Starting phenix.real_space_refine on Thu Feb 22 05:32:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mem_23792/02_2024/7mem_23792_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mem_23792/02_2024/7mem_23792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mem_23792/02_2024/7mem_23792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mem_23792/02_2024/7mem_23792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mem_23792/02_2024/7mem_23792_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mem_23792/02_2024/7mem_23792_trim.pdb" } resolution = 3.2 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= 0.056 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: 5 Type Number sf(0) Gaussians S 75 5.16 5 C 10602 2.51 5 N 2859 2.21 5 O 3318 1.98 5 H 16044 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32898 Number of models: 1 Model: "" Number of chains: 21 Chain: "E" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4974 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 19, 'TRANS': 301} Chain: "L" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1629 Classifications: {'peptide': 107} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1763 Classifications: {'peptide': 120} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "D" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2520 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "C" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4974 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 19, 'TRANS': 301} Chain: "J" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1629 Classifications: {'peptide': 107} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "G" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1763 Classifications: {'peptide': 120} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "A" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2520 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "F" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4974 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 19, 'TRANS': 301} Chain: "K" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1629 Classifications: {'peptide': 107} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1763 Classifications: {'peptide': 120} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "B" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2520 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "M" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "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: "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 Time building chain proxies: 14.39, per 1000 atoms: 0.44 Number of scatterers: 32898 At special positions: 0 Unit cell: (138.02, 140.08, 152.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 O 3318 8.00 N 2859 7.00 C 10602 6.00 H 16044 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS A 137 " distance=2.02 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.05 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.02 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS F 14 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS B 137 " distance=2.02 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.05 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.02 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 148 " distance=2.04 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 277 " distance=2.05 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 76 " distance=2.02 Simple disulfide: pdb=" SG CYS F 97 " - pdb=" SG CYS F 139 " distance=2.03 Simple disulfide: pdb=" SG CYS F 281 " - pdb=" SG CYS F 305 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG R 1 " - " NAG R 2 " BETA1-6 " NAG M 1 " - " FUC M 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG O 1 " - " FUC O 2 " " NAG Q 1 " - " FUC Q 2 " Time building additional restraints: 26.03 Conformation dependent library (CDL) restraints added in 3.4 seconds 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 51 sheets defined 20.6% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 77 Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 159 through 169 removed outlier: 4.461A pdb=" N GLU D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLU D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'A' and resid 37 through 58 Processing helix chain 'A' and resid 74 through 127 Processing helix chain 'A' and resid 145 through 154 Processing helix chain 'A' and resid 159 through 169 removed outlier: 4.462A pdb=" N GLU A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLU A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 72 Processing helix chain 'F' and resid 73 through 77 Processing helix chain 'F' and resid 104 through 112 Processing helix chain 'F' and resid 187 through 195 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 159 through 169 removed outlier: 4.461A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 36 removed outlier: 6.533A pdb=" N CYS A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.095A pdb=" N LEU E 51 " --> pdb=" O HIS E 