Starting phenix.real_space_refine on Wed Feb 21 12:53:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asd_11892/02_2024/7asd_11892_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asd_11892/02_2024/7asd_11892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asd_11892/02_2024/7asd_11892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asd_11892/02_2024/7asd_11892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asd_11892/02_2024/7asd_11892_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asd_11892/02_2024/7asd_11892_neut_updated.pdb" } resolution = 3.5 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= 0.003 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 144 5.16 5 C 19144 2.51 5 N 4960 2.21 5 O 6048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AA ARG 23": "NH1" <-> "NH2" Residue "AA ARG 184": "NH1" <-> "NH2" Residue "AA GLU 208": "OE1" <-> "OE2" Residue "AA ARG 284": "NH1" <-> "NH2" Residue "AA ARG 342": "NH1" <-> "NH2" Residue "AA ARG 415": "NH1" <-> "NH2" Residue "AA ARG 423": "NH1" <-> "NH2" Residue "BA ARG 23": "NH1" <-> "NH2" Residue "BA ARG 184": "NH1" <-> "NH2" Residue "BA GLU 208": "OE1" <-> "OE2" Residue "BA ARG 284": "NH1" <-> "NH2" Residue "BA ARG 342": "NH1" <-> "NH2" Residue "BA ARG 415": "NH1" <-> "NH2" Residue "BA ARG 423": "NH1" <-> "NH2" Residue "CA ARG 23": "NH1" <-> "NH2" Residue "CA ARG 184": "NH1" <-> "NH2" Residue "CA GLU 208": "OE1" <-> "OE2" Residue "CA ARG 284": "NH1" <-> "NH2" Residue "CA ARG 342": "NH1" <-> "NH2" Residue "CA ARG 415": "NH1" <-> "NH2" Residue "CA ARG 423": "NH1" <-> "NH2" Residue "DA ARG 23": "NH1" <-> "NH2" Residue "DA ARG 184": "NH1" <-> "NH2" Residue "DA GLU 208": "OE1" <-> "OE2" Residue "DA ARG 284": "NH1" <-> "NH2" Residue "DA ARG 342": "NH1" <-> "NH2" Residue "DA ARG 415": "NH1" <-> "NH2" Residue "DA ARG 423": "NH1" <-> "NH2" Residue "EA ARG 23": "NH1" <-> "NH2" Residue "EA ARG 184": "NH1" <-> "NH2" Residue "EA GLU 208": "OE1" <-> "OE2" Residue "EA ARG 284": "NH1" <-> "NH2" Residue "EA ARG 342": "NH1" <-> "NH2" Residue "EA ARG 415": "NH1" <-> "NH2" Residue "EA ARG 423": "NH1" <-> "NH2" Residue "FA ARG 23": "NH1" <-> "NH2" Residue "FA ARG 184": "NH1" <-> "NH2" Residue "FA GLU 208": "OE1" <-> "OE2" Residue "FA ARG 284": "NH1" <-> "NH2" Residue "FA ARG 342": "NH1" <-> "NH2" Residue "FA ARG 415": "NH1" <-> "NH2" Residue "FA ARG 423": "NH1" <-> "NH2" Residue "GA ARG 23": "NH1" <-> "NH2" Residue "GA ARG 184": "NH1" <-> "NH2" Residue "GA GLU 208": "OE1" <-> "OE2" Residue "GA ARG 284": "NH1" <-> "NH2" Residue "GA ARG 342": "NH1" <-> "NH2" Residue "GA ARG 415": "NH1" <-> "NH2" Residue "GA ARG 423": "NH1" <-> "NH2" Residue "HA ARG 23": "NH1" <-> "NH2" Residue "HA ARG 184": "NH1" <-> "NH2" Residue "HA GLU 208": "OE1" <-> "OE2" Residue "HA ARG 284": "NH1" <-> "NH2" Residue "HA ARG 342": "NH1" <-> "NH2" Residue "HA ARG 415": "NH1" <-> "NH2" Residue "HA ARG 423": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30296 Number of models: 1 Model: "" Number of chains: 48 Chain: "AA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "AB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "BA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "BB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "CA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "CB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "DA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "DB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "EA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "EB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "FA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "FB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "GA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "GB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "HA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "HB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: "BA" 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: 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: "CA" 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: 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: "DA" 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: 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: "EA" 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: "E" 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: "FA" 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: "F" 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: "GA" 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: 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: "HA" 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: 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: "AA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "AB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "BB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Chain: "CA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "CB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Chain: "DA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "DB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Chain: "EA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "EB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Chain: "FA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "FB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Chain: "GA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "GB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Chain: "HA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "HB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 16 residue: pdb=" N AHISAA 172 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHISAA 172 " occ=0.50 residue: pdb=" N AHISAA 294 " occ=0.60 ... (18 atoms not shown) pdb=" NE2BHISAA 294 " occ=0.40 residue: pdb=" N AHISBA 172 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHISBA 172 " occ=0.50 residue: pdb=" N AHISBA 294 " occ=0.60 ... (18 atoms not shown) pdb=" NE2BHISBA 294 " occ=0.40 residue: pdb=" N AHISCA 172 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHISCA 172 " occ=0.50 residue: pdb=" N AHISCA 294 " occ=0.60 ... (18 atoms not shown) pdb=" NE2BHISCA 294 " occ=0.40 residue: pdb=" N AHISDA 172 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHISDA 172 " occ=0.50 residue: pdb=" N AHISDA 294 " occ=0.60 ... (18 atoms not shown) pdb=" NE2BHISDA 294 " occ=0.40 residue: pdb=" N AHISEA 172 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHISEA 172 " occ=0.50 residue: pdb=" N AHISEA 294 " occ=0.60 ... (18 atoms not shown) pdb=" NE2BHISEA 294 " occ=0.40 residue: pdb=" N AHISFA 172 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHISFA 172 " occ=0.50 residue: pdb=" N AHISFA 294 " occ=0.60 ... (18 atoms not shown) pdb=" NE2BHISFA 294 " occ=0.40 ... (remaining 4 not shown) Time building chain proxies: 28.02, per 1000 atoms: 0.92 Number of scatterers: 30296 At special positions: 0 Unit cell: (149.334, 151.723, 127.83, 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 144 16.00 O 6048 8.00 N 4960 7.00 C 19144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYSAA 118 " - pdb=" SG CYSAA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSAA 132 " - pdb=" SG CYSAA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSAA 329 " - pdb=" SG CYSAA 416 " distance=2.03 Simple disulfide: pdb=" SG CYSBA 118 " - pdb=" SG CYSBA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSBA 132 " - pdb=" SG CYSBA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSBA 329 " - pdb=" SG CYSBA 416 " distance=2.03 Simple disulfide: pdb=" SG CYSCA 118 " - pdb=" SG CYSCA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSCA 132 " - pdb=" SG CYSCA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSCA 329 " - pdb=" SG CYSCA 416 " distance=2.03 Simple disulfide: pdb=" SG CYSDA 118 " - pdb=" SG CYSDA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSDA 132 " - pdb=" SG CYSDA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSDA 329 " - pdb=" SG CYSDA 416 " distance=2.03 Simple disulfide: pdb=" SG CYSEA 118 " - pdb=" SG CYSEA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSEA 132 " - pdb=" SG CYSEA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSEA 329 " - pdb=" SG CYSEA 416 " distance=2.03 Simple disulfide: pdb=" SG CYSFA 118 " - pdb=" SG CYSFA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSFA 132 " - pdb=" SG CYSFA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSFA 329 " - pdb=" SG CYSFA 416 " distance=2.03 Simple disulfide: pdb=" SG CYSGA 118 " - pdb=" SG CYSGA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSGA 132 " - pdb=" SG CYSGA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSGA 329 " - pdb=" SG CYSGA 416 " distance=2.03 Simple disulfide: pdb=" SG CYSHA 118 " - pdb=" SG CYSHA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSHA 132 " - pdb=" SG CYSHA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSHA 329 " - pdb=" SG CYSHA 416 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " 