Starting phenix.real_space_refine on Mon Mar 18 12:28:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v8m_8644/03_2024/5v8m_8644.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v8m_8644/03_2024/5v8m_8644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v8m_8644/03_2024/5v8m_8644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v8m_8644/03_2024/5v8m_8644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v8m_8644/03_2024/5v8m_8644.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v8m_8644/03_2024/5v8m_8644.pdb" } resolution = 4.4 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= 0.006 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 120 5.16 5 C 12987 2.51 5 N 3423 2.21 5 O 4305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20835 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3493 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "B" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "F" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3493 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "I" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "R" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "T" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "G" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3493 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "J" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "S" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "U" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} 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: "D" 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: 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: "K" 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: "M" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "N" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "e" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "k" 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: "l" 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: "m" 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: "n" 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: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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: "q" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "r" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "s" 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: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "w" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "x" 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: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 60 residue: pdb=" C1 NAG K 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG K 1 " occ=0.00 residue: pdb=" C1 NAG K 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG K 2 " occ=0.00 residue: pdb=" C1 NAG M 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG M 1 " occ=0.00 residue: pdb=" C1 NAG M 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG M 2 " occ=0.00 residue: pdb=" C1 BMA M 3 " occ=0.00 ... (9 atoms not shown) pdb=" O6 BMA M 3 " occ=0.00 residue: pdb=" C1 MAN M 4 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN M 4 " occ=0.00 residue: pdb=" C1 MAN M 5 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN M 5 " occ=0.00 residue: pdb=" C1 MAN M 6 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN M 6 " occ=0.00 residue: pdb=" C1 MAN M 7 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN M 7 " occ=0.00 residue: pdb=" C1 MAN N 6 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN N 6 " occ=0.00 residue: pdb=" C1 MAN N 7 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN N 7 " occ=0.00 residue: pdb=" C1 MAN N 8 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN N 8 " occ=0.00 ... (remaining 48 not shown) Time building chain proxies: 11.32, per 1000 atoms: 0.54 Number of scatterers: 20835 At special positions: 0 Unit cell: (149.34, 144.1, 121.83, 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 120 16.00 O 4305 8.00 N 3423 7.00 C 12987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.19 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.11 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.19 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.11 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.04 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.04 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.07 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.19 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.11 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.04 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN N 4 " - " MAN N 5 " " MAN d 4 " - " MAN d 5 " " MAN e 4 " - " MAN e 5 " " MAN q 4 " - " MAN q 5 " " MAN r 4 " - " MAN r 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " MAN M 6 " - " MAN M 7 " " BMA N 3 " - " MAN N 4 " " MAN N 6 " - " MAN N 7 " " BMA V 3 " - " MAN V 6 " " MAN V 4 " - " MAN V 5 " " BMA d 3 " - " MAN d 4 " " MAN d 6 " - " MAN d 7 " " BMA e 3 " - " MAN e 4 " " MAN e 6 " - " MAN e 7 " " BMA i 3 " - " MAN i 6 " " MAN i 4 " - " MAN i 5 " " BMA q 3 " - " MAN q 4 " " MAN q 6 " - " MAN q 7 " " BMA r 3 " - " MAN r 4 " " MAN r 6 " - " MAN r 7 " " BMA v 3 " - " MAN v 6 " " MAN v 4 " - " MAN v 5 " ALPHA1-6 " BMA M 3 " - " MAN M 6 " " BMA N 3 " - " MAN N 6 " " MAN N 6 " - " MAN N 8 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA d 3 " - " MAN d 6 " " BMA e 3 " - " MAN e 6 " " MAN e 6 " - " MAN e 8 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " BMA q 3 " - " MAN q 6 " " BMA r 3 " - " MAN r 6 " " MAN r 6 " - " MAN r 8 " " BMA v 3 " - " MAN v 4 " " BMA w 3 " - " MAN w 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 604 " - " ASN A 133 " " NAG A 611 " - " ASN A 234 " " NAG A 633 " - " ASN A 339 " " NAG A 634 " - " ASN A 355 " " NAG A 645 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 