.713A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AC4, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AC5, first strand: chain 'C' and resid 158 through 162 Processing sheet with id=AC6, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.587A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.120A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.254A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.795A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 466 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 302 through 308 removed outlier: 6.643A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 423 through 424 removed outlier: 4.168A pdb=" N ILE C 424 " --> pdb=" O MET C 434 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.635A pdb=" N TYR D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 65 " --> pdb=" O ASN D 72 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.813A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.571A pdb=" N GLN E 72 " --> pdb=" O THR E 77 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AD5, first strand: chain 'E' and resid 49 through 52 removed outlier: 3.610A pdb=" N TRP E 50 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN E 58 " --> pdb=" O TRP E 50 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 603 through 609 removed outlier: 7.347A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.692A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD9, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.713A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 129 through 130 Processing sheet with id=AE2, first strand: chain 'I' and resid 154 through 155 Processing sheet with id=AE3, first strand: chain 'I' and resid 158 through 162 Processing sheet with id=AE4, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.585A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 271 through 273 removed outlier: 7.118A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.256A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.795A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU I 466 " --> pdb=" O ILE I 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 302 through 308 removed outlier: 6.645A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 423 through 424 removed outlier: 4.089A pdb=" N ILE I 424 " --> pdb=" O MET I 434 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.635A pdb=" N TYR J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER J 65 " --> pdb=" O ASN J 72 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.812A pdb=" N ILE J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.571A pdb=" N GLN K 72 " --> pdb=" O THR K 77 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AF3, first strand: chain 'K' and resid 49 through 52 removed outlier: 3.610A pdb=" N TRP K 50 " --> pdb=" O ASN K 58 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.13 Time building geometry restraints manager: 8.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3554 1.32 - 1.45: 5923 1.45 - 1.57: 11589 1.57 - 1.69: 0 1.69 - 1.82: 186 Bond restraints: 21252 Sorted by residual: bond pdb=" N CYS G 201 " pdb=" CA CYS G 201 " ideal model delta sigma weight residual 1.463 1.392 0.071 1.27e-02 6.20e+03 3.11e+01 bond pdb=" CA SER I 199 " pdb=" CB SER I 199 " ideal model delta sigma weight residual 1.532 1.450 0.081 1.56e-02 4.11e+03 2.71e+01 bond pdb=" N CYS I 201 " pdb=" CA CYS I 201 " ideal model delta sigma weight residual 1.460 1.402 0.058 1.20e-02 6.94e+03 2.35e+01 bond pdb=" CA SER C 199 " pdb=" CB SER C 199 " ideal model delta sigma weight residual 1.532 1.451 0.081 1.68e-02 3.54e+03 2.35e+01 bond pdb=" CA SER G 199 " pdb=" CB SER G 199 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.69e-02 3.50e+03 2.05e+01 ... (remaining 21247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 27156 2.18 - 4.36: 1402 4.36 - 6.53: 217 6.53 - 8.71: 60 8.71 - 10.89: 19 Bond angle restraints: 28854 Sorted by residual: angle pdb=" C ASN I 156 " pdb=" CA ASN I 156 " pdb=" CB ASN I 156 " ideal model delta sigma weight residual 111.68 100.79 10.89 1.67e+00 3.59e-01 4.25e+01 angle pdb=" C ASN C 156 " pdb=" CA ASN C 156 " pdb=" CB ASN C 156 " ideal model delta sigma weight residual 111.68 100.85 10.83 1.67e+00 3.59e-01 4.20e+01 angle pdb=" C ASN G 156 " pdb=" CA ASN G 156 " pdb=" CB ASN G 156 " ideal model delta sigma weight residual 111.68 100.86 10.82 1.67e+00 3.59e-01 4.19e+01 angle pdb=" CA ALA I 200 " pdb=" C ALA I 200 " pdb=" O ALA I 200 " ideal model delta sigma weight residual 121.11 115.25 5.86 1.13e+00 7.83e-01 2.69e+01 angle pdb=" N LEU A 663 " pdb=" CA LEU A 663 " pdb=" C LEU A 663 " ideal model delta sigma weight residual 111.28 105.83 5.45 1.09e+00 8.42e-01 2.50e+01 ... (remaining 28849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.87: 13242 21.87 - 43.74: 935 43.74 - 65.60: 142 65.60 - 87.47: 96 87.47 - 109.34: 60 Dihedral angle restraints: 14475 sinusoidal: 7533 harmonic: 6942 Sorted by residual: dihedral pdb=" CB CYS K 32 " pdb=" SG CYS K 32 " pdb=" SG CYS K 98 " pdb=" CB CYS K 98 " ideal model delta sinusoidal sigma weight residual -86.00 -13.56 -72.44 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS H 32 " pdb=" SG CYS H 32 " pdb=" SG CYS H 98 " pdb=" CB CYS H 98 " ideal model delta sinusoidal sigma weight residual -86.00 -13.57 -72.43 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS E 32 " pdb=" SG CYS E 32 " pdb=" SG CYS E 98 " pdb=" CB CYS E 98 " ideal model delta sinusoidal sigma weight residual -86.00 -13.60 -72.40 1 1.00e+01 1.00e-02 6.70e+01 ... (remaining 14472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.288: 3518 0.288 - 0.576: 55 0.576 - 0.864: 6 0.864 - 1.152: 3 1.152 - 1.441: 3 Chirality restraints: 3585 Sorted by residual: chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.96 -1.44 2.00e-02 2.50e+03 5.19e+03 chirality pdb=" C1 BMA V 3 " pdb=" O4 NAG V 2 " pdb=" C2 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.96 -1.44 2.00e-02 2.50e+03 5.16e+03 chirality pdb=" C1 BMA d 3 " pdb=" O4 NAG d 2 " pdb=" C2 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-02 2.50e+03 5.13e+03 ... (remaining 3582 not shown) Planarity restraints: 3558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 2 " 0.308 2.00e-02 2.50e+03 2.59e-01 8.41e+02 pdb=" C7 NAG h 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG h 2 " 0.190 2.00e-02 2.50e+03 pdb=" N2 NAG h 2 " -0.445 2.00e-02 2.50e+03 pdb=" O7 NAG h 2 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " 0.308 2.00e-02 2.50e+03 2.59e-01 8.40e+02 pdb=" C7 NAG R 2 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " 0.190 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " -0.444 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " 0.307 2.00e-02 2.50e+03 2.59e-01 8.39e+02 pdb=" C7 NAG Z 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " 0.190 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " -0.443 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " 0.030 2.00e-02 2.50e+03 ... (remaining 3555 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4427 2.77 - 3.30: 17738 3.30 - 3.84: 32644 3.84 - 4.37: 37378 4.37 - 4.90: 66247 Nonbonded interactions: 158434 Sorted by model distance: nonbonded pdb=" OG SER D 63 " pdb=" OG1 THR D 74 " model vdw 2.241 3.040 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.241 3.040 nonbonded pdb=" OG SER J 63 " pdb=" OG1 THR J 74 " model vdw 2.241 3.040 nonbonded pdb=" O ASP B 632 " pdb=" OG SER B 636 " model vdw 2.306 3.040 nonbonded pdb=" O ASP A 632 " pdb=" OG SER A 636 " model vdw 2.307 3.040 ... (remaining 158429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'g' selection = chain 'j' } ncs_group { reference = chain 'N' selection = chain 'V' selection = chain 