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 G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGEA 1 " - " NAGEA 2 " " NAGFA 1 " - " NAGFA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " NAG-ASN " NAG A 1 " - " ASNAA 177 " " NAG B 1 " - " ASNBA 177 " " NAG C 1 " - " ASNCA 177 " " NAG D 1 " - " ASNDA 177 " " NAG E 1 " - " ASNEA 177 " " NAG F 1 " - " ASNFA 177 " " NAG G 1 " - " ASNGA 177 " " NAG H 1 " - " ASNHA 177 " " NAGAA 1 " - " ASNAA 144 " " NAGAA 502 " - " ASNAA 28 " " NAGBA 1 " - " ASNBA 144 " " NAGBA 502 " - " ASNBA 28 " " NAGCA 1 " - " ASNCA 144 " " NAGCA 502 " - " ASNCA 28 " " NAGDA 1 " - " ASNDA 144 " " NAGDA 502 " - " ASNDA 28 " " NAGEA 1 " - " ASNEA 144 " " NAGEA 502 " - " ASNEA 28 " " NAGFA 1 " - " ASNFA 144 " " NAGFA 502 " - " ASNFA 28 " " NAGGA 1 " - " ASNGA 144 " " NAGGA 502 " - " ASNGA 28 " " NAGHA 1 " - " ASNHA 144 " " NAGHA 502 " - " ASNHA 28 " Time building additional restraints: 12.60 Conformation dependent library (CDL) restraints added in 9.8 seconds 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7008 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 56 sheets defined 16.8% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.45 Creating SS restraints... Processing helix chain 'AA' and resid 47 through 56 Processing helix chain 'AA' and resid 110 through 113 No H-bonds generated for 'chain 'AA' and resid 110 through 113' Processing helix chain 'AA' and resid 172 through 175 No H-bonds generated for 'chain 'AA' and resid 172 through 175' Processing helix chain 'AA' and resid 229 through 231 No H-bonds generated for 'chain 'AA' and resid 229 through 231' Processing helix chain 'AA' and resid 235 through 237 No H-bonds generated for 'chain 'AA' and resid 235 through 237' Processing helix chain 'AA' and resid 280 through 283 Processing helix chain 'AA' and resid 368 through 372 removed outlier: 3.976A pdb=" N ARGAA 371 " --> pdb=" O ILEAA 368 " (cutoff:3.500A) Processing helix chain 'AA' and resid 385 through 390 Processing helix chain 'AA' and resid 407 through 410 No H-bonds generated for 'chain 'AA' and resid 407 through 410' Processing helix chain 'AB' and resid 35 through 51 Processing helix chain 'AB' and resid 57 through 73 Processing helix chain 'BA' and resid 47 through 56 Processing helix chain 'BA' and resid 110 through 113 No H-bonds generated for 'chain 'BA' and resid 110 through 113' Processing helix chain 'BA' and resid 172 through 175 No H-bonds generated for 'chain 'BA' and resid 172 through 175' Processing helix chain 'BA' and resid 229 through 231 No H-bonds generated for 'chain 'BA' and resid 229 through 231' Processing helix chain 'BA' and resid 235 through 237 No H-bonds generated for 'chain 'BA' and resid 235 through 237' Processing helix chain 'BA' and resid 280 through 283 Processing helix chain 'BA' and resid 368 through 372 removed outlier: 3.975A pdb=" N ARGBA 371 " --> pdb=" O ILEBA 368 " (cutoff:3.500A) Processing helix chain 'BA' and resid 385 through 390 Processing helix chain 'BA' and resid 407 through 410 No H-bonds generated for 'chain 'BA' and resid 407 through 410' Processing helix chain 'BB' and resid 35 through 51 Processing helix chain 'BB' and resid 57 through 73 Processing helix chain 'CA' and resid 47 through 56 Processing helix chain 'CA' and resid 110 through 113 No H-bonds generated for 'chain 'CA' and resid 110 through 113' Processing helix chain 'CA' and resid 172 through 175 No H-bonds generated for 'chain 'CA' and resid 172 through 175' Processing helix chain 'CA' and resid 229 through 231 No H-bonds generated for 'chain 'CA' and resid 229 through 231' Processing helix chain 'CA' and resid 235 through 237 No H-bonds generated for 'chain 'CA' and resid 235 through 237' Processing helix chain 'CA' and resid 280 through 283 Processing helix chain 'CA' and resid 368 through 372 removed outlier: 3.976A pdb=" N ARGCA 371 " --> pdb=" O ILECA 368 " (cutoff:3.500A) Processing helix chain 'CA' and resid 385 through 390 Processing helix chain 'CA' and resid 407 through 410 No H-bonds generated for 'chain 'CA' and resid 407 through 410' Processing helix chain 'CB' and resid 35 through 51 Processing helix chain 'CB' and resid 57 through 73 Processing helix chain 'DA' and resid 47 through 56 Processing helix chain 'DA' and resid 110 through 113 No H-bonds generated for 'chain 'DA' and resid 110 through 113' Processing helix chain 'DA' and resid 172 through 175 No H-bonds generated for 'chain 'DA' and resid 172 through 175' Processing helix chain 'DA' and resid 229 through 231 No H-bonds generated for 'chain 'DA' and resid 229 through 231' Processing helix chain 'DA' and resid 235 through 237 No H-bonds generated for 'chain 'DA' and resid 235 through 237' Processing helix chain 'DA' and resid 280 through 283 Processing helix chain 'DA' and resid 368 through 372 removed outlier: 3.975A pdb=" N ARGDA 371 " --> pdb=" O ILEDA 368 " (cutoff:3.500A) Processing helix chain 'DA' and resid 385 through 390 Processing helix chain 'DA' and resid 407 through 410 No H-bonds generated for 'chain 'DA' and resid 407 through 410' Processing helix chain 'DB' and resid 35 through 51 Processing helix chain 'DB' and resid 57 through 73 Processing helix chain 'EA' and resid 47 through 56 Processing helix chain 'EA' and resid 110 through 113 No H-bonds generated for 'chain 'EA' and resid 110 through 113' Processing helix chain 'EA' and resid 172 through 175 No H-bonds generated for 'chain 'EA' and resid 172 through 175' Processing helix chain 'EA' and resid 229 through 231 No H-bonds generated for 'chain 'EA' and resid 229 through 231' Processing helix chain 'EA' and resid 235 through 237 No H-bonds generated for 'chain 'EA' and resid 235 through 237' Processing helix chain 'EA' and resid 280 through 283 Processing helix chain 'EA' and resid 368 through 372 removed outlier: 3.976A pdb=" N ARGEA 371 " --> pdb=" O ILEEA 368 " (cutoff:3.500A) Processing helix chain 'EA' and resid 385 through 390 Processing helix chain 'EA' and resid 407 through 410 No H-bonds generated for 'chain 'EA' and resid 407 through 410' Processing helix chain 'EB' and resid 35 through 51 Processing helix chain 'EB' and resid 57 through 73 Processing helix chain 'FA' and resid 47 through 56 Processing helix chain 'FA' and resid 110 through 113 No H-bonds generated for 'chain 'FA' and resid 110 through 113' Processing helix chain 'FA' and resid 172 through 175 No H-bonds generated for 'chain 'FA' and resid 172 through 175' Processing helix chain 'FA' and resid 229 through 231 No H-bonds generated for 'chain 'FA' and resid 229 through 231' Processing helix chain 'FA' and resid 235 through 237 No H-bonds generated for 'chain 'FA' and resid 235 through 237' Processing helix chain 'FA' and resid 280 through 283 Processing helix chain 'FA' and resid 368 through 372 removed outlier: 3.976A pdb=" N ARGFA 371 " --> pdb=" O ILEFA 368 " (cutoff:3.500A) Processing helix chain 'FA' and resid 385 through 390 Processing helix chain 'FA' and resid 407 through 410 No H-bonds generated for 'chain 'FA' and resid 407 through 410' Processing helix chain 'FB' and resid 35 through 51 Processing helix chain 'FB' and resid 57 through 73 Processing helix chain 'GA' and resid 47 through 56 Processing helix chain 'GA' and resid 110 through 113 No H-bonds generated for 'chain 'GA' and resid 110 through 113' Processing helix chain 'GA' and resid 172 through 175 No H-bonds generated for 'chain 'GA' and resid 172 through 175' Processing helix chain 'GA' and resid 229 through 231 No H-bonds generated for 'chain 'GA' and resid 229 through 231' Processing helix chain 'GA' and resid 235 through 237 No H-bonds generated for 'chain 'GA' and resid 235 through 237' Processing helix chain 'GA' and resid 280 through 283 Processing helix chain 'GA' and resid 368 through 372 removed outlier: 3.976A pdb=" N ARGGA 371 " --> pdb=" O ILEGA 368 " (cutoff:3.500A) Processing helix chain 'GA' and resid 385 through 390 Processing helix chain 'GA' and resid 407 through 410 No H-bonds generated for 'chain 'GA' and resid 407 through 410' Processing helix chain 'GB' and resid 35 through 51 Processing helix chain 'GB' and resid 57 through 73 Processing helix chain 'HA' and resid 47 through 56 Processing helix chain 'HA' and resid 110 through 113 No H-bonds generated for 'chain 'HA' and resid 110 through 113' Processing helix chain 'HA' and resid 172 through 175 No H-bonds generated for 'chain 'HA' and resid 172 through 175' Processing helix chain 'HA' and resid 229 through 231 No H-bonds generated for 'chain 'HA' and resid 229 through 231' Processing helix chain 'HA' and resid 235 through 237 No H-bonds generated for 'chain 'HA' and resid 235 through 237' Processing helix chain 'HA' and resid 280 through 283 Processing helix chain 'HA' and resid 368 through 372 removed outlier: 3.976A pdb=" N ARGHA 371 " --> pdb=" O ILEHA 368 " (cutoff:3.500A) Processing helix chain 'HA' and resid 385 through 390 Processing helix chain 'HA' and resid 407 