275 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.395A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 115 through 122 removed outlier: 6.954A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 115 through 122 removed outlier: 6.954A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.339A pdb=" N ALA E 138 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N ALA E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'E' and resid 286 through 288 removed outlier: 4.192A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 7 removed outlier: 5.590A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.692A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 89 through 90 removed outlier: 3.637A pdb=" N THR L 97 " --> pdb=" O HIS L 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.950A pdb=" N MET H 34 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N MET H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.608A pdb=" N PHE H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 31 through 36 removed outlier: 6.533A pdb=" N CYS D 137 " --> pdb=" O ILE D 133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 64 through 65 removed outlier: 4.191A pdb=" N CYS F 281 " --> pdb=" O ILE F 288 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 31 through 36 removed outlier: 6.534A pdb=" N CYS B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC4, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC5, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC6, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.095A pdb=" N LEU C 51 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.395A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.954A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.954A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.338A pdb=" N ALA C 138 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N ALA C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD3, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.191A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 5 through 7 removed outlier: 5.590A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER J 67 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.692A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 89 through 90 removed outlier: 3.637A pdb=" N THR J 97 " --> pdb=" O HIS J 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.950A pdb=" N MET G 34 " --> pdb=" O MET G 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N MET G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.608A pdb=" N PHE G 102 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AE2, first strand: chain 'F' and resid 39 through 41 Processing sheet with id=AE3, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AE4, first strand: chain 'F' and resid 51 through 54 removed outlier: 6.095A pdb=" N LEU F 51 " --> pdb=" O HIS F 275 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N CYS F 277 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 59 through 60 removed outlier: 6.395A pdb=" N LEU F 59 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE F 87 " --> pdb=" O ILE F 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'F' and resid 115 through 122 removed outlier: 6.954A pdb=" N TYR F 256 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU F 179 " --> pdb=" O TYR F 256 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU F 179 " --> pdb=" O PRO F 254 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 115 through 122 removed outlier: 6.954A pdb=" N TYR F 256 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU F 179 " --> pdb=" O TYR F 256 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 136 through 141 removed outlier: 7.339A pdb=" N ALA F 138 " --> pdb=" O ALA F 144 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N ALA F 144 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 164 through 169 Processing sheet with id=AF1, first strand: chain 'K' and resid 5 through 7 removed outlier: 5.590A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER K 67 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.692A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 89 through 90 removed outlier: 3.637A pdb=" N THR K 97 " --> pdb=" O HIS K 90 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.950A pdb=" N MET I 34 " --> pdb=" O MET I 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N MET I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.608A pdb=" N PHE I 102 " --> pdb=" O LYS I 94 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 1980 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: 13.50 Time building geometry restraints manager: 27.