1 " - " ASN A 88 " " NAG D 1 " - " ASN A 156 " " NAG E 1 " - " ASN A 160 " " NAG F 604 " - " ASN F 133 " " NAG F 611 " - " ASN F 234 " " NAG F 631 " - " ASN F 355 " " NAG F 634 " - " ASN F 339 " " NAG F 645 " - " ASN F 392 " " NAG G 604 " - " ASN G 133 " " NAG G 611 " - " ASN G 234 " " NAG G 633 " - " ASN G 339 " " NAG G 634 " - " ASN G 355 " " NAG G 645 " - " ASN G 392 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 637 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 637 " " NAG K 1 " - " ASN A 197 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 276 " " NAG O 1 " - " ASN A 295 " " NAG P 1 " - " ASN A 301 " " NAG Q 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 363 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN L 72 " " NAG Z 1 " - " ASN F 88 " " NAG a 1 " - " ASN F 156 " " NAG b 1 " - " ASN F 160 " " NAG c 1 " - " ASN F 197 " " NAG d 1 " - " ASN F 262 " " NAG e 1 " - " ASN F 276 " " NAG f 1 " - " ASN F 295 " " NAG g 1 " - " ASN F 301 " " NAG h 1 " - " ASN F 332 " " NAG i 1 " - " ASN F 363 " " NAG j 1 " - " ASN F 386 " " NAG k 1 " - " ASN F 448 " " NAG l 1 " - " ASN T 72 " " NAG m 1 " - " ASN G 88 " " NAG n 1 " - " ASN G 156 " " NAG o 1 " - " ASN G 160 " " NAG p 1 " - " ASN G 197 " " NAG q 1 " - " ASN G 262 " " NAG r 1 " - " ASN G 276 " " NAG s 1 " - " ASN G 295 " " NAG t 1 " - " ASN G 301 " " NAG u 1 " - " ASN G 332 " " NAG v 1 " - " ASN G 363 " " NAG w 1 " - " ASN G 386 " " NAG x 1 " - " ASN G 448 " " NAG y 1 " - " ASN U 72 " Time building additional restraints: 10.74 Conformation dependent library (CDL) restraints added in 3.4 seconds 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4422 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 54 sheets defined 24.0% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.824A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.865A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.500A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.967A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.745A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.582A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 597 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'F' and resid 99 through 117 removed outlier: 3.824A pdb=" N ILE F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 removed outlier: 3.864A pdb=" N VAL F 127 " --> pdb=" O PRO F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 151 Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 377 through 381 removed outlier: 3.501A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 392 Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.967A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 528 Processing helix chain 'I' and resid 529 through 534 removed outlier: 3.745A pdb=" N SER I 534 " --> pdb=" O MET I 530 " (cutoff:3.500A) Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.581A pdb=" N ARG I 542 " --> pdb=" O THR I 538 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 597 Processing helix chain 'I' and resid 611 through 615 Processing helix chain 'I' and resid 618 through 624 Processing helix chain 'I' and resid 627 through 636 Processing helix chain 'I' and resid 638 through 649 Processing helix chain 'I' and resid 650 through 663 Processing helix chain 'R' and resid 28 through 32 Processing helix chain 'R' and resid 60 through 64 Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'T' and resid 79 through 83 Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.824A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.864A pdb=" N VAL G 127 " --> pdb=" O PRO G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 151 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 377 through 381 removed outlier: 3.500A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 392 Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.966A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 528 Processing helix chain 'J' and resid 529 through 534 removed outlier: 3.745A pdb=" N SER J 534 " --> pdb=" O MET J 530 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.581A pdb=" N ARG J 542 " --> pdb=" O THR J 538 " (cutoff:3.500A) Processing helix chain 'J' and resid 571 through 597 Processing helix chain 'J' and resid 611 through 615 Processing helix chain 'J' and resid 618 through 624 Processing helix chain 'J' and resid 627 through 636 Processing helix chain 'J' and resid 638 through 649 Processing helix chain 'J' and resid 650 through 663 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 83 through 87 Processing helix chain 'U' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.863A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.056A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 394 through 395 removed outlier: 6.669A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.198A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 376 removed outlier: 4.339A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 316 through 323 removed outlier: 4.411A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.820A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.198A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.593A pdb=" N ALA H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.593A pdb=" N ALA H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.730A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AC1, first strand: chain 'F' and resid 35 through 40 Processing sheet with id=AC2, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.863A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 91 through 92 Processing sheet with id=AC5, first strand: chain 'F' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain 'F' and resid 181 through 183 Processing sheet with id=AC7, first strand: chain 'F' and resid 201 through 202 Processing sheet with