through 410 No H-bonds generated for 'chain 'HA' and resid 407 through 410' Processing helix chain 'HB' and resid 35 through 51 Processing helix chain 'HB' and resid 57 through 73 Processing sheet with id= A, first strand: chain 'AA' and resid 69 through 72 removed outlier: 5.185A pdb=" N ILEAA 76 " --> pdb=" O ILEAA 93 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'AA' and resid 127 through 129 removed outlier: 6.508A pdb=" N ASPAA 158 " --> pdb=" O LEUAA 164 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEUAA 164 " --> pdb=" O ASPAA 158 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'AA' and resid 222 through 227 Processing sheet with id= D, first strand: chain 'AA' and resid 239 through 242 Processing sheet with id= E, first strand: chain 'AA' and resid 264 through 267 Processing sheet with id= F, first strand: chain 'AA' and resid 309 through 311 removed outlier: 3.603A pdb=" N ALAAA 345 " --> pdb=" O LEUAA 327 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYSAA 329 " --> pdb=" O THRAA 343 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N THRAA 343 " --> pdb=" O CYSAA 329 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'AA' and resid 32 through 37 removed outlier: 7.035A pdb=" N ILEAA 402 " --> pdb=" O LEUAA 34 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLUAA 36 " --> pdb=" O PHEAA 400 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHEAA 400 " --> pdb=" O GLUAA 36 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SERAA 356 " --> pdb=" O LEUAA 381 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'BA' and resid 69 through 72 removed outlier: 5.185A pdb=" N ILEBA 76 " --> pdb=" O ILEBA 93 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'BA' and resid 127 through 129 removed outlier: 6.508A pdb=" N ASPBA 158 " --> pdb=" O LEUBA 164 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEUBA 164 " --> pdb=" O ASPBA 158 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'BA' and resid 222 through 227 Processing sheet with id= K, first strand: chain 'BA' and resid 239 through 242 Processing sheet with id= L, first strand: chain 'BA' and resid 264 through 267 Processing sheet with id= M, first strand: chain 'BA' and resid 309 through 311 removed outlier: 3.601A pdb=" N ALABA 345 " --> pdb=" O LEUBA 327 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYSBA 329 " --> pdb=" O THRBA 343 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THRBA 343 " --> pdb=" O CYSBA 329 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'BA' and resid 32 through 37 removed outlier: 7.034A pdb=" N ILEBA 402 " --> pdb=" O LEUBA 34 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLUBA 36 " --> pdb=" O PHEBA 400 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHEBA 400 " --> pdb=" O GLUBA 36 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SERBA 356 " --> pdb=" O LEUBA 381 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'CA' and resid 69 through 72 removed outlier: 5.186A pdb=" N ILECA 76 " --> pdb=" O ILECA 93 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'CA' and resid 127 through 129 removed outlier: 6.508A pdb=" N ASPCA 158 " --> pdb=" O LEUCA 164 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEUCA 164 " --> pdb=" O ASPCA 158 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'CA' and resid 222 through 227 Processing sheet with id= R, first strand: chain 'CA' and resid 239 through 242 Processing sheet with id= S, first strand: chain 'CA' and resid 264 through 267 Processing sheet with id= T, first strand: chain 'CA' and resid 309 through 311 removed outlier: 3.602A pdb=" N ALACA 345 " --> pdb=" O LEUCA 327 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N CYSCA 329 " --> pdb=" O THRCA 343 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THRCA 343 " --> pdb=" O CYSCA 329 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'CA' and resid 32 through 37 removed outlier: 7.035A pdb=" N ILECA 402 " --> pdb=" O LEUCA 34 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLUCA 36 " --> pdb=" O PHECA 400 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHECA 400 " --> pdb=" O GLUCA 36 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SERCA 356 " --> pdb=" O LEUCA 381 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'DA' and resid 69 through 72 removed outlier: 5.185A pdb=" N ILEDA 76 " --> pdb=" O ILEDA 93 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'DA' and resid 127 through 129 removed outlier: 6.508A pdb=" N ASPDA 158 " --> pdb=" O LEUDA 164 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEUDA 164 " --> pdb=" O ASPDA 158 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'DA' and resid 222 through 227 Processing sheet with id= Y, first strand: chain 'DA' and resid 239 through 242 Processing sheet with id= Z, first strand: chain 'DA' and resid 264 through 267 Processing sheet with id= AA, first strand: chain 'DA' and resid 309 through 311 removed outlier: 3.601A pdb=" N ALADA 345 " --> pdb=" O LEUDA 327 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYSDA 329 " --> pdb=" O THRDA 343 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N THRDA 343 " --> pdb=" O CYSDA 329 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'DA' and resid 32 through 37 removed outlier: 7.034A pdb=" N ILEDA 402 " --> pdb=" O LEUDA 34 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLUDA 36 " --> pdb=" O PHEDA 400 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHEDA 400 " --> pdb=" O GLUDA 36 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SERDA 356 " --> pdb=" O LEUDA 381 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'EA' and resid 69 through 72 removed outlier: 5.185A pdb=" N ILEEA 76 " --> pdb=" O ILEEA 93 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'EA' and resid 127 through 129 removed outlier: 6.508A pdb=" N ASPEA 158 " --> pdb=" O LEUEA 164 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEUEA 164 " --> pdb=" O ASPEA 158 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'EA' and resid 222 through 227 Processing sheet with id= AF, first strand: chain 'EA' and resid 239 through 242 Processing sheet with id= AG, first strand: chain 'EA' and resid 264 through 267 Processing sheet with id= AH, first strand: chain 'EA' and resid 309 through 311 removed outlier: 3.602A pdb=" N ALAEA 345 " --> pdb=" O LEUEA 327 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYSEA 329 " --> pdb=" O THREA 343 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THREA 343 " --> pdb=" O CYSEA 329 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'EA' and resid 32 through 37 removed outlier: 7.035A pdb=" N ILEEA 402 " --> pdb=" O LEUEA 34 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLUEA 36 " --> pdb=" O PHEEA 400 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHEEA 400 " --> pdb=" O GLUEA 36 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SEREA 356 " --> pdb=" O LEUEA 381 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'FA' and resid 69 through 72 removed outlier: 5.185A pdb=" N ILEFA 76 " --> pdb=" O ILEFA 93 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'FA' and resid 127 through 129 removed outlier: 6.509A pdb=" N ASPFA 158 " --> pdb=" O LEUFA 164 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEUFA 164 " --> pdb=" O ASPFA 158 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'FA' and resid 222 through 227 Processing sheet with id= AM, first strand: chain 'FA' and resid 239 through 242 Processing sheet with id= AN, first strand: chain 'FA' and resid 264 through 267 Processing sheet with id= AO, first strand: chain 'FA' and resid 309 through 311 removed outlier: 3.602A pdb=" N ALAFA 345 " --> pdb=" O LEUFA 327 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYSFA 329 " --> pdb=" O THRFA 343 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THRFA 343 " --> pdb=" O CYSFA 329 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'FA' and resid 32 through 37 removed outlier: 7.035A pdb=" N ILEFA 402 " --> pdb=" O LEUFA 34 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLUFA 36 " --> pdb=" O PHEFA 400 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHEFA 400 " --> pdb=" O GLUFA 36 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SERFA 356 " --> pdb=" O LEUFA 381 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'GA' and resid 69 through 72 removed outlier: 5.185A pdb=" N ILEGA 76 " --> pdb=" O ILEGA 93 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'GA' and resid 127 through 129 removed outlier: 6.509A pdb=" N ASPGA 158 " --> pdb=" O LEUGA 164 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEUGA 164 " --> pdb=" O ASPGA 158 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'GA' and resid 222 through 227 Processing sheet with id= AT, first strand: chain 'GA' and resid 239 through 242 Processing sheet with id= AU, first strand: chain 'GA' and resid 264 through 267 Processing sheet with id= AV, first strand: chain 'GA' and resid 309 