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.00: 755 1.00 - 1.23: 16007 1.23 - 1.45: 8058 1.45 - 1.67: 8363 1.67 - 1.90: 102 Bond restraints: 33285 Sorted by residual: bond pdb=" NE2 HIS K 32 " pdb=" HE2 HIS K 32 " ideal model delta sigma weight residual 0.860 1.055 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" NE2 HIS J 32 " pdb=" HE2 HIS J 32 " ideal model delta sigma weight residual 0.860 1.055 -0.195 2.00e-02 2.50e+03 9.49e+01 bond pdb=" NE2 HIS L 32 " pdb=" HE2 HIS L 32 " ideal model delta sigma weight residual 0.860 1.055 -0.195 2.00e-02 2.50e+03 9.48e+01 bond pdb=" NE ARG C 224 " pdb=" HE ARG C 224 " ideal model delta sigma weight residual 0.860 1.050 -0.190 2.00e-02 2.50e+03 9.05e+01 bond pdb=" NE ARG E 224 " pdb=" HE ARG E 224 " ideal model delta sigma weight residual 0.860 1.050 -0.190 2.00e-02 2.50e+03 9.04e+01 ... (remaining 33280 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.55: 1608 106.55 - 113.43: 36457 113.43 - 120.31: 12638 120.31 - 127.19: 8833 127.19 - 134.07: 275 Bond angle restraints: 59811 Sorted by residual: angle pdb=" CA ASP I 96 " pdb=" CB ASP I 96 " pdb=" CG ASP I 96 " ideal model delta sigma weight residual 112.60 104.66 7.94 1.00e+00 1.00e+00 6.31e+01 angle pdb=" CA ASP H 96 " pdb=" CB ASP H 96 " pdb=" CG ASP H 96 " ideal model delta sigma weight residual 112.60 104.68 7.92 1.00e+00 1.00e+00 6.27e+01 angle pdb=" CA ASP G 96 " pdb=" CB ASP G 96 " pdb=" CG ASP G 96 " ideal model delta sigma weight residual 112.60 104.70 7.90 1.00e+00 1.00e+00 6.24e+01 angle pdb=" C HIS F 184 " pdb=" N PRO F 185 " pdb=" CA PRO F 185 " ideal model delta sigma weight residual 119.78 127.85 -8.07 1.03e+00 9.43e-01 6.14e+01 angle pdb=" C HIS C 184 " pdb=" N PRO C 185 " pdb=" CA PRO C 185 " ideal model delta sigma weight residual 119.78 127.83 -8.05 1.03e+00 9.43e-01 6.11e+01 ... (remaining 59806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 15318 17.53 - 35.05: 486 35.05 - 52.58: 198 52.58 - 70.11: 99 70.11 - 87.64: 18 Dihedral angle restraints: 16119 sinusoidal: 8802 harmonic: 7317 Sorted by residual: dihedral pdb=" CA SER C 265 " pdb=" C SER C 265 " pdb=" N GLY C 266 " pdb=" CA GLY C 266 " ideal model delta harmonic sigma weight residual 180.00 -146.01 -33.99 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA SER F 265 " pdb=" C SER F 265 " pdb=" N GLY F 266 " pdb=" CA GLY F 266 " ideal model delta harmonic sigma weight residual 180.00 -146.03 -33.97 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA SER E 265 " pdb=" C SER E 265 " pdb=" N GLY E 266 " pdb=" CA GLY E 266 " ideal model delta harmonic sigma weight residual -180.00 -146.04 -33.96 0 5.00e+00 4.00e-02 4.61e+01 ... (remaining 16116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1934 0.110 - 0.220: 549 0.220 - 0.329: 64 0.329 - 0.439: 15 0.439 - 0.549: 3 Chirality restraints: 2565 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.34e+02 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.30e+02 ... (remaining 2562 not shown) Planarity restraints: 5019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 1 " 0.367 2.00e-02 2.50e+03 3.13e-01 1.22e+03 pdb=" C7 NAG Q 1 " -0.103 2.00e-02 2.50e+03 pdb=" C8 NAG Q 1 " 0.060 2.00e-02 2.50e+03 pdb=" N2 NAG Q 1 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG Q 1 " 0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " -0.367 2.00e-02 2.50e+03 3.13e-01 1.22e+03 pdb=" C7 NAG O 1 " 0.104 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " -0.060 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " 0.541 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " -0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.367 2.00e-02 2.50e+03 3.13e-01 1.22e+03 pdb=" C7 NAG M 1 " 0.103 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.060 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.541 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.218 2.00e-02 2.50e+03 ... (remaining 5016 not shown) Histogram of nonbonded interaction distances: 0.55 - 1.36: 18 1.36 - 2.17: 2439 2.17 - 2.98: 86716 2.98 - 3.79: 146268 3.79 - 4.60: 240361 Warning: very small nonbonded interaction distances. Nonbonded interactions: 475802 Sorted by model distance: nonbonded pdb="HD21 ASN C 278 " pdb=" C1 NAG C 401 " model vdw 0.546 2.750 nonbonded pdb="HD21 ASN E 278 " pdb=" C1 NAG E 401 " model vdw 0.546 2.750 nonbonded pdb="HD21 ASN F 278 " pdb=" C1 NAG F 401 " model vdw 0.547 2.750 nonbonded pdb="HD21 ASN C 94 " pdb=" C1 NAG P 1 " model vdw 0.554 2.750 nonbonded pdb="HD21 ASN E 94 " pdb=" C1 NAG N 1 " model vdw 0.554 2.750 ... (remaining 475797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.500 Extract box with map and model: 8.710 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 103.290 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 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 : 0.019 0.109 17241 Z= 1.249 Angle : 1.719 12.822 23361 Z= 1.145 Chirality : 0.103 0.549 2565 Planarity : 0.014 0.313 2991 Dihedral : 10.410 87.637 6528 Min Nonbonded Distance : 1.511 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.80 (0.17), residues: 2100 helix: 0.82 (0.25), residues: 369 sheet: 0.45 (0.20), residues: 537 loop : 0.64 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.009 TRP I 103 HIS 0.010 0.002 HIS F 275 PHE 0.028 0.007 PHE E 118 TYR 0.070 0.011 TYR D 34 ARG 0.010 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 533 time to evaluate : 2.966 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 71 LEU cc_start: 