id=AC8, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.056A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 394 through 395 removed outlier: 6.668A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.197A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 374 through 376 removed outlier: 4.339A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 316 through 323 removed outlier: 4.410A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.819A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.197A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AD5, first strand: chain 'R' and resid 10 through 11 removed outlier: 6.593A pdb=" N ALA R 10 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 10 through 11 removed outlier: 6.593A pdb=" N ALA R 10 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL R 102 " --> pdb=" O ARG R 94 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 4 through 6 Processing sheet with id=AD8, first strand: chain 'T' and resid 10 through 11 removed outlier: 6.729A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 10 through 11 Processing sheet with id=AE1, first strand: chain 'G' and resid 35 through 40 Processing sheet with id=AE2, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AE3, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.863A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 91 through 92 Processing sheet with id=AE5, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AE6, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AE7, first strand: chain 'G' and resid 201 through 202 Processing sheet with id=AE8, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.057A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 394 through 395 removed outlier: 6.669A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.197A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 374 through 376 removed outlier: 4.339A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 316 through 323 removed outlier: 4.411A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 271 through 273 removed outlier: 6.820A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.197A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 5 through 6 Processing sheet with id=AF5, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.594A pdb=" N ALA S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE S 34 " --> pdb=" O TRP S 50 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TRP S 50 " --> pdb=" O ILE S 34 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.594A pdb=" N ALA S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL S 102 " --> pdb=" O ARG S 94 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 4 through 6 Processing sheet with id=AF8, first strand: chain 'U' and resid 10 through 11 removed outlier: 6.730A pdb=" N TRP U 35 " --> pdb=" O LEU U 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 10 through 11 849 hydrogen bonds defined for protein. 2025 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.87 Time building geometry restraints manager: 11.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5451 1.33 - 1.45: 5952 1.45 - 1.58: 9675 1.58 - 1.71: 9 1.71 - 1.83: 162 Bond restraints: 21249 Sorted by residual: bond pdb=" CA PHE S 78 " pdb=" C PHE S 78 " ideal model delta sigma weight residual 1.522 1.465 0.056 1.21e-02 6.83e+03 2.15e+01 bond pdb=" CA PHE H 78 " pdb=" C PHE H 78 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.21e-02 6.83e+03 2.11e+01 bond pdb=" CA PHE R 78 " pdb=" C PHE R 78 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.21e-02 6.83e+03 2.06e+01 bond pdb=" C3 MAN e 5 " pdb=" C4 MAN e 5 " ideal model delta sigma weight residual 1.524 1.615 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C3 MAN N 5 " pdb=" C4 MAN N 5 " ideal model delta sigma weight residual 1.524 1.615 -0.091 2.00e-02 2.50e+03 2.05e+01 ... (remaining 21244 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.34: 570 105.34 - 112.56: 11151 112.56 - 119.78: 8210 119.78 - 127.00: 8636 127.00 - 134.22: 302 Bond angle restraints: 28869 Sorted by residual: angle pdb=" C LYS G 252 " pdb=" N PRO G 253 " pdb=" CA PRO G 253 " ideal model delta sigma weight residual 120.12 131.59 -11.47 1.11e+00 8.12e-01 1.07e+02 angle pdb=" C LYS A 252 " pdb=" N PRO A 253 " pdb=" CA PRO A 253 " ideal model delta sigma weight residual 120.12 131.53 -11.41 1.11e+00 8.12e-01 1.06e+02 angle pdb=" C LYS F 252 " pdb=" N PRO F 253 " pdb=" CA PRO F 253 " ideal model delta sigma weight residual 120.12 131.52 -11.40 1.11e+00 8.12e-01 1.05e+02 angle pdb=" C CYS A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta sigma weight residual 119.56 129.03 -9.47 1.01e+00 9.80e-01 8.79e+01 angle pdb=" C CYS F 239 " pdb=" N PRO F 240 " pdb=" CA PRO F 240 " ideal model delta sigma weight residual 119.56 129.00 -9.44 1.01e+00 9.80e-01 8.74e+01 ... (remaining 28864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 13890 22.84 - 45.68: 456 45.68 - 68.52: 162 68.52 - 91.37: 96 91.37 - 114.21: 42 Dihedral angle restraints: 14646 sinusoidal: 7794 harmonic: 6852 Sorted by residual: dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.22 44.22 1 1.00e+01 1.00e-02 2.72e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.22 44.22 1 1.00e+01 1.00e-02 2.72e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.22 44.22 1 1.00e+01 1.00e-02 2.72e+01 ... (remaining 14643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.176: 3318 0.176 - 0.351: 282 0.351 - 0.527: 51 0.527 - 0.702: 3 0.702 - 0.878: 3 Chirality restraints: 3657 Sorted by residual: chirality pdb=" C1 MAN e 6 " pdb=" O6 BMA e 3 " pdb=" C2 MAN e 6 " pdb=" O5 MAN e 6 " both_signs ideal model delta sigma weight residual False 2.40 1.52 0.88 2.00e-02 2.50e+03 1.93e+03 chirality pdb=" C1 MAN N 6 " pdb=" O6 BMA N 3 " pdb=" C2 MAN N 6 " pdb=" O5 MAN N 6 " both_signs ideal model delta sigma weight residual False 2.40 1.52 0.88 