through 311 removed outlier: 3.601A pdb=" N ALAGA 345 " --> pdb=" O LEUGA 327 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYSGA 329 " --> pdb=" O THRGA 343 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THRGA 343 " --> pdb=" O CYSGA 329 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'GA' and resid 32 through 37 removed outlier: 7.035A pdb=" N ILEGA 402 " --> pdb=" O LEUGA 34 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLUGA 36 " --> pdb=" O PHEGA 400 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHEGA 400 " --> pdb=" O GLUGA 36 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SERGA 356 " --> pdb=" O LEUGA 381 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'HA' and resid 69 through 72 removed outlier: 5.186A pdb=" N ILEHA 76 " --> pdb=" O ILEHA 93 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'HA' and resid 127 through 129 removed outlier: 6.509A pdb=" N ASPHA 158 " --> pdb=" O LEUHA 164 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEUHA 164 " --> pdb=" O ASPHA 158 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'HA' and resid 222 through 227 Processing sheet with id= BA, first strand: chain 'HA' and resid 239 through 242 Processing sheet with id= BB, first strand: chain 'HA' and resid 264 through 267 Processing sheet with id= BC, first strand: chain 'HA' and resid 309 through 311 removed outlier: 3.602A pdb=" N ALAHA 345 " --> pdb=" O LEUHA 327 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYSHA 329 " --> pdb=" O THRHA 343 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THRHA 343 " --> pdb=" O CYSHA 329 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'HA' and resid 32 through 37 removed outlier: 7.035A pdb=" N ILEHA 402 " --> pdb=" O LEUHA 34 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLUHA 36 " --> pdb=" O PHEHA 400 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHEHA 400 " --> pdb=" O GLUHA 36 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SERHA 356 " --> pdb=" O LEUHA 381 " (cutoff:3.500A) 872 hydrogen bonds defined for protein. 2376 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: 10.95 Time building geometry restraints manager: 13.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9864 1.35 - 1.47: 7159 1.47 - 1.58: 13689 1.58 - 1.70: 0 1.70 - 1.82: 224 Bond restraints: 30936 Sorted by residual: bond pdb=" O3 SO4FA 503 " pdb=" S SO4FA 503 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" O3 SO4GA 503 " pdb=" S SO4GA 503 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" O3 SO4HA 503 " pdb=" S SO4HA 503 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" O4 SO4AA 503 " pdb=" S SO4AA 503 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" O4 SO4BA 503 " pdb=" S SO4BA 503 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 3.91e+00 ... (remaining 30931 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.89: 872 106.89 - 113.66: 17903 113.66 - 120.44: 10867 120.44 - 127.22: 12206 127.22 - 133.99: 312 Bond angle restraints: 42160 Sorted by residual: angle pdb=" C ASNBA 196 " pdb=" N THRBA 197 " pdb=" CA THRBA 197 " ideal model delta sigma weight residual 120.82 125.76 -4.94 1.50e+00 4.44e-01 1.08e+01 angle pdb=" C ASNAA 196 " pdb=" N THRAA 197 " pdb=" CA THRAA 197 " ideal model delta sigma weight residual 120.82 125.75 -4.93 1.50e+00 4.44e-01 1.08e+01 angle pdb=" C ASNCA 196 " pdb=" N THRCA 197 " pdb=" CA THRCA 197 " ideal model delta sigma weight residual 120.82 125.75 -4.93 1.50e+00 4.44e-01 1.08e+01 angle pdb=" C ASNFA 196 " pdb=" N THRFA 197 " pdb=" CA THRFA 197 " ideal model delta sigma weight residual 120.82 125.73 -4.91 1.50e+00 4.44e-01 1.07e+01 angle pdb=" C ASNEA 196 " pdb=" N THREA 197 " pdb=" CA THREA 197 " ideal model delta sigma weight residual 120.82 125.70 -4.88 1.50e+00 4.44e-01 1.06e+01 ... (remaining 42155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.61: 19246 21.61 - 43.21: 586 43.21 - 64.82: 72 64.82 - 86.43: 48 86.43 - 108.03: 32 Dihedral angle restraints: 19984 sinusoidal: 9144 harmonic: 10840 Sorted by residual: dihedral pdb=" CB CYSEA 132 " pdb=" SG CYSEA 132 " pdb=" SG CYSEA 195 " pdb=" CB CYSEA 195 " ideal model delta sinusoidal sigma weight residual -86.00 -131.06 45.06 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYSGA 132 " pdb=" SG CYSGA 132 " pdb=" SG CYSGA 195 " pdb=" CB CYSGA 195 " ideal model delta sinusoidal sigma weight residual -86.00 -131.04 45.04 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYSBA 132 " pdb=" SG CYSBA 132 " pdb=" SG CYSBA 195 " pdb=" CB CYSBA 195 " ideal model delta sinusoidal sigma weight residual -86.00 -131.04 45.04 1 1.00e+01 1.00e-02 2.82e+01 ... (remaining 19981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 4699 0.105 - 0.210: 189 0.210 - 0.316: 40 0.316 - 0.421: 0 0.421 - 0.526: 16 Chirality restraints: 4944 Sorted by residual: chirality pdb=" C14 94RFA 501 " pdb=" C13 94RFA 501 " pdb=" C15 94RFA 501 " pdb=" C8 94RFA 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.85 0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" C14 94RBA 501 " pdb=" C13 94RBA 501 " pdb=" C15 94RBA 501 " pdb=" C8 94RBA 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.85 0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" C14 94RAA 501 " pdb=" C13 94RAA 501 " pdb=" C15 94RAA 501 " pdb=" C8 94RAA 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.85 0.52 2.00e-01 2.50e+01 6.89e+00 ... (remaining 4941 not shown) Planarity restraints: 5360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRPHA 72 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C TRPHA 72 " 0.023 2.00e-02 2.50e+03 pdb=" O TRPHA 72 " -0.009 2.00e-02 2.50e+03 pdb=" N HISHA 73 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRPGA 72 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C TRPGA 72 " -0.023 2.00e-02 2.50e+03 pdb=" O TRPGA 72 " 0.009 2.00e-02 2.50e+03 pdb=" N HISGA 73 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRPEA 72 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C TRPEA 72 " 0.023 2.00e-02 2.50e+03 pdb=" O TRPEA 72 " -0.009 2.00e-02 2.50e+03 pdb=" N HISEA 73 " -0.008 2.00e-02 2.50e+03 ... (remaining 5357 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 828 2.70 - 3.25: 29261 3.25 - 3.80: 46139 3.80 - 4.35: 63211 4.35 - 4.90: 105725 Nonbonded interactions: 245164 Sorted by model distance: nonbonded pdb=" OG SERGA 325 " pdb=" O LEUGA 351 " model vdw 2.153 2.440 nonbonded pdb=" OG SEREA 325 " pdb=" O LEUEA 351 " model vdw 2.153 2.440 nonbonded pdb=" OG SERCA 325 " pdb=" O LEUCA 351 " model vdw 2.153 2.440 nonbonded pdb=" OG SERDA 325 " pdb=" O LEUDA 351 " model vdw 2.153 2.440 nonbonded pdb=" OG SERAA 325 " pdb=" O LEUAA 351 " model vdw 2.154 2.440 ... (remaining 245159 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'AA' and (resid 20 through 171 or resid 173 through 293 or resid 295 thro \ ugh 432 or resid 1 through 2 or resid 501 through 503)) selection = (chain 'BA' and (resid 20 through 171 or resid 173 through 293 or resid 295 thro \ ugh 432 or resid 1 through 2 or resid 501 through 503)) selection = (chain 'CA' and (resid 20 through 171 or resid 173 through 293 or resid 295 thro \ ugh 432 or resid 1 through 2 or resid 501 through 503)) selection = (chain 'DA' and (resid 20 through 171 or resid 173 through 293 or resid 295 thro \ ugh 432 or resid 1 through 2 or resid 501 through 503)) selection = (chain 'EA' and (resid 20 through 171 or resid 173 through 293 or resid 295 thro \ ugh 432 or resid 1 through 2 or resid 501 through 503)) selection = (chain 'FA' and (resid 20 through 171 or resid 173 through 293 or resid 295 thro \ ugh 432 or resid 1 through 2 or resid 501 through 503)) selection = (chain 'GA' and (resid 20 through 171 or resid 173 through 293 or resid 295 thro \ ugh 432 or resid 1 through 2 or resid 501 through 503)) selection = (chain 'HA' and (resid 20 through 171 or resid 173 through 293 or resid 295 thro \ ugh 432 or resid 1 through 2 or resid 501 through 503)) } ncs_group { reference = chain 'AB' selection = chain 'BB' selection = chain 'CB' selection = chain 'DB' selection = chain 'EB' selection = chain 'FB' selection = chain 'GB' selection = chain 'HB' } 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=0.40 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 11.310 Check model and map are aligned: 0.510 Set scattering table: 0.280 Process input model: 97.440 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 0.003 0.040 30936 Z= 0.213 Angle : 0.684 8.482 42160 Z= 0.355 Chirality : 0.059 0.526 4944 Planarity : 0.003 0.029 5336 Dihedral : 11.932 108.032 12904 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.16 % Allowed : 4.56 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.30 (0.14), residues: 3680 helix: 1.46 (0.22), residues: 680 sheet: 1.17 (0.16), residues: 1056 loop : -0.85 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPDA 72 HIS 0.002 0.001 HISGA 217 PHE 0.009 0.001 PHEFA 157 TYR 0.008 0.001 TYRHA 377 ARG 0.002 0.000 ARGHA 415 