'd' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'W' selection = chain 'Z' selection = chain 'e' selection = chain 'h' } ncs_group { reference = chain 'P' selection = chain 'X' selection = chain 'f' } ncs_group { reference = chain 'S' selection = chain 'a' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.250 Process input model: 54.320 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 21432 Z= 0.428 Angle : 1.680 52.335 29349 Z= 0.704 Chirality : 0.103 1.441 3585 Planarity : 0.015 0.259 3498 Dihedral : 17.431 109.340 9870 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.79 % Favored : 92.05 % Rotamer: Outliers : 1.23 % Allowed : 8.13 % Favored : 90.64 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.43 (0.13), residues: 2376 helix: -4.82 (0.08), residues: 390 sheet: -3.18 (0.16), residues: 720 loop : -3.48 (0.13), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 50 HIS 0.011 0.002 HIS I 249 PHE 0.018 0.002 PHE G 53 TYR 0.028 0.002 TYR G 435 ARG 0.004 0.001 ARG K 71 Details of bonding type rmsd link_NAG-ASN : bond 0.01080 ( 60) link_NAG-ASN : angle 3.15426 ( 180) link_ALPHA1-6 : bond 0.02991 ( 15) link_ALPHA1-6 : angle 14.65742 ( 45) link_BETA1-4 : bond 0.04759 ( 39) link_BETA1-4 : angle 17.09320 ( 117) link_ALPHA1-2 : bond 0.00123 ( 6) link_ALPHA1-2 : angle 3.98839 ( 18) link_ALPHA1-3 : bond 0.00624 ( 15) link_ALPHA1-3 : angle 3.30322 ( 45) hydrogen bonds : bond 0.26357 ( 531) hydrogen bonds : angle 10.46124 ( 1386) SS BOND : bond 0.00622 ( 45) SS BOND : angle 1.68388 ( 90) covalent geometry : bond 0.00850 (21252) covalent geometry : angle 1.11983 (28854) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 278 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 603 ILE cc_start: 0.8994 (mt) cc_final: 0.8700 (tt) REVERT: B 632 ASP cc_start: 0.8695 (t70) cc_final: 0.8336 (t0) REVERT: B 651 ASN cc_start: 0.8180 (t0) cc_final: 0.7492 (p0) REVERT: G 166 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7112 (ttp-170) REVERT: L 17 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7906 (mt-10) REVERT: L 54 ARG cc_start: 0.7985 (mtm110) cc_final: 0.7780 (ptp-110) REVERT: H 76 ASP cc_start: 0.7987 (p0) cc_final: 0.7764 (p0) REVERT: A 603 ILE cc_start: 0.8960 (mt) cc_final: 0.8661 (tt) REVERT: A 632 ASP cc_start: 0.8630 (t70) cc_final: 0.8316 (t0) REVERT: A 633 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8850 (mtmm) REVERT: A 651 ASN cc_start: 0.8059 (t0) cc_final: 0.7439 (p0) REVERT: C 114 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7574 (tm-30) REVERT: C 166 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.7159 (ttp-110) REVERT: C 426 MET cc_start: 0.8615 (tpp) cc_final: 0.8397 (tpt) REVERT: D 17 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7775 (mt-10) REVERT: D 42 GLN cc_start: 0.8356 (mt0) cc_final: 0.8062 (mt0) REVERT: D 75 ILE cc_start: 0.7683 (mt) cc_final: 0.7459 (tt) REVERT: F 603 ILE cc_start: 0.8980 (mt) cc_final: 0.8614 (tt) REVERT: F 632 ASP cc_start: 0.8873 (t70) cc_final: 0.8520 (t0) REVERT: F 651 ASN cc_start: 0.8177 (t0) cc_final: 0.7600 (p0) REVERT: I 100 MET cc_start: 0.9090 (mtp) cc_final: 0.8804 (mtt) REVERT: I 166 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7096 (ttp-110) REVERT: I 424 ILE cc_start: 0.8563 (pt) cc_final: 0.8299 (pt) REVERT: I 426 MET cc_start: 0.8697 (tpp) cc_final: 0.8477 (tpt) REVERT: J 17 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7709 (mt-10) REVERT: J 24 ARG cc_start: 0.7936 (tpt90) cc_final: 0.7622 (tpt170) REVERT: J 42 GLN cc_start: 0.8357 (mt0) cc_final: 0.7945 (mp10) REVERT: J 60 ASP cc_start: 0.8413 (m-30) cc_final: 0.8201 (m-30) REVERT: K 76 ASP cc_start: 0.8102 (p0) cc_final: 0.7857 (p0) REVERT: K 96 LYS cc_start: 0.9229 (tttm) cc_final: 0.8810 (tttm) outliers start: 26 outliers final: 10 residues processed: 302 average time/residue: 0.3843 time to fit residues: 171.4974 Evaluate