2.00e-02 2.50e+03 1.92e+03 chirality pdb=" C1 MAN r 6 " pdb=" O6 BMA r 3 " pdb=" C2 MAN r 6 " pdb=" O5 MAN r 6 " both_signs ideal model delta sigma weight residual False 2.40 1.53 0.87 2.00e-02 2.50e+03 1.91e+03 ... (remaining 3654 not shown) Planarity restraints: 3534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 363 " -0.195 2.00e-02 2.50e+03 2.62e-01 8.61e+02 pdb=" CG ASN A 363 " 0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN A 363 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 363 " 0.443 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.319 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 363 " 0.195 2.00e-02 2.50e+03 2.62e-01 8.61e+02 pdb=" CG ASN G 363 " -0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN G 363 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN G 363 " -0.443 2.00e-02 2.50e+03 pdb=" C1 NAG v 1 " 0.319 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 363 " -0.195 2.00e-02 2.50e+03 2.62e-01 8.60e+02 pdb=" CG ASN F 363 " 0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN F 363 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN F 363 " 0.443 2.00e-02 2.50e+03 pdb=" C1 NAG i 1 " -0.319 2.00e-02 2.50e+03 ... (remaining 3531 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 1204 2.68 - 3.23: 21423 3.23 - 3.79: 33682 3.79 - 4.34: 43612 4.34 - 4.90: 69605 Nonbonded interactions: 169526 Sorted by model distance: nonbonded pdb=" OD1 ASN A 363 " pdb=" O SER A 364 " model vdw 2.124 3.040 nonbonded pdb=" OD1 ASN F 363 " pdb=" O SER F 364 " model vdw 2.124 3.040 nonbonded pdb=" OD1 ASN G 363 " pdb=" O SER G 364 " model vdw 2.124 3.040 nonbonded pdb=" O ARG L 66 " pdb=" CD1 TRP L 67 " model vdw 2.212 3.260 nonbonded pdb=" O ARG T 66 " pdb=" CD1 TRP T 67 " model vdw 2.212 3.260 ... (remaining 169521 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 'F' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'Z' selection = chain 'm' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'H' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'L' selection = chain 'T' selection = chain 'U' } ncs_group { reference = (chain 'M' and resid 5 through 7) selection = (chain 'N' and resid 6 through 8) selection = (chain 'V' and resid 4 through 6) selection = (chain 'd' and resid 5 through 7) selection = (chain 'e' and resid 6 through 8) selection = (chain 'i' and resid 4 through 6) selection = (chain 'q' and resid 5 through 7) selection = (chain 'r' and resid 6 through 8) selection = (chain 'v' and resid 4 through 6) } ncs_group { reference = chain 'W' selection = chain 'j' selection = chain 'w' } 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=0.00 max=1.00 mean=0.97 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: 0.840 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: 0.010 Extract box with map and model: 4.920 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 58.390 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 : 0.015 0.091 21249 Z= 0.989 Angle : 1.860 12.634 28869 Z= 1.156 Chirality : 0.114 0.878 3657 Planarity : 0.012 0.087 3474 Dihedral : 15.328 114.207 10107 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.14 % Allowed : 0.43 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.18), residues: 2328 helix: -0.54 (0.23), residues: 390 sheet: 0.73 (0.18), residues: 717 loop : 3.10 (0.19), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.008 TRP F 479 HIS 0.009 0.003 HIS A 72 PHE 0.022 0.005 PHE S 78 TYR 0.048 0.005 TYR R 76 ARG 0.005 0.001 ARG G 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 391 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8165 (ttt) cc_final: 0.7889 (ttm) REVERT: A 117 LYS cc_start: 0.9082 (mttt) cc_final: 0.8834 (mmmm) REVERT: A 150 MET cc_start: 0.8458 (mmm) cc_final: 0.8246 (mmm) REVERT: A 161 MET cc_start: 0.8982 (tmm) cc_final: 0.8692 (tmm) REVERT: B 633 LYS cc_start: 0.9162 (mttt) cc_final: 0.8818 (tppt) REVERT: B 647 GLU cc_start: 0.8918 (tt0) cc_final: 0.8404 (tt0) REVERT: H 73 PHE cc_start: 0.8529 (m-80) cc_final: 0.8200 (m-80) REVERT: L 33 LEU cc_start: 0.9481 (tp) cc_final: 0.9218 (tp) REVERT: F 180 ASP cc_start: 0.8685 (m-30) cc_final: 0.8474 (m-30) REVERT: F 217 TYR cc_start: 0.8413 (m-80) cc_final: 0.8011 (m-80) REVERT: F 434 MET cc_start: 0.8610 (ptm) cc_final: 0.8162 (ppp) REVERT: F 435 TYR cc_start: 0.8897 (t80) cc_final: 0.8637 (t80) REVERT: I 633 LYS cc_start: 0.9158 (mttt) cc_final: 0.8792 (tppp) REVERT: I 647 GLU cc_start: 0.8891 (tt0) cc_final: 0.8368 (tt0) REVERT: R 73 PHE cc_start: 0.8412 (m-80) cc_final: 0.8136 (m-80) REVERT: T 33 LEU cc_start: 0.9514 (tp) cc_final: 0.9097 (tp) REVERT: T 58 VAL cc_start: 0.8125 (t) cc_final: 0.7807 (t) REVERT: G 217 TYR cc_start: 0.8322 (m-80) cc_final: 0.7961 (m-80) REVERT: J 538 THR cc_start: 0.8248 (p) cc_final: 0.8045 (p) REVERT: J 610 TRP cc_start: 0.7018 (p-90) cc_final: 0.6687 (p-90) REVERT: J 633 LYS cc_start: 0.9103 (mttt) cc_final: 0.8873 (tppp) REVERT: J 647 GLU cc_start: 0.8678 (tt0) cc_final: 0.8012 (tt0) REVERT: S 73 PHE cc_start: 0.8519 (m-80) cc_final: 0.8143 (m-80) REVERT: U 33 LEU cc_start: 0.9538 (tp) cc_final: 0.9275 (tp) REVERT: U 104 LEU cc_start: 0.8905 (mt) cc_final: 0.8626 (mt) outliers start: 3 outliers final: 3 residues processed: 394 average time/residue: 0.3668 time to fit residues: 212.6460 Evaluate side-chains 197 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 194 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 209 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 428 GLN ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 ASN F 428 GLN G 80 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21249 Z= 0.259 Angle : 0.841 10.064 28869 Z= 0.420 Chirality : 0.049 0.289 3657 Planarity : 0.006 0.053 3474 Dihedral : 14.543 76.593 5661 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.19 % Allowed : 1.15 