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 349 time to evaluate : 3.107 Fit side-chains revert: symmetry clash REVERT: AA 202 MET cc_start: 0.7514 (mtp) cc_final: 0.6451 (mtm) REVERT: AB 56 SER cc_start: 0.9257 (t) cc_final: 0.8980 (p) REVERT: BA 202 MET cc_start: 0.7444 (mtp) cc_final: 0.6928 (mtp) REVERT: BA 242 ILE cc_start: 0.7837 (mt) cc_final: 0.7298 (mt) REVERT: BA 353 MET cc_start: 0.8262 (tpt) cc_final: 0.8002 (tpt) REVERT: BB 68 LEU cc_start: 0.9064 (mt) cc_final: 0.8753 (mt) REVERT: DA 261 MET cc_start: 0.7755 (ttp) cc_final: 0.7326 (ttm) REVERT: DB 56 SER cc_start: 0.9014 (t) cc_final: 0.8628 (p) REVERT: FA 207 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6780 (p0) REVERT: FB 56 SER cc_start: 0.9164 (t) cc_final: 0.8886 (p) REVERT: GA 301 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7992 (tt) REVERT: GB 56 SER cc_start: 0.9131 (t) cc_final: 0.8761 (p) REVERT: HA 242 ILE cc_start: 0.7879 (mt) cc_final: 0.7326 (mt) REVERT: HA 353 MET cc_start: 0.8310 (tpt) cc_final: 0.8051 (tpt) REVERT: HA 361 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7273 (mt-10) outliers start: 72 outliers final: 7 residues processed: 418 average time/residue: 0.3796 time to fit residues: 265.8735 Evaluate side-chains 192 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 183 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 150 CYS Chi-restraints excluded: chain AA residue 207 ASP Chi-restraints excluded: chain DA residue 150 CYS Chi-restraints excluded: chain DA residue 207 ASP Chi-restraints excluded: chain FA residue 150 CYS Chi-restraints excluded: chain FA residue 207 ASP Chi-restraints excluded: chain GA residue 150 CYS Chi-restraints excluded: chain GA residue 207 ASP Chi-restraints excluded: chain GA residue 301 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 8.9990 chunk 272 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 184 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 282 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 210 optimal weight: 4.9990 chunk 326 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 35 HIS ** AA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 64 ASN AA 299 GLN AB 41 GLN AB 62 GLN AB 66 ASN ** BA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 64 ASN BA 167 GLN BA 299 GLN BB 75 ASN ** CA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 64 ASN CA 167 GLN ** CA 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 299 GLN ** CB 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 35 HIS ** DA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 64 ASN DA 299 GLN DB 62 GLN DB 66 ASN ** EA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 64 ASN EA 167 GLN ** EA 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EA 299 GLN ** EB 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 35 HIS ** FA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 64 ASN FA 299 GLN FB 62 GLN FB 66 ASN GA 35 HIS ** GA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GA 64 ASN GA 299 GLN GB 62 GLN GB 66 ASN ** HA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 64 ASN ** HA 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HA 299 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 30936 Z= 0.437 Angle : 0.659 7.913 42160 Z= 0.334 Chirality : 0.046 0.199 4944 Planarity : 0.004 0.050 5336 Dihedral : 9.135 59.912 6014 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.41 % Allowed : 8.51 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.09 (0.14), residues: 3680 helix: 0.93 (0.21), residues: 680 sheet: 0.77 (0.16), residues: 1120 loop : -0.96 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAA 72 HIS 0.008 0.002 HISHA 217 PHE 0.020 0.002 PHECA 231 TYR 0.018 0.002 TYRHA 276 ARG 0.011 0.001 ARGBA 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 184 time to evaluate : 3.037 Fit side-chains REVERT: BA 202 MET cc_start: 0.6950 (mtp) cc_final: 0.6419 (mtp) REVERT: BA 353 MET cc_start: 0.8357 (tpt) cc_final: 0.7951 (tpt) REVERT: DA 261 MET cc_start: 0.7895 (ttp) cc_final: 0.7520 (ttm) REVERT: DB 59 LEU cc_start: 0.8206 (tp) cc_final: 0.7959 (tp) REVERT: EA 149 MET cc_start: 0.7806 (tmm) cc_final: 0.7397 (tmm) REVERT: FA 80 MET cc_start: 0.8977 (tpp) cc_final: 0.8650 (mmm) REVERT: GA 301 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8185 (tt) REVERT: GB 59 LEU cc_start: 0.8306 (tp) cc_final: 0.8082 (tp) REVERT: HA 353 MET cc_start: 0.8444 (tpt) cc_final: 0.8023 (tpt) outliers start: 47 outliers final: 38 residues processed: 223 average time/residue: 0.3681 time to fit residues: 142.6708 Evaluate side-chains 196 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 157 time to evaluate : 3.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 89 SER Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AA residue 154 LEU Chi-restraints excluded: chain AA residue 207 ASP Chi-restraints excluded: chain AA residue 256 MET Chi-restraints excluded: chain AB residue 38 VAL Chi-restraints excluded: chain AB residue 58 VAL Chi-restraints excluded: chain BA residue 90 LEU Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BB residue 71 LEU Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 242 ILE Chi-restraints excluded: chain CB residue 71 LEU Chi-restraints excluded: chain DA residue 69 ILE Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DA residue 202 MET Chi-restraints excluded: chain DA residue 207 ASP Chi-restraints excluded: chain DB residue 38 VAL Chi-restraints excluded: chain DB residue 58 VAL Chi-restraints excluded: chain EA residue 90 LEU Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 207 ASP Chi-restraints excluded: chain FA residue 69 ILE Chi-restraints excluded: chain FA residue 89 SER Chi-restraints excluded: chain FA residue 150 CYS Chi-restraints excluded: chain FB residue 38 VAL Chi-restraints excluded: chain FB residue 58 VAL Chi-restraints excluded: chain GA residue 69 ILE Chi-restraints excluded: chain GA residue 89 SER Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 125 SER Chi-restraints excluded: chain GA residue 207 ASP Chi-restraints excluded: chain GA residue 301 ILE Chi-restraints excluded: chain GB residue 38 VAL Chi-restraints excluded: chain GB residue 58 VAL Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HB residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 222 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 327 optimal weight: 2.9990 chunk 353 optimal weight: 2.9990 chunk 291 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 262 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 64 ASN AB 41 GLN AB 66 ASN BA 35 HIS ** BA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 35 HIS ** CA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 64 ASN DB 66 ASN EA 35 HIS EA 63 ASN ** EB 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 62 GLN FB 66 ASN ** GA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 66 ASN HA 35 HIS ** HA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 167 GLN ** HB 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30936 Z= 0.229 Angle : 0.508 6.602 42160 Z= 0.261 Chirality : 0.042 0.184 4944 Planarity : 0.003 0.037 5336 Dihedral : 7.452 55.716 6009 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.17 % Allowed : 9.47 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.08 (0.14), residues: 3680 helix: 1.08 (0.21), residues: 680 sheet: 0.68 (0.16), residues: 1096 loop : -0.92 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPEA 37 HIS 0.004 0.001 HISHA 217 PHE 0.012 0.001 PHEHA 157 TYR 0.010 0.001 TYRBA 276 ARG 0.013 0.000 ARGBA 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 178 time to evaluate : 3.602 Fit side-chains REVERT: AA 80 MET cc_start: 0.8723 (mmm) cc_final: 0.8482 (mmm) REVERT: BA 353 MET cc_start: 0.8412 (tpt) cc_final: 0.8014 (tpt) REVERT: BB 73 ASP cc_start: 0.8126 (t0) cc_final: 0.7920 (t0) REVERT: DA 403 MET cc_start: 0.8554 (mtm) cc_final: 0.8283 (mtm) REVERT: DB 59 LEU cc_start: 0.8112 (tp) cc_final: 0.7902 (tp) REVERT: EA 149 MET cc_start: 0.7706 (tmm) cc_final: 0.7402 (tmm) REVERT: FA 80 MET cc_start: 0.8952 (tpp) cc_final: 0.8621 (mmm) REVERT: FA 207 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6618 (p0) REVERT: GA 301 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8141 (tt) REVERT: GA 403 MET cc_start: 0.8562 (mtm) cc_final: 0.8285 (mtm) REVERT: HA 353 MET cc_start: 0.8416 (tpt) cc_final: 0.8008 (tpt) outliers start: 39 outliers final: 31 residues processed: 214 average time/residue: 0.3529 time to fit residues: 131.0913 Evaluate side-chains 201 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 4.