side-chains 198 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 430 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 112 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 114 GLN L 6 GLN H 3 GLN A 590 GLN C 114 GLN D 6 GLN E 3 GLN ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN J 6 GLN K 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.101521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.081563 restraints weight = 44017.091| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.93 r_work: 0.3183 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21432 Z= 0.169 Angle : 0.795 11.749 29349 Z= 0.362 Chirality : 0.048 0.341 3585 Planarity : 0.005 0.048 3498 Dihedral : 13.441 77.040 5347 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.89 % Allowed : 11.16 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.14), residues: 2376 helix: -3.25 (0.17), residues: 408 sheet: -2.57 (0.18), residues: 717 loop : -3.02 (0.15), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 50 HIS 0.011 0.001 HIS K 102 PHE 0.014 0.001 PHE I 53 TYR 0.015 0.001 TYR A 638 ARG 0.008 0.000 ARG J 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 60) link_NAG-ASN : angle 2.56837 ( 180) link_ALPHA1-6 : bond 0.00401 ( 15) link_ALPHA1-6 : angle 2.09008 ( 45) link_BETA1-4 : bond 0.00652 ( 39) link_BETA1-4 : angle 2.55099 ( 117) link_ALPHA1-2 : bond 0.01216 ( 6) link_ALPHA1-2 : angle 2.32436 ( 18) link_ALPHA1-3 : bond 0.00903 ( 15) link_ALPHA1-3 : angle 1.77855 ( 45) hydrogen bonds : bond 0.04690 ( 531) hydrogen bonds : angle 6.13673 ( 1386) SS BOND : bond 0.00388 ( 45) SS BOND : angle 1.61687 ( 90) covalent geometry : bond 0.00384 (21252) covalent geometry : angle 0.74288 (28854) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8528 (t70) cc_final: 0.8236 (t0) REVERT: G 114 GLN cc_start: 0.8466 (tm130) cc_final: 0.8101 (tm-30) REVERT: G 166 ARG cc_start: 0.7837 (mmm-85) cc_final: 0.7215 (ttp-170) REVERT: L 97 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7186 (pt0) REVERT: H 76 ASP cc_start: 0.7752 (p0) cc_final: 0.7498 (p0) REVERT: H 87 THR cc_start: 0.9098 (m) cc_final: 0.8747 (p) REVERT: A 632 ASP cc_start: 0.8325 (t70) cc_final: 0.8102 (t0) REVERT: C 114 GLN cc_start: 0.8472 (tm130) cc_final: 0.8145 (tm-30) REVERT: C 166 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7353 (ttp-110) REVERT: D 97 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7255 (pt0) REVERT: E 75 GLN cc_start: 0.8874 (mt0) cc_final: 0.8655 (mt0) REVERT: E 87 THR cc_start: 0.9043 (m) cc_final: 0.8807 (p) REVERT: F 616 ASN cc_start: 0.8441 (p0) cc_final: 0.8205 (p0) REVERT: F 632 ASP cc_start: 0.8647 (t70) cc_final: 0.8318 (t0) REVERT: F 655 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7375 (mmmt) REVERT: I 166 ARG cc_start: 0.7872 (mmm-85) cc_final: 0.7226 (ttp-110) REVERT: J 97 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7252 (pt0) REVERT: K 76 ASP cc_start: 0.7987 (p0) cc_final: 0.7689 (p0) outliers start: 40 outliers final: 26 residues processed: 247 average time/residue: 0.3133 time to fit residues: 121.9560 Evaluate side-chains 214 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 130 optimal weight: 0.0870 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 175 optimal weight: 0.0570 chunk 35 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.0078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN A 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.100052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.078561 restraints weight = 46472.152| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.41 r_work: 0.3193 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21432 Z= 0.132 Angle : 0.742 17.064 29349 Z= 0.337 Chirality : 0.048 0.348 3585 Planarity : 0.004 0.036 3498 Dihedral : 11.326 63.758 5340 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.74 % Allowed : 12.58 