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.18), residues: 2328 helix: 1.15 (0.27), residues: 372 sheet: 0.45 (0.18), residues: 759 loop : 2.17 (0.19), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP S 103 HIS 0.004 0.001 HIS F 85 PHE 0.019 0.002 PHE L 62 TYR 0.017 0.002 TYR J 586 ARG 0.004 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 311 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.9732 (mt) cc_final: 0.9486 (tt) REVERT: A 377 ASN cc_start: 0.8384 (t0) cc_final: 0.8135 (t0) REVERT: A 434 MET cc_start: 0.8695 (ppp) cc_final: 0.8166 (ppp) REVERT: B 584 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8335 (tm-30) REVERT: B 586 TYR cc_start: 0.9129 (t80) cc_final: 0.8906 (t80) REVERT: B 610 TRP cc_start: 0.7115 (p-90) cc_final: 0.6779 (p-90) REVERT: B 633 LYS cc_start: 0.9180 (mttt) cc_final: 0.8933 (tppt) REVERT: H 5 LEU cc_start: 0.8885 (tp) cc_final: 0.8613 (tt) REVERT: H 23 GLU cc_start: 0.8217 (mp0) cc_final: 0.7936 (mp0) REVERT: H 28 ASN cc_start: 0.8218 (p0) cc_final: 0.7969 (p0) REVERT: H 43 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8315 (mp-120) REVERT: H 100 TRP cc_start: 0.9540 (m-10) cc_final: 0.9040 (m-10) REVERT: L 33 LEU cc_start: 0.9544 (tp) cc_final: 0.9150 (tp) REVERT: L 46 LEU cc_start: 0.8517 (tt) cc_final: 0.7765 (tt) REVERT: F 150 MET cc_start: 0.7852 (mmm) cc_final: 0.7354 (mmm) REVERT: F 180 ASP cc_start: 0.8573 (m-30) cc_final: 0.8279 (m-30) REVERT: F 377 ASN cc_start: 0.8579 (t0) cc_final: 0.8278 (t0) REVERT: F 434 MET cc_start: 0.8503 (ptm) cc_final: 0.8277 (ptm) REVERT: I 530 MET cc_start: 0.8133 (ttm) cc_final: 0.7800 (ttm) REVERT: I 584 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8379 (tm-30) REVERT: I 626 MET cc_start: 0.7346 (ptp) cc_final: 0.7049 (ptt) REVERT: I 648 GLU cc_start: 0.8830 (tp30) cc_final: 0.8173 (tp30) REVERT: R 5 LEU cc_start: 0.8851 (tp) cc_final: 0.7582 (tt) REVERT: R 23 GLU cc_start: 0.8157 (mp0) cc_final: 0.7306 (mp0) REVERT: R 28 ASN cc_start: 0.8315 (p0) cc_final: 0.7954 (p0) REVERT: R 100 TRP cc_start: 0.9496 (m-10) cc_final: 0.8776 (m-10) REVERT: T 33 LEU cc_start: 0.9521 (tp) cc_final: 0.9102 (tp) REVERT: T 46 LEU cc_start: 0.8410 (tt) cc_final: 0.7719 (tt) REVERT: G 377 ASN cc_start: 0.8533 (t0) cc_final: 0.8258 (t0) REVERT: G 435 TYR cc_start: 0.8946 (t80) cc_final: 0.8707 (t80) REVERT: J 584 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8191 (tm-30) REVERT: J 647 GLU cc_start: 0.8449 (tt0) cc_final: 0.8211 (tt0) REVERT: S 82 LYS cc_start: 0.8316 (mttt) cc_final: 0.7968 (mptt) REVERT: S 95 GLN cc_start: 0.9243 (tt0) cc_final: 0.8973 (tt0) REVERT: S 100 TRP cc_start: 0.9485 (m-10) cc_final: 0.8819 (m-10) REVERT: S 109 VAL cc_start: 0.9256 (t) cc_final: 0.8909 (t) outliers start: 4 outliers final: 0 residues processed: 315 average time/residue: 0.3442 time to fit residues: 162.3399 Evaluate side-chains 201 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 227 optimal weight: 0.4980 chunk 187 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN L 24 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 ASN R 59 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 618 ASN ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21249 Z= 0.280 Angle : 0.779 9.712 28869 Z= 0.385 Chirality : 0.047 0.252 3657 Planarity : 0.005 0.052 3474 Dihedral : 11.692 66.887 5661 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.19 % Allowed : 1.58 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2328 helix: 1.12 (0.27), residues: 387 sheet: 0.27 (0.17), residues: 753 loop : 1.52 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 103 HIS 0.005 0.001 HIS F 85 PHE 0.032 0.002 PHE R 73 TYR 0.028 0.002 TYR T 49 ARG 0.009 0.001 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 261 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8757 (tpp) cc_final: 0.8502 (tpp) REVERT: A 108 ILE cc_start: 0.9503 (pt) cc_final: 0.9274 (mt) REVERT: A 109 ILE cc_start: 0.9782 (mt) cc_final: 0.9443 (tt) REVERT: A 377 ASN cc_start: 0.8499 (t0) cc_final: 0.8163 (t0) REVERT: A 434 MET cc_start: 0.8852 (ppp) cc_final: 0.8304 (ppp) REVERT: B 584 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8375 (tm-30) REVERT: H 23 GLU cc_start: 0.8107 (mp0) cc_final: 0.7848 (mp0) REVERT: H 100 TRP cc_start: 0.9541 (m-10) cc_final: 0.8998 (m-10) REVERT: F 150 MET cc_start: 0.8160 (mmm) cc_final: 0.7909 (mmm) REVERT: F 180 ASP cc_start: 0.8624 (m-30) cc_final: 0.8325 (m-30) REVERT: F 377 ASN cc_start: 0.8755 (t0) cc_final: 0.8320 (t0) REVERT: F 434 MET cc_start: 0.8589 (ptm) cc_final: 0.8295 (ptm) REVERT: I 584 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8369 (tm-30) REVERT: T 47 LEU cc_start: 0.8590 (mm) cc_final: 0.8339 (mm) REVERT: T 53 LYS cc_start: 0.9452 (mtmm) cc_final: 0.9196 (ptmt) REVERT: G 377 ASN cc_start: 0.8701 (t0) cc_final: 0.8403 (t0) REVERT: J 584 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8296 (tm-30) REVERT: J 610 TRP cc_start: 0.7154 (p-90) cc_final: 0.6668 (p-90) REVERT: J 648 GLU cc_start: 0.8713 (tp30) cc_final: 0.8038 (tp30) REVERT: U 33 LEU cc_start: 0.9592 (tp) cc_final: 0.9170 (tp) REVERT: U 34 ASN cc_start: 0.8972 (m-40) cc_final: 0.8679 (t0) REVERT: U 42 LYS cc_start: 0.9251 (mtmt) cc_final: 0.8835 (ptmm) outliers start: 4 outliers final: 0 residues processed: 265 average time/residue: 0.3441 time to fit residues: 137.4174 Evaluate side-chains 177 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 10.0000 chunk 158 optimal weight: 0.0370 chunk 109 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 223 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS I 640 GLN T 24 GLN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 374 HIS J 640 GLN S 1 GLN S 28 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21249 Z= 0.230 Angle : 0.708 9.762 28869 Z= 0.347 Chirality : 0.046 0.275 3657 Planarity : 0.004 0.048 3474 Dihedral : 9.916 61.068 5661 