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 89 SER Chi-restraints excluded: chain AA residue 150 CYS Chi-restraints excluded: chain AA residue 207 ASP Chi-restraints excluded: chain AB residue 38 VAL Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 188 LEU Chi-restraints excluded: chain BA residue 378 ILE Chi-restraints excluded: chain BB residue 58 VAL Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 195 CYS Chi-restraints excluded: chain CA residue 242 ILE Chi-restraints excluded: chain CA residue 378 ILE Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DA residue 150 CYS Chi-restraints excluded: chain DA residue 207 ASP Chi-restraints excluded: chain DB residue 38 VAL Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 195 CYS Chi-restraints excluded: chain EA residue 378 ILE Chi-restraints excluded: chain FA residue 207 ASP Chi-restraints excluded: chain FB residue 38 VAL Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 150 CYS Chi-restraints excluded: chain GA residue 207 ASP Chi-restraints excluded: chain GA residue 301 ILE Chi-restraints excluded: chain GB residue 38 VAL Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 195 CYS Chi-restraints excluded: chain HA residue 378 ILE Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 0.9990 chunk 246 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 219 optimal weight: 3.9990 chunk 328 optimal weight: 4.9990 chunk 347 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 311 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 64 ASN AB 62 GLN BA 63 ASN ** BA 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 63 ASN ** CA 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 64 ASN DB 62 GLN ** EA 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 62 GLN FB 66 ASN ** GA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 62 GLN ** HA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30936 Z= 0.237 Angle : 0.507 8.662 42160 Z= 0.261 Chirality : 0.042 0.183 4944 Planarity : 0.003 0.052 5336 Dihedral : 6.714 51.352 6008 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.38 % Allowed : 10.16 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.07 (0.14), residues: 3680 helix: 1.12 (0.21), residues: 680 sheet: 0.63 (0.16), residues: 1096 loop : -0.89 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPBA 37 HIS 0.004 0.001 HISBA 217 PHE 0.010 0.001 PHEHA 393 TYR 0.011 0.001 TYRBA 276 ARG 0.004 0.000 ARGBA 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 177 time to evaluate : 3.408 Fit side-chains REVERT: BA 353 MET cc_start: 0.8415 (tpt) cc_final: 0.8012 (tpt) REVERT: DA 403 MET cc_start: 0.8560 (mtm) cc_final: 0.8288 (mtm) REVERT: DB 59 LEU cc_start: 0.8180 (tp) cc_final: 0.7945 (tp) REVERT: GA 301 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8260 (tt) REVERT: HA 202 MET cc_start: 0.7469 (mtp) cc_final: 0.7194 (mmt) REVERT: HA 353 MET cc_start: 0.8422 (tpt) cc_final: 0.7935 (tpt) outliers start: 46 outliers final: 37 residues processed: 219 average time/residue: 0.3568 time to fit residues: 137.1130 Evaluate side-chains 208 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 170 time to evaluate : 3.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AA residue 150 CYS Chi-restraints excluded: chain AA residue 154 LEU Chi-restraints excluded: chain AA residue 207 ASP Chi-restraints excluded: chain AA residue 256 MET Chi-restraints excluded: chain AB residue 58 VAL Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 253 ILE Chi-restraints excluded: chain BA residue 256 MET Chi-restraints excluded: chain BA residue 378 ILE Chi-restraints excluded: chain BB residue 58 VAL Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 195 CYS Chi-restraints excluded: chain CA residue 242 ILE Chi-restraints excluded: chain CA residue 256 MET Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DA residue 150 CYS Chi-restraints excluded: chain DA residue 207 ASP Chi-restraints excluded: chain DB residue 58 VAL Chi-restraints excluded: chain EA residue 90 LEU Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 195 CYS Chi-restraints excluded: chain EA residue 256 MET Chi-restraints excluded: chain EA residue 378 ILE Chi-restraints excluded: chain FB residue 58 VAL Chi-restraints excluded: chain GA residue 89 SER Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 125 SER Chi-restraints excluded: chain GA residue 150 CYS Chi-restraints excluded: chain GA residue 207 ASP Chi-restraints excluded: chain GA residue 301 ILE Chi-restraints excluded: chain GB residue 58 VAL Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 378 ILE Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 259 optimal weight: 3.9990 chunk 143 optimal weight: 0.4980 chunk 296 optimal weight: 0.9980 chunk 240 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 312 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 62 GLN ** BA 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 62 GLN DB 66 ASN ** FA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 66 ASN ** GA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 62 GLN ** HA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30936 Z= 0.128 Angle : 0.465 10.275 42160 Z= 0.239 Chirality : 0.041 0.181 4944 Planarity : 0.003 0.034 5336 Dihedral : 6.312 52.920 6008 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.17 % Allowed : 10.55 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.06 (0.14), residues: 3680 helix: 1.26 (0.21), residues: 680 sheet: 0.74 (0.16), residues: 1080 loop : -0.84 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPEA 37 HIS 0.003 0.001 HISBA 217 PHE 0.008 0.001 PHECA 157 TYR 0.010 0.001 TYRHA 377 ARG 0.004 0.000 ARGFA 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 174 time to evaluate : 3.154 Fit side-chains REVERT: BA 353 MET cc_start: 0.8396 (tpt) cc_final: 0.7987 (tpt) REVERT: CA 353 MET cc_start: 0.8060 (tpt) cc_final: 0.7805 (tpt) REVERT: DA 80 MET cc_start: 0.8170 (mmm) cc_final: 0.7887 (mmm) REVERT: DA 403 MET cc_start: 0.8587 (mtm) cc_final: 0.8311 (mtm) REVERT: EA 80 MET cc_start: 0.7488 (mmm) cc_final: 0.7186 (mmm) REVERT: FA 207 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6595 (p0) REVERT: GA 301 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8095 (tt) REVERT: GA 403 MET cc_start: 0.8589 (mtm) cc_final: 0.8307 (mtm) REVERT: HA 202 MET cc_start: 0.7433 (mtp) cc_final: 0.7170 (mmt) REVERT: HA 240 MET cc_start: 0.7835 (ptp) cc_final: 0.7575 (ptp) REVERT: HA 353 MET cc_start: 0.8390 (tpt) cc_final: 0.7979 (tpt) outliers start: 39 outliers final: 30 residues processed: 210 average time/residue: 0.3538 time to fit residues: 129.4381 Evaluate side-chains 200 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 73 HIS Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AA residue 150 CYS Chi-restraints excluded: chain AA residue 207 ASP Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 188 LEU Chi-restraints excluded: chain BA residue 195 CYS Chi-restraints excluded: chain BA residue 253 ILE Chi-restraints excluded: chain BA residue 256 MET Chi-restraints excluded: chain BB residue 58 VAL Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 195 CYS Chi-restraints excluded: chain CA residue 242 ILE Chi-restraints excluded: chain CA residue 256 MET Chi-restraints excluded: chain CA residue 378 ILE Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DA residue 150 CYS Chi-restraints excluded: chain DA residue 207 ASP Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 195 CYS Chi-restraints excluded: chain EA residue 256 MET Chi-restraints excluded: chain FA residue 207 ASP Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 150 CYS Chi-restraints excluded: chain GA residue 207 ASP Chi-restraints excluded: chain GA residue 301 ILE Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 195 CYS Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.9990 chunk 313 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 348 optimal weight: 2.9990 chunk 289 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 62 GLN CA 63 ASN ** DA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 290 GLN DB 62 GLN DB 66 ASN EA 63 ASN ** FA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 290 GLN ** GA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 62 GLN HA 63 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 30936 Z= 0.363 Angle : 0.569 9.824 42160 Z= 0.291 Chirality : 0.044 0.205 4944 Planarity : 0.004 0.040 5336 Dihedral : 6.812 58.953 6008 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.35 % Allowed : 10.37 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.19 (0.14), residues: 3680 helix: 0.98 (0.21), residues: 680 sheet: 0.51 (0.16), residues: 1096 loop : -0.91 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPDA 37 HIS 0.005 0.002 HISBA 217 PHE 0.016 0.002 PHEBA 157 TYR 0.016 0.002 TYRFA 276 ARG 0.005 0.001 ARGFA 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 167 time to evaluate : 3.218 Fit side-chains REVERT: BA 80 MET cc_start: 0.7484 (mmm) cc_final: 0.7043 (mmm) REVERT: BA 353 MET cc_start: 0.8377 (tpt) cc_final: 0.7903 (tpt) REVERT: CA 80 MET cc_start: 0.7462 (mmm) cc_final: 0.7010 (mmm) REVERT: CA 353 MET cc_start: 0.8209 (tpt) cc_final: 0.7905 (tpt) REVERT: GA 301 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8259 (tt) REVERT: HA 240 MET cc_start: 0.7914 (ptp) cc_final: 