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.16), residues: 2376 helix: -1.91 (0.23), residues: 387 sheet: -2.04 (0.19), residues: 672 loop : -2.63 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 112 HIS 0.006 0.001 HIS E 102 PHE 0.010 0.001 PHE G 53 TYR 0.017 0.001 TYR A 638 ARG 0.009 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 60) link_NAG-ASN : angle 2.24520 ( 180) link_ALPHA1-6 : bond 0.00670 ( 15) link_ALPHA1-6 : angle 1.87576 ( 45) link_BETA1-4 : bond 0.00476 ( 39) link_BETA1-4 : angle 2.16051 ( 117) link_ALPHA1-2 : bond 0.00991 ( 6) link_ALPHA1-2 : angle 2.32392 ( 18) link_ALPHA1-3 : bond 0.00941 ( 15) link_ALPHA1-3 : angle 1.66674 ( 45) hydrogen bonds : bond 0.03557 ( 531) hydrogen bonds : angle 5.26728 ( 1386) SS BOND : bond 0.00242 ( 45) SS BOND : angle 2.52180 ( 90) covalent geometry : bond 0.00302 (21252) covalent geometry : angle 0.69055 (28854) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 201 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8833 (mtp) cc_final: 0.8500 (mtp) REVERT: B 632 ASP cc_start: 0.8940 (t70) cc_final: 0.8625 (t0) REVERT: G 114 GLN cc_start: 0.8437 (tm130) cc_final: 0.8118 (tm-30) REVERT: G 166 ARG cc_start: 0.8082 (mmm-85) cc_final: 0.7175 (ttp-170) REVERT: L 54 ARG cc_start: 0.7876 (ptp-110) cc_final: 0.7639 (mtm110) REVERT: H 76 ASP cc_start: 0.8070 (p0) cc_final: 0.7854 (p0) REVERT: H 87 THR cc_start: 0.9061 (m) cc_final: 0.8856 (p) REVERT: A 616 ASN cc_start: 0.8736 (p0) cc_final: 0.8277 (p0) REVERT: A 632 ASP cc_start: 0.8806 (t70) cc_final: 0.8517 (t0) REVERT: C 114 GLN cc_start: 0.8481 (tm130) cc_final: 0.8210 (tm-30) REVERT: F 616 ASN cc_start: 0.8740 (p0) cc_final: 0.8505 (p0) REVERT: F 632 ASP cc_start: 0.8999 (t70) cc_final: 0.8654 (t0) REVERT: F 655 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7357 (mmmt) REVERT: I 166 ARG cc_start: 0.8167 (mmm-85) cc_final: 0.7087 (ttp-110) REVERT: J 42 GLN cc_start: 0.8013 (mt0) cc_final: 0.7568 (mp10) REVERT: J 97 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.6668 (pm20) REVERT: K 20 ILE cc_start: 0.8928 (pt) cc_final: 0.8682 (pt) REVERT: K 76 ASP cc_start: 0.8199 (p0) cc_final: 0.7929 (p0) REVERT: K 96 LYS cc_start: 0.9182 (tttm) cc_final: 0.8831 (tttm) outliers start: 58 outliers final: 25 residues processed: 249 average time/residue: 0.3059 time to fit residues: 121.3387 Evaluate side-chains 206 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 227 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.100074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.079272 restraints weight = 47101.039| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.32 r_work: 0.3195 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 21432 Z= 0.147 Angle : 0.713 11.698 29349 Z= 0.322 Chirality : 0.048 0.363 3585 Planarity : 0.004 0.042 3498 Dihedral : 10.159 59.771 5339 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.36 % Allowed : 14.14 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.16), residues: 2376 helix: -1.20 (0.26), residues: 357 sheet: -1.77 (0.20), residues: 669 loop : -2.39 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 100B HIS 0.004 0.001 HIS G 249 PHE 0.010 0.001 PHE G 53 TYR 0.020 0.001 TYR A 638 ARG 0.009 0.000 ARG D 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 60) link_NAG-ASN : angle 2.21146 ( 180) link_ALPHA1-6 : bond 0.00749 ( 15) link_ALPHA1-6 : angle 1.85748 ( 45) link_BETA1-4 : bond 0.00448 ( 39) link_BETA1-4 : angle 2.02044 ( 117) link_ALPHA1-2 : bond 0.00938 ( 6) link_ALPHA1-2 : angle 2.24501 ( 18) link_ALPHA1-3 : bond 0.00950 ( 15) link_ALPHA1-3 : angle 1.68971 ( 45) hydrogen bonds : bond 0.03245 ( 531) hydrogen bonds : angle 4.92624 ( 1386) SS BOND : bond 0.00202 ( 45) SS BOND : angle 2.03132 ( 90) covalent geometry : bond 0.00347 (21252) covalent geometry : angle 0.66695 (28854) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8934 (t70) cc_final: 0.8624 (t0) REVERT: B 648 GLU cc_start: 0.8540 (pm20) cc_final: 0.8151 (pm20) REVERT: B 659 ASP cc_start: 0.8357 (m-30) cc_final: 0.8095 (t0) REVERT: G 114 GLN cc_start: 0.8419 (tm130) cc_final: 0.8128 (tm-30) REVERT: G 166 ARG cc_start: 0.8052 (mmm-85) cc_final: 0.7236 (ttp-110) REVERT: L 97 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7183 (pt0) REVERT: H 101 GLU cc_start: 0.8637 (tt0) cc_final: 0.8359 (tm-30) REVERT: A 616 ASN cc_start: 0.8656 (p0) cc_final: 0.8183 (p0) REVERT: A 632 ASP cc_start: 0.8805 (t70) cc_final: 0.8533 (t0) REVERT: C 114 GLN cc_start: 0.8473 (tm130) cc_final: 0.8189 (tm-30) REVERT: D 97 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7234 (pt0) REVERT: E 76 ASP cc_start: 0.8613 (t0) cc_final: 0.8279 (t0) REVERT: F 632 ASP cc_start: 0.9006 (t70) cc_final: 0.8677 (t0) REVERT: F 655 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7334 (mmmt) REVERT: I 166 ARG cc_start: 0.8159 (mmm-85) cc_final: 0.7124 (ttp-110) REVERT: J 54 ARG cc_start: 0.8340 (mtm110) cc_final: 0.8126 (mtm110) REVERT: J 97 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.6649 (pm20) REVERT: K 76 ASP cc_start: 0.8162 (p0) cc_final: 0.7902 (p0) REVERT: K 96 LYS cc_start: 0.9144 (tttm) cc_final: 0.8760 (ttpp) outliers start: 50 outliers final: 32 residues processed: 224 average time/residue: 0.2880 time to fit residues: 103.2792 Evaluate side-chains 210 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.1568 > 50: distance: 22 - 25: 17.722 distance: 25 - 26: 15.292 distance: 25 - 138: 20.360 distance: 26 - 27: 11.158 distance: 26 - 29: 15.177 distance: 27 - 28: 16.623 distance: 27 - 39: 4.756 distance: 29 - 30: 9.421 distance: 30 - 31: 4.241 distance: 30 - 32: 3.831 distance: 31 - 33: 7.412 distance: 32 - 34: 6.574 distance: 32 - 35: 6.555 distance: 33 - 34: 5.788 distance: 34 - 36: 8.185 distance: 35 - 37: 6.186 distance: 36 - 38: 5.261 distance: 37 - 38: 10.199 distance: 39 - 40: 11.761 distance: 39 - 193: 6.297 distance: 40 - 41: 7.781 distance: 40 - 43: 16.551 distance: 41 - 42: 19.545 distance: 41 - 51: 12.978 distance: 42 - 190: 21.501 distance: 44 - 45: 10.057 distance: 44 - 46: 9.004 distance: 45 - 47: 11.153 distance: 46 - 48: 11.640 distance: 47 - 49: 11.608 distance: 48 - 49: 7.419 distance: 49 - 50: 8.560 distance: 51 - 52: 16.972 distance: 52 - 53: 12.469 distance: 52 - 55: 14.368 distance: 53 - 54: 13.053 distance: 53 - 60: 22.133 distance: 55 - 56: 16.240 distance: 56 - 57: 10.548 distance: 60 - 61: 25.888 distance: 60 - 175: 19.299 distance: 61 - 62: 23.438 distance: 61 - 64: 29.537 distance: 62 - 63: 12.863 distance: 62 - 69: 17.038 distance: 63 - 172: 22.317 distance: 64 - 65: 18.600 distance: 65 - 66: 6.520 distance: 66 - 67: 9.962 distance: 66 - 68: 11.242 distance: 69 - 70: 10.539 distance: 70 - 71: 8.556 distance: 70 - 73: 17.240 distance: 71 - 72: 11.657 distance: 71 - 80: 20.360 distance: 73 - 74: 17.546 distance: 74 - 75: 4.879 distance: 75 - 76: 5.122 distance: 76 - 77: 3.571 distance: 77 - 78: 4.859 distance: 77 - 79: 6.009 distance: 80 - 81: 26.680 distance: 80 - 86: 19.411 distance: 81 - 82: 10.097 distance: 81 - 84: 18.763 distance: 82 - 83: 14.287 distance: 82 - 87: 21.060 distance: 84 - 85: 14.031 distance: 85 - 86: 26.909 distance: 87 - 88: 6.784 distance: 88 - 89: 26.919 distance: 89 - 90: 18.200 distance: 89 - 91: 29.152 distance: 91 - 92: 21.611 distance: 92 - 93: 32.285 distance: 92 - 95: 20.696 distance: 93 - 94: 26.534 distance: 93 - 100: 61.158 distance: 96 - 97: 5.880 distance: 97 - 99: 8.940 distance: 100 - 101: 50.246 distance: 101 - 102: 42.827 distance: 101 - 104: 16.282 distance: 102 - 103: 27.121 distance: 102 - 105: 20.094 distance: 105 - 106: 47.189 distance: 105 - 111: 10.667 distance: 106 - 107: 36.585 distance: 106 - 109: 6.736 distance: 107 - 112: 34.263 distance: 109 - 110: 44.278 distance: 110 - 111: 39.236