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.10 % Allowed : 1.48 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.18), residues: 2328 helix: 1.69 (0.27), residues: 369 sheet: 0.27 (0.17), residues: 783 loop : 1.25 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 100 HIS 0.004 0.001 HIS A 85 PHE 0.020 0.001 PHE H 73 TYR 0.015 0.001 TYR U 49 ARG 0.008 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8382 (t0) cc_final: 0.8113 (t0) REVERT: A 434 MET cc_start: 0.8793 (ppp) cc_final: 0.8249 (ppp) REVERT: B 584 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8442 (tm-30) REVERT: H 23 GLU cc_start: 0.8225 (mp0) cc_final: 0.8015 (mp0) REVERT: H 82 LYS cc_start: 0.8491 (mttt) cc_final: 0.8137 (mmtt) REVERT: L 47 LEU cc_start: 0.8955 (mm) cc_final: 0.8077 (tp) REVERT: L 87 PHE cc_start: 0.7297 (m-10) cc_final: 0.6917 (m-10) REVERT: F 161 MET cc_start: 0.9029 (tmm) cc_final: 0.8777 (tmm) REVERT: F 377 ASN cc_start: 0.8648 (t0) cc_final: 0.8330 (t0) REVERT: F 434 MET cc_start: 0.8685 (ptm) cc_final: 0.8457 (ptm) REVERT: I 530 MET cc_start: 0.8534 (mmm) cc_final: 0.8050 (mmm) REVERT: I 584 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8434 (tm-30) REVERT: R 5 LEU cc_start: 0.8959 (tt) cc_final: 0.8443 (tt) REVERT: R 23 GLU cc_start: 0.8094 (mp0) cc_final: 0.7305 (mp0) REVERT: R 82 LYS cc_start: 0.8216 (mttt) cc_final: 0.7989 (mmtt) REVERT: R 100 TRP cc_start: 0.9121 (m-10) cc_final: 0.8630 (m-10) REVERT: T 34 ASN cc_start: 0.8084 (t0) cc_final: 0.7714 (t0) REVERT: G 377 ASN cc_start: 0.8581 (t0) cc_final: 0.8292 (t0) REVERT: J 584 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8309 (tm-30) REVERT: J 610 TRP cc_start: 0.7032 (p-90) cc_final: 0.6642 (p-90) REVERT: S 76 TYR cc_start: 0.8792 (m-80) cc_final: 0.8350 (m-80) REVERT: U 42 LYS cc_start: 0.9280 (mtmt) cc_final: 0.8962 (ptmm) REVERT: U 46 LEU cc_start: 0.8885 (pt) cc_final: 0.8521 (tt) outliers start: 2 outliers final: 0 residues processed: 242 average time/residue: 0.3439 time to fit residues: 127.1615 Evaluate side-chains 168 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 190 optimal weight: 0.7980 chunk 154 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 21249 Z= 0.329 Angle : 0.761 9.817 28869 Z= 0.372 Chirality : 0.047 0.263 3657 Planarity : 0.005 0.076 3474 Dihedral : 9.418 59.936 5661 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.10 % Allowed : 1.72 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2328 helix: 1.26 (0.26), residues: 387 sheet: 0.33 (0.18), residues: 723 loop : 0.89 (0.19), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP I 571 HIS 0.007 0.001 HIS G 85 PHE 0.024 0.002 PHE F 53 TYR 0.012 0.002 TYR U 49 ARG 0.010 0.001 ARG G 298 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 221 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8899 (tpp) cc_final: 0.8563 (tpp) REVERT: A 108 ILE cc_start: 0.9537 (OUTLIER) cc_final: 0.9173 (mm) REVERT: A 150 MET cc_start: 0.8340 (mmm) cc_final: 0.7922 (mmm) REVERT: A 377 ASN cc_start: 0.8392 (t0) cc_final: 0.8179 (t0) REVERT: A 434 MET cc_start: 0.8903 (ppp) cc_final: 0.8439 (ppp) REVERT: B 584 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8454 (tm-30) REVERT: B 633 LYS cc_start: 0.9279 (mmmt) cc_final: 0.9075 (mtpt) REVERT: H 23 GLU cc_start: 0.8163 (mp0) cc_final: 0.7921 (mp0) REVERT: H 28 ASN cc_start: 0.8522 (p0) cc_final: 0.7367 (p0) REVERT: H 45 LEU cc_start: 0.9237 (mt) cc_final: 0.9036 (mt) REVERT: H 82 LYS cc_start: 0.8504 (mttt) cc_final: 0.8268 (mmtt) REVERT: F 377 ASN cc_start: 0.8735 (t0) cc_final: 0.8453 (t0) REVERT: F 434 MET cc_start: 0.8729 (ptm) cc_final: 0.8445 (ptm) REVERT: I 530 MET cc_start: 0.8637 (mmm) cc_final: 0.8160 (mmm) REVERT: I 584 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8465 (tm-30) REVERT: I 610 TRP cc_start: 0.6933 (p-90) cc_final: 0.6466 (p-90) REVERT: R 23 GLU cc_start: 0.8120 (mp0) cc_final: 0.7529 (mp0) REVERT: G 161 MET cc_start: 0.9049 (tmm) cc_final: 0.8717 (tmm) REVERT: G 377 ASN cc_start: 0.8633 (t0) cc_final: 0.8394 (t0) REVERT: J 584 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8408 (tm-30) REVERT: J 610 TRP cc_start: 0.7117 (p-90) cc_final: 0.6623 (p-90) REVERT: S 27 TYR cc_start: 0.8776 (p90) cc_final: 0.8542 (p90) REVERT: S 71 TRP cc_start: 0.8588 (p-90) cc_final: 0.8135 (p-90) REVERT: U 46 LEU cc_start: 0.8963 (pt) cc_final: 0.8725 (pt) outliers start: 2 outliers final: 0 residues processed: 223 average time/residue: 0.3372 time to fit residues: 116.6295 Evaluate side-chains 157 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 185 optimal weight: 0.4980 chunk 103 optimal weight: 0.0980 chunk 18 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21249 Z= 0.247 Angle : 0.690 9.826 28869 Z= 0.341 Chirality : 0.045 0.283 3657 Planarity : 0.004 0.039 3474 Dihedral : 8.830 58.542 5661 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.05 % Allowed : 1.10 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.18), residues: 2328 helix: 1.42 (0.27), residues: 387 sheet: 0.08 (0.17), residues: 798 loop : 0.86 (0.20), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 103 HIS 0.004 0.001 HIS G 85 PHE 0.012 0.001 PHE T 62 TYR 0.020 0.002 TYR T 36 ARG 0.006 0.000 ARG G 298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8196 (mtp) cc_final: 0.7968 (mtp) REVERT: A 104 MET cc_start: 0.8877 (tpp) cc_final: 0.8530 (tpp) REVERT: A 150 MET cc_start: 0.8377 (mmm) cc_final: 0.8076 (mmm) REVERT: B 546 SER cc_start: 0.8601 (m) cc_final: 0.8253 (p) REVERT: B 584 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8437 (tm-30) REVERT: H 23 GLU cc_start: 0.8178 (mp0) cc_final: 0.7875 (mp0) REVERT: H 82 LYS cc_start: 0.8610 (mttt) cc_final: 0.8296 (mmtt) REVERT: F 161 MET cc_start: 0.9032 (tmm) cc_final: 0.8792 (tmm) REVERT: I 530 MET cc_start: 0.8664 (mmm) cc_final: 0.8318 (mmm) REVERT: I 546 SER cc_start: 0.8910 (m) cc_final: 0.8428 (p) REVERT: I 584 