0.7617 (ptp) REVERT: HA 353 MET cc_start: 0.8382 (tpt) cc_final: 0.7840 (tpt) outliers start: 45 outliers final: 43 residues processed: 207 average time/residue: 0.3592 time to fit residues: 129.5471 Evaluate side-chains 207 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 163 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 89 SER Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AA residue 150 CYS Chi-restraints excluded: chain AA residue 154 LEU Chi-restraints excluded: chain AA residue 207 ASP Chi-restraints excluded: chain AB residue 58 VAL Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 125 SER Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 188 LEU Chi-restraints excluded: chain BA residue 195 CYS Chi-restraints excluded: chain BA residue 253 ILE Chi-restraints excluded: chain BA residue 256 MET Chi-restraints excluded: chain BA residue 378 ILE Chi-restraints excluded: chain BB residue 58 VAL Chi-restraints excluded: chain BB residue 73 ASP Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 195 CYS Chi-restraints excluded: chain CA residue 242 ILE Chi-restraints excluded: chain CA residue 256 MET Chi-restraints excluded: chain CA residue 378 ILE Chi-restraints excluded: chain CB residue 71 LEU Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DA residue 150 CYS Chi-restraints excluded: chain DA residue 207 ASP Chi-restraints excluded: chain DB residue 58 VAL Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 378 ILE Chi-restraints excluded: chain FA residue 150 CYS Chi-restraints excluded: chain FB residue 58 VAL Chi-restraints excluded: chain GA residue 89 SER Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 125 SER Chi-restraints excluded: chain GA residue 150 CYS Chi-restraints excluded: chain GA residue 207 ASP Chi-restraints excluded: chain GA residue 301 ILE Chi-restraints excluded: chain GB residue 58 VAL Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 195 CYS Chi-restraints excluded: chain HA residue 256 MET Chi-restraints excluded: chain HA residue 378 ILE Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 254 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 293 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 346 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 290 GLN AB 62 GLN AB 66 ASN BA 63 ASN ** DA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GA 290 GLN GB 41 GLN GB 62 GLN GB 66 ASN HA 63 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 30936 Z= 0.359 Angle : 0.570 13.972 42160 Z= 0.290 Chirality : 0.044 0.197 4944 Planarity : 0.004 0.043 5336 Dihedral : 6.875 56.362 6008 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.56 % Allowed : 10.22 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.14), residues: 3680 helix: 0.82 (0.21), residues: 680 sheet: 0.38 (0.16), residues: 1096 loop : -0.92 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPDA 37 HIS 0.005 0.001 HISHA 217 PHE 0.014 0.002 PHECA 157 TYR 0.014 0.002 TYRBA 276 ARG 0.007 0.001 ARGBA 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 164 time to evaluate : 3.335 Fit side-chains REVERT: BA 353 MET cc_start: 0.8331 (tpt) cc_final: 0.7802 (tpt) REVERT: CA 353 MET cc_start: 0.8208 (tpt) cc_final: 0.7949 (tpt) REVERT: EA 149 MET cc_start: 0.7687 (tmm) cc_final: 0.7287 (tmm) REVERT: FA 207 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6663 (p0) REVERT: GA 301 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8294 (tt) REVERT: HA 240 MET cc_start: 0.8025 (ptp) cc_final: 0.7718 (ptp) REVERT: HA 353 MET cc_start: 0.8376 (tpt) cc_final: 0.7858 (tpt) outliers start: 52 outliers final: 50 residues processed: 211 average time/residue: 0.3525 time to fit residues: 129.7593 Evaluate side-chains 215 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 163 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 73 HIS Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AA residue 150 CYS Chi-restraints excluded: chain AA residue 154 LEU Chi-restraints excluded: chain AA residue 207 ASP Chi-restraints excluded: chain AB residue 58 VAL Chi-restraints excluded: chain BA residue 90 LEU Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 188 LEU Chi-restraints excluded: chain BA residue 195 CYS Chi-restraints excluded: chain BA residue 253 ILE Chi-restraints excluded: chain BA residue 256 MET Chi-restraints excluded: chain BA residue 378 ILE Chi-restraints excluded: chain BB residue 58 VAL Chi-restraints excluded: chain BB residue 73 ASP Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 195 CYS Chi-restraints excluded: chain CA residue 242 ILE Chi-restraints excluded: chain CA residue 256 MET Chi-restraints excluded: chain CA residue 351 LEU Chi-restraints excluded: chain CA residue 378 ILE Chi-restraints excluded: chain CB residue 71 LEU Chi-restraints excluded: chain DA residue 89 SER Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DA residue 150 CYS Chi-restraints excluded: chain DA residue 207 ASP Chi-restraints excluded: chain DB residue 58 VAL Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 125 SER Chi-restraints excluded: chain EA residue 195 CYS Chi-restraints excluded: chain EA residue 253 ILE Chi-restraints excluded: chain EA residue 256 MET Chi-restraints excluded: chain EA residue 378 ILE Chi-restraints excluded: chain FA residue 150 CYS Chi-restraints excluded: chain FA residue 207 ASP Chi-restraints excluded: chain FB residue 58 VAL Chi-restraints excluded: chain GA residue 89 SER Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 125 SER Chi-restraints excluded: chain GA residue 150 CYS Chi-restraints excluded: chain GA residue 207 ASP Chi-restraints excluded: chain GA residue 301 ILE Chi-restraints excluded: chain GB residue 41 GLN Chi-restraints excluded: chain GB residue 58 VAL Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 195 CYS Chi-restraints excluded: chain HA residue 256 MET Chi-restraints excluded: chain HA residue 378 ILE Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 220 optimal weight: 0.9980 chunk 236 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 66 ASN ** DA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 30936 Z= 0.254 Angle : 0.524 12.117 42160 Z= 0.267 Chirality : 0.042 0.193 4944 Planarity : 0.003 0.040 5336 Dihedral : 6.714 56.406 6008 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.53 % Allowed : 10.31 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.14), residues: 3680 helix: 0.90 (0.21), residues: 680 sheet: 0.49 (0.16), residues: 1080 loop : -0.90 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPEA 37 HIS 0.005 0.001 HISBA 217 PHE 0.011 0.001 PHEHA 157 TYR 0.010 0.001 TYRHA 377 ARG 0.005 0.000 ARGBA 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 167 time to evaluate : 3.253 Fit side-chains REVERT: BA 353 MET cc_start: 0.8319 (tpt) cc_final: 0.7783 (tpt) REVERT: CA 353 MET cc_start: 0.8191 (tpt) cc_final: 0.7933 (tpt) REVERT: DA 403 MET cc_start: 0.8611 (mtm) cc_final: 0.8335 (mtm) REVERT: EA 202 MET cc_start: 0.7843 (tpp) cc_final: 0.7049 (mmm) REVERT: GA 301 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8318 (tt) REVERT: HA 240 MET cc_start: 0.8065 (ptp) cc_final: 0.7765 (ptp) REVERT: HA 353 MET cc_start: 0.8355 (tpt) cc_final: 0.7844 (tpt) outliers start: 51 outliers final: 48 residues processed: 214 average time/residue: 0.3464 time to fit residues: 130.5663 Evaluate side-chains 214 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 165 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 73 HIS Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AA residue 150 CYS Chi-restraints excluded: chain AA residue 154 LEU Chi-restraints excluded: chain AA residue 207 ASP Chi-restraints excluded: chain AB residue 58 VAL Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 125 SER Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 188 LEU Chi-restraints excluded: chain BA residue 195 CYS Chi-restraints excluded: chain BA residue 253 ILE Chi-restraints excluded: chain BA residue 256 MET Chi-restraints excluded: chain BA residue 378 ILE Chi-restraints excluded: chain BB residue 58 VAL Chi-restraints excluded: chain BB residue 73 ASP Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 195 CYS Chi-restraints excluded: chain CA residue 242 ILE Chi-restraints excluded: chain CA residue 253 ILE Chi-restraints excluded: chain CA residue 256 MET Chi-restraints excluded: chain CA residue 378 ILE Chi-restraints excluded: chain CB residue 71 LEU Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DA residue 150 CYS Chi-restraints excluded: chain DA residue 207 ASP Chi-restraints excluded: chain DB residue 58 VAL Chi-restraints excluded: chain EA residue 90 LEU Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 195 CYS Chi-restraints excluded: chain EA residue 378 ILE Chi-restraints excluded: chain EB residue 37 ASP Chi-restraints excluded: chain FA residue 150 CYS Chi-restraints excluded: chain FA residue 207 ASP Chi-restraints excluded: chain FB residue 58 VAL Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 125 SER Chi-restraints excluded: chain GA residue 150 CYS Chi-restraints excluded: chain GA residue 207 ASP Chi-restraints excluded: chain GA residue 301 ILE Chi-restraints excluded: chain GB residue 58 VAL Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 195 CYS Chi-restraints excluded: chain HA residue 256 MET Chi-restraints excluded: chain HA residue 378 ILE Chi-restraints excluded: chain HB residue 37 ASP Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 303 optimal weight: 4.9990 chunk 323 optimal weight: 0.0170 chunk 194 optimal weight: 8.9990 chunk 140 optimal weight: 0.9980 chunk 253 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 292 optimal weight: 5.9990 chunk 305 optimal weight: 2.9990 chunk 322 optimal weight: 0.8980 overall best weight: 1.