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8477 (tm-30) REVERT: I 610 TRP cc_start: 0.6907 (p-90) cc_final: 0.6381 (p-90) REVERT: R 5 LEU cc_start: 0.8974 (tt) cc_final: 0.8529 (tt) REVERT: R 23 GLU cc_start: 0.8226 (mp0) cc_final: 0.7536 (mp0) REVERT: T 47 LEU cc_start: 0.8685 (mm) cc_final: 0.8319 (mm) REVERT: G 161 MET cc_start: 0.9019 (tmm) cc_final: 0.8745 (tmm) REVERT: J 530 MET cc_start: 0.8909 (mmm) cc_final: 0.8519 (mmm) REVERT: J 584 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8371 (tm-30) REVERT: J 610 TRP cc_start: 0.6964 (p-90) cc_final: 0.6455 (p-90) REVERT: S 71 TRP cc_start: 0.8619 (p-90) cc_final: 0.8297 (p-90) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.3144 time to fit residues: 110.4896 Evaluate side-chains 166 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 124 optimal weight: 0.2980 chunk 222 optimal weight: 7.9990 chunk 139 optimal weight: 0.0470 chunk 135 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21249 Z= 0.176 Angle : 0.658 9.784 28869 Z= 0.324 Chirality : 0.045 0.289 3657 Planarity : 0.004 0.037 3474 Dihedral : 8.384 59.235 5661 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.05 % Allowed : 0.53 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.18), residues: 2328 helix: 1.65 (0.28), residues: 384 sheet: 0.26 (0.17), residues: 780 loop : 0.91 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 628 HIS 0.004 0.001 HIS F 374 PHE 0.013 0.001 PHE R 73 TYR 0.017 0.001 TYR T 36 ARG 0.006 0.000 ARG H 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8120 (mtp) cc_final: 0.7875 (mtp) REVERT: A 104 MET cc_start: 0.8936 (tpp) cc_final: 0.8426 (tpp) REVERT: A 150 MET cc_start: 0.8288 (mmm) cc_final: 0.8062 (mmm) REVERT: A 161 MET cc_start: 0.8908 (tmm) cc_final: 0.8558 (tmm) REVERT: B 546 SER cc_start: 0.8620 (m) cc_final: 0.8258 (p) REVERT: B 571 TRP cc_start: 0.7849 (m-10) cc_final: 0.7540 (m-10) REVERT: B 584 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8407 (tm-30) REVERT: H 23 GLU cc_start: 0.8208 (mp0) cc_final: 0.7940 (mp0) REVERT: F 150 MET cc_start: 0.7863 (mmm) cc_final: 0.7558 (mmm) REVERT: I 530 MET cc_start: 0.8714 (mmm) cc_final: 0.8393 (mmm) REVERT: I 546 SER cc_start: 0.8922 (m) cc_final: 0.8413 (p) REVERT: I 584 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8449 (tm-30) REVERT: I 610 TRP cc_start: 0.7136 (p-90) cc_final: 0.6798 (p-90) REVERT: R 5 LEU cc_start: 0.8973 (tt) cc_final: 0.8753 (tt) REVERT: R 23 GLU cc_start: 0.8256 (mp0) cc_final: 0.7631 (mp0) REVERT: G 161 MET cc_start: 0.8953 (tmm) cc_final: 0.8642 (tmm) REVERT: J 584 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8365 (tm-30) REVERT: J 610 TRP cc_start: 0.6955 (p-90) cc_final: 0.6512 (p-90) REVERT: S 71 TRP cc_start: 0.8572 (p-90) cc_final: 0.8287 (p-90) REVERT: U 2 ILE cc_start: 0.9614 (mp) cc_final: 0.9068 (tp) REVERT: U 36 TYR cc_start: 0.8747 (m-80) cc_final: 0.8464 (m-80) REVERT: U 46 LEU cc_start: 0.8878 (pt) cc_final: 0.8461 (tt) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.3317 time to fit residues: 122.3402 Evaluate side-chains 173 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 175 optimal weight: 0.4980 chunk 202 optimal weight: 5.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN R 28 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 21249 Z= 0.328 Angle : 0.739 9.861 28869 Z= 0.363 Chirality : 0.046 0.277 3657 Planarity : 0.004 0.042 3474 Dihedral : 8.343 59.611 5661 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.05 % Allowed : 0.57 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.17), residues: 2328 helix: 1.21 (0.27), residues: 387 sheet: 0.26 (0.18), residues: 714 loop : 0.62 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 628 HIS 0.006 0.001 HIS A 85 PHE 0.020 0.002 PHE H 73 TYR 0.018 0.002 TYR G 217 ARG 0.007 0.001 ARG S 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 2.648 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.8247 (mtp) cc_final: 0.7997 (mtp) REVERT: A 104 MET cc_start: 0.8748 (tpp) cc_final: 0.8209 (tpp) REVERT: A 125 LEU cc_start: 0.9623 (mm) cc_final: 0.9318 (mt) REVERT: A 150 MET cc_start: 0.8367 (mmm) cc_final: 0.8132 (mmm) REVERT: B 546 SER cc_start: 0.8814 (m) cc_final: 0.8481 (p) REVERT: B 548 ILE cc_start: 0.7384 (tp) cc_final: 0.7181 (tp) REVERT: B 584 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8493 (tm-30) REVERT: B 610 TRP cc_start: 0.6976 (p-90) cc_final: 0.6606 (p-90) REVERT: H 23 GLU cc_start: 0.8226 (mp0) cc_final: 0.7959 (mp0) REVERT: L 2 ILE cc_start: 0.9531 (mp) cc_final: 0.8824 (tp) REVERT: F 150 MET cc_start: 0.7963 (mmm) cc_final: 0.7681 (mmm) REVERT: F 161 MET cc_start: 0.9037 (tmm) cc_final: 0.8761 (tmm) REVERT: I 530 MET cc_start: 0.8826 (mmm) cc_final: 0.8515 (mmm) REVERT: I 546 SER cc_start: 0.8901 (m) cc_final: 0.8512 (p) REVERT: I 584 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8501 (tm-30) REVERT: I 610 TRP cc_start: 0.7226 (p-90) cc_final: 0.6563 (p-90) REVERT: R 5 LEU cc_start: 0.8993 (tt) cc_final: 0.8785 (tt) REVERT: R 23 GLU cc_start: 0.8292 (mp0) cc_final: 0.7694 (mp0) REVERT: R 31 ASP cc_start: 0.8266 (t0) cc_final: 0.7966 (t0) REVERT: R 32 TYR cc_start: 0.8897 (m-80) cc_final: 0.8465 (m-80) REVERT: R 71 TRP cc_start: 0.8574 (p-90) cc_final: 0.8192 (p-90) REVERT: T 55 GLU cc_start: 0.7893 (pp20) cc_final: 0.7596 (pp20) REVERT: G 161 MET cc_start: 0.8956 (tmm) cc_final: 0.8704 (tmm) REVERT: J 546 SER cc_start: 0.8915 (m) cc_final: 0.8642 (p) REVERT: J 584 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8459 (tm-30) REVERT: J 610 TRP cc_start: 0.7201 (p-90) cc_final: 0.6548 (p-90) REVERT: S 71 TRP cc_start: 0.8592 (p-90) cc_final: 0.8351 (p-90) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.3150 time to fit residues: 108.4021 Evaluate side-chains 161 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 21249 Z= 0.193 Angle : 0.661 15.148 28869 Z= 0.327 