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 62 GLN BA 63 ASN CA 63 ASN ** DA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 41 GLN DB 62 GLN DB 66 ASN EA 63 ASN ** EA 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 30936 Z= 0.204 Angle : 0.502 11.033 42160 Z= 0.255 Chirality : 0.041 0.192 4944 Planarity : 0.003 0.038 5336 Dihedral : 6.543 59.500 6008 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.53 % Allowed : 10.52 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.13 (0.14), residues: 3680 helix: 1.02 (0.21), residues: 680 sheet: 0.51 (0.16), residues: 1080 loop : -0.84 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPEA 37 HIS 0.004 0.001 HISEA 217 PHE 0.010 0.001 PHECA 157 TYR 0.010 0.001 TYRHA 377 ARG 0.003 0.000 ARGEA 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 169 time to evaluate : 3.590 Fit side-chains REVERT: BA 353 MET cc_start: 0.8341 (tpt) cc_final: 0.7816 (tpt) REVERT: CA 353 MET cc_start: 0.8172 (tpt) cc_final: 0.7928 (tpt) REVERT: DA 403 MET cc_start: 0.8608 (mtm) cc_final: 0.8335 (mtm) REVERT: GA 403 MET cc_start: 0.8611 (mtm) cc_final: 0.8336 (mtm) REVERT: HA 240 MET cc_start: 0.8097 (ptp) cc_final: 0.7782 (ptp) REVERT: HA 353 MET cc_start: 0.8316 (tpt) cc_final: 0.7786 (tpt) outliers start: 51 outliers final: 48 residues processed: 216 average time/residue: 0.3597 time to fit residues: 133.8821 Evaluate side-chains 217 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 169 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 73 HIS Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AA residue 150 CYS Chi-restraints excluded: chain AA residue 154 LEU Chi-restraints excluded: chain AA residue 207 ASP Chi-restraints excluded: chain AB residue 58 VAL Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 125 SER Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 188 LEU Chi-restraints excluded: chain BA residue 195 CYS Chi-restraints excluded: chain BA residue 253 ILE Chi-restraints excluded: chain BA residue 256 MET Chi-restraints excluded: chain BA residue 378 ILE Chi-restraints excluded: chain BB residue 58 VAL Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 195 CYS Chi-restraints excluded: chain CA residue 242 ILE Chi-restraints excluded: chain CA residue 253 ILE Chi-restraints excluded: chain CA residue 256 MET Chi-restraints excluded: chain CA residue 378 ILE Chi-restraints excluded: chain CB residue 71 LEU Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DA residue 150 CYS Chi-restraints excluded: chain DA residue 207 ASP Chi-restraints excluded: chain DB residue 41 GLN Chi-restraints excluded: chain DB residue 58 VAL Chi-restraints excluded: chain EA residue 90 LEU Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 195 CYS Chi-restraints excluded: chain EA residue 256 MET Chi-restraints excluded: chain EA residue 378 ILE Chi-restraints excluded: chain FA residue 150 CYS Chi-restraints excluded: chain FA residue 207 ASP Chi-restraints excluded: chain FB residue 58 VAL Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 125 SER Chi-restraints excluded: chain GA residue 150 CYS Chi-restraints excluded: chain GA residue 207 ASP Chi-restraints excluded: chain GB residue 58 VAL Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 195 CYS Chi-restraints excluded: chain HA residue 256 MET Chi-restraints excluded: chain HA residue 378 ILE Chi-restraints excluded: chain HB residue 37 ASP Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 9.9990 chunk 341 optimal weight: 0.9990 chunk 208 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 358 optimal weight: 10.0000 chunk 330 optimal weight: 0.8980 chunk 285 optimal weight: 0.0010 chunk 29 optimal weight: 2.9990 chunk 220 optimal weight: 0.4980 chunk 175 optimal weight: 0.0870 overall best weight: 0.4966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 62 GLN AB 66 ASN ** BA 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BA 264 ASN CA 264 ASN ** DA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EA 264 ASN ** FA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 66 ASN HB 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 30936 Z= 0.113 Angle : 0.469 10.870 42160 Z= 0.238 Chirality : 0.040 0.185 4944 Planarity : 0.003 0.044 5336 Dihedral : 5.998 54.946 6006 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.02 % Allowed : 11.03 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.02 (0.14), residues: 3680 helix: 1.13 (0.21), residues: 672 sheet: 0.67 (0.16), residues: 1088 loop : -0.77 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPCA 37 HIS 0.002 0.001 HISBA 217 PHE 0.008 0.001 PHEEA 157 TYR 0.012 0.001 TYRHA 377 ARG 0.005 0.000 ARGBA 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 3.549 Fit side-chains REVERT: BA 353 MET cc_start: 0.8363 (tpt) cc_final: 0.7881 (tpt) REVERT: CA 149 MET cc_start: 0.7884 (tmm) cc_final: 0.7603 (tmm) REVERT: CA 353 MET cc_start: 0.8221 (tpt) cc_final: 0.7936 (tpt) REVERT: DA 403 MET cc_start: 0.8588 (mtm) cc_final: 0.8327 (mtm) REVERT: GA 403 MET cc_start: 0.8599 (mtm) cc_final: 0.8325 (mtm) REVERT: HA 240 MET cc_start: 0.8072 (ptp) cc_final: 0.7751 (ptp) REVERT: HA 353 MET cc_start: 0.8300 (tpt) cc_final: 0.7755 (tpt) outliers start: 34 outliers final: 28 residues processed: 201 average time/residue: 0.3744 time to fit residues: 130.1868 Evaluate side-chains 193 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 3.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 73 HIS Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AA residue 154 LEU Chi-restraints excluded: chain AA residue 207 ASP Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 253 ILE Chi-restraints excluded: chain BA residue 256 MET Chi-restraints excluded: chain BB residue 58 VAL Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 242 ILE Chi-restraints excluded: chain CA residue 256 MET Chi-restraints excluded: chain CA residue 378 ILE Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DA residue 207 ASP Chi-restraints excluded: chain DB residue 58 VAL Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 195 CYS Chi-restraints excluded: chain FA residue 150 CYS Chi-restraints excluded: chain FA residue 207 ASP Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 125 SER Chi-restraints excluded: chain GA residue 150 CYS Chi-restraints excluded: chain GA residue 207 ASP Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 195 CYS Chi-restraints excluded: chain HB residue 37 ASP Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 0.0570 chunk 304 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 263 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 79 optimal weight: 0.0370 chunk 286 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 293 optimal weight: 0.0870 chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 264 ASN CA 264 ASN ** DA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 264 ASN ** FA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 62 GLN ** GA 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 62 GLN ** HA 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HB 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.094013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.070730 restraints weight = 256480.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.075820 restraints weight = 94076.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.075635 restraints weight = 55001.245| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30936 Z= 0.159 Angle : 0.469 10.598 42160 Z= 0.239 Chirality : 0.040 0.173 4944 Planarity : 0.003 0.034 5336 Dihedral : 5.979 53.161 6006 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.93 % Allowed : 11.48 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.06 (0.14), residues: 3680 helix: 1.18 (0.22), residues: 672 sheet: 0.69 (0.16), residues: 1088 loop : -0.75 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPEA 37 HIS 0.004 0.001 HISHA 217 PHE 0.009 0.001 PHEAA 157 TYR 0.011 0.001 TYRHA 377 ARG 0.004 0.000 ARGBA 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4730.06 seconds wall clock time: 91 minutes 16.06 seconds (5476.06 seconds total)