Chirality : 0.045 0.291 3657 Planarity : 0.004 0.037 3474 Dihedral : 7.877 59.076 5661 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.05 % Allowed : 0.48 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.18), residues: 2328 helix: 1.51 (0.28), residues: 384 sheet: 0.32 (0.18), residues: 768 loop : 0.76 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 628 HIS 0.004 0.001 HIS G 216 PHE 0.019 0.001 PHE H 73 TYR 0.024 0.001 TYR G 217 ARG 0.008 0.000 ARG S 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8092 (mtp) cc_final: 0.7844 (mtp) REVERT: A 104 MET cc_start: 0.8821 (tpp) cc_final: 0.8247 (tpp) REVERT: A 125 LEU cc_start: 0.9624 (mm) cc_final: 0.9390 (mt) REVERT: A 161 MET cc_start: 0.8885 (tmm) cc_final: 0.8594 (tmm) REVERT: A 434 MET cc_start: 0.8541 (ptm) cc_final: 0.8273 (ttm) REVERT: B 546 SER cc_start: 0.8742 (m) cc_final: 0.8390 (p) REVERT: B 548 ILE cc_start: 0.7448 (tp) cc_final: 0.7191 (tp) REVERT: B 584 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8483 (tm-30) REVERT: H 71 TRP cc_start: 0.8516 (p-90) cc_final: 0.8177 (p-90) REVERT: L 2 ILE cc_start: 0.9519 (mp) cc_final: 0.8814 (tp) REVERT: F 150 MET cc_start: 0.8011 (mmm) cc_final: 0.7716 (mmm) REVERT: F 161 MET cc_start: 0.9000 (tmm) cc_final: 0.8788 (tmm) REVERT: I 530 MET cc_start: 0.8780 (mmm) cc_final: 0.8540 (mmm) REVERT: I 546 SER cc_start: 0.8852 (m) cc_final: 0.8428 (p) REVERT: I 584 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8478 (tm-30) REVERT: I 610 TRP cc_start: 0.7019 (p-90) cc_final: 0.6490 (p-90) REVERT: R 71 TRP cc_start: 0.8594 (p-90) cc_final: 0.8291 (p-90) REVERT: G 161 MET cc_start: 0.8921 (tmm) cc_final: 0.8643 (tmm) REVERT: J 584 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8380 (tm-30) REVERT: J 610 TRP cc_start: 0.6963 (p-90) cc_final: 0.6469 (p-90) REVERT: U 4 MET cc_start: 0.7553 (mtm) cc_final: 0.6904 (mtm) REVERT: U 46 LEU cc_start: 0.8990 (pt) cc_final: 0.8674 (tt) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.3129 time to fit residues: 110.3575 Evaluate side-chains 162 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 5.9990 chunk 133 optimal weight: 0.0770 chunk 104 optimal weight: 20.0000 chunk 152 optimal weight: 8.9990 chunk 230 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 141 optimal weight: 0.4980 chunk 112 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 overall best weight: 1.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21249 Z= 0.190 Angle : 0.652 11.074 28869 Z= 0.321 Chirality : 0.044 0.280 3657 Planarity : 0.004 0.038 3474 Dihedral : 7.604 59.332 5661 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.05 % Allowed : 0.10 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 2328 helix: 1.47 (0.28), residues: 384 sheet: 0.32 (0.18), residues: 780 loop : 0.70 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP I 571 HIS 0.004 0.001 HIS G 216 PHE 0.010 0.001 PHE U 62 TYR 0.025 0.001 TYR G 217 ARG 0.009 0.000 ARG S 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8112 (mtp) cc_final: 0.7875 (mtp) REVERT: A 104 MET cc_start: 0.8724 (tpp) cc_final: 0.8169 (tpp) REVERT: A 125 LEU cc_start: 0.9628 (mm) cc_final: 0.9392 (mt) REVERT: A 161 MET cc_start: 0.8890 (tmm) cc_final: 0.8608 (tmm) REVERT: B 546 SER cc_start: 0.8861 (m) cc_final: 0.8467 (p) REVERT: B 548 ILE cc_start: 0.7473 (tp) cc_final: 0.7253 (tp) REVERT: B 584 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8471 (tm-30) REVERT: L 2 ILE cc_start: 0.9513 (mp) cc_final: 0.8791 (tp) REVERT: L 21 ILE cc_start: 0.8657 (pt) cc_final: 0.8386 (pt) REVERT: F 150 MET cc_start: 0.7980 (mmm) cc_final: 0.7692 (mmm) REVERT: F 161 MET cc_start: 0.8942 (tmm) cc_final: 0.8653 (tmm) REVERT: F 377 ASN cc_start: 0.8647 (t0) cc_final: 0.8443 (t0) REVERT: I 530 MET cc_start: 0.8453 (mmm) cc_final: 0.8205 (mmm) REVERT: I 546 SER cc_start: 0.8829 (m) cc_final: 0.8417 (p) REVERT: I 584 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8512 (tm-30) REVERT: I 610 TRP cc_start: 0.7057 (p-90) cc_final: 0.6498 (p-90) REVERT: R 32 TYR cc_start: 0.8797 (m-80) cc_final: 0.8524 (m-80) REVERT: R 71 TRP cc_start: 0.8517 (p-90) cc_final: 0.8215 (p-90) REVERT: G 161 MET cc_start: 0.8963 (tmm) cc_final: 0.8676 (tmm) REVERT: G 271 MET cc_start: 0.8826 (mmm) cc_final: 0.7997 (mtp) REVERT: J 543 ASN cc_start: 0.8905 (m-40) cc_final: 0.8686 (m-40) REVERT: J 584 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8361 (tm-30) REVERT: J 610 TRP cc_start: 0.6999 (p-90) cc_final: 0.6517 (p-90) REVERT: U 2 ILE cc_start: 0.9411 (mp) cc_final: 0.8913 (tp) REVERT: U 46 LEU cc_start: 0.9005 (pt) cc_final: 0.8756 (tt) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.3370 time to fit residues: 117.7823 Evaluate side-chains 166 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.0270 chunk 183 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 188 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.057486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.048631 restraints weight = 112807.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.049921 restraints weight = 65725.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.050851 restraints weight = 45680.311| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21249 Z= 0.162 Angle : 0.643 10.239 28869 Z= 0.315 Chirality : 0.044 0.281 3657 Planarity : 0.004 0.037 3474 Dihedral : 7.368 59.558 5661 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.05 % Allowed : 0.24 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.18), residues: 2328 helix: 1.51 (0.28), residues: 384 sheet: 0.45 (0.18), residues: 771 loop : 0.69 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 628 HIS 0.007 0.001 HIS G 216 PHE 0.018 0.001 PHE T 62 TYR 0.024 0.001 TYR G 217 ARG 0.009 0.000 ARG S 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3519.36 seconds wall clock time: 65 minutes 18.25 seconds (3918.25 seconds total)