0.8416 (mt) cc_final: 0.8195 (mt) REVERT: D 158 ASP cc_start: 0.8883 (t0) cc_final: 0.8665 (t0) REVERT: C 71 LEU cc_start: 0.8513 (mt) cc_final: 0.8258 (mt) REVERT: J 14 PHE cc_start: 0.7632 (p90) cc_final: 0.7180 (p90) REVERT: A 158 ASP cc_start: 0.8871 (t0) cc_final: 0.8639 (t0) REVERT: F 17 TYR cc_start: 0.5855 (p90) cc_final: 0.5424 (p90) REVERT: F 71 LEU cc_start: 0.8566 (mt) cc_final: 0.8263 (mt) REVERT: F 131 ASP cc_start: 0.7454 (t0) cc_final: 0.7244 (t0) REVERT: K 82 ASP cc_start: 0.7864 (m-30) cc_final: 0.7462 (m-30) REVERT: B 158 ASP cc_start: 0.8884 (t0) cc_final: 0.8671 (t0) outliers start: 0 outliers final: 0 residues processed: 533 average time/residue: 0.7584 time to fit residues: 578.8202 Evaluate side-chains 307 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 ASN E 278 ASN E 298 HIS C 278 ASN C 298 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 ASN F 298 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17241 Z= 0.214 Angle : 0.714 8.521 23361 Z= 0.387 Chirality : 0.046 0.254 2565 Planarity : 0.004 0.028 2991 Dihedral : 6.585 47.407 2661 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.29 % Favored : 97.57 % Rotamer: Outliers : 1.64 % Allowed : 8.16 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.66 (0.17), residues: 2100 helix: 2.30 (0.26), residues: 360 sheet: -0.07 (0.19), residues: 594 loop : 0.22 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 69 HIS 0.009 0.001 HIS B 72 PHE 0.025 0.002 PHE G 100 TYR 0.015 0.002 TYR B 141 ARG 0.005 0.001 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 344 time to evaluate : 2.784 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: 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: 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: D 158 ASP cc_start: 0.8835 (t0) cc_final: 0.8549 (t0) REVERT: J 14 PHE cc_start: 0.7364 (p90) cc_final: 0.6292 (p90) REVERT: J 17 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7626 (m-30) REVERT: A 120 GLU cc_start: 0.9238 (mt-10) cc_final: 0.9004 (mm-30) REVERT: A 158 ASP cc_start: 0.8751 (t0) cc_final: 0.8443 (t0) REVERT: F 17 TYR cc_start: 0.5442 (p90) cc_final: 0.5117 (p90) REVERT: F 105 TYR cc_start: 0.7340 (t80) cc_final: 0.7076 (t80) REVERT: K 18 ARG cc_start: 0.7136 (ttt-90) cc_final: 0.6912 (ttt-90) REVERT: B 27 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8350 (pp30) REVERT: B 120 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8977 (mm-30) REVERT: B 158 ASP cc_start: 0.8822 (t0) cc_final: 0.8532 (t0) outliers start: 30 outliers final: 18 residues processed: 358 average time/residue: 0.7118 time to fit residues: 367.7489 Evaluate side-chains 317 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 298 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 278 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 278 ASN Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 278 ASN Chi-restraints excluded: chain K residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 206 optimal weight: 0.4980 chunk 170 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 153 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17241 Z= 0.238 Angle : 0.614 6.198 23361 Z= 0.333 Chirality : 0.043 0.148 2565 Planarity : 0.004 0.045 2991 Dihedral : 6.067 49.177 2661 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.59 % Allowed : 9.58 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.43 (0.17), residues: 2100 helix: 2.35 (0.27), residues: 363 sheet: -0.23 (0.19), residues: 579 loop : -0.02 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 69 HIS 0.006 0.001 HIS B 72 PHE 0.021 0.002 PHE I 100 TYR 0.017 0.002 TYR I 79 ARG 0.006 0.001 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 312 time to evaluate : 2.922 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 158 ASP cc_start: 0.8827 (t0) cc_final: 0.8508 (t0) REVERT: J 14 PHE cc_start: 0.7387 (p90) cc_final: 0.6375 (p90) REVERT: J 17 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: J 36 TYR cc_start: 0.8239 (m-80) cc_final: 0.7964 (m-80) REVERT: A 132 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7495 (mp0) REVERT: A 158 ASP cc_start: 0.8663 (t0) cc_final: 0.8329 (t0) REVERT: F 17 TYR cc_start: 0.5631 (p90) cc_final: 0.5240 (p90) REVERT: F 101 ASP cc_start: 0.7525 (t0) cc_final: 0.7300 (t0) REVERT: B 27 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8356 (pp30) REVERT: B 119 TYR cc_start: 0.8224 (t80) cc_final: 0.7862 (t80) REVERT: B 120 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8995 (mm-30) REVERT: B 158 ASP cc_start: 0.8654 (t0) cc_final: 0.8324 (t0) outliers start: 29 outliers final: 20 residues processed: 326 average time/residue: 0.7095 time to fit residues: 333.4872 Evaluate side-chains 295 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 274 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 156 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 181 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17241 Z= 0.213 Angle : 0.554 5.306 23361 Z= 0.303 Chirality : 0.042 0.162 2565 Planarity : 0.004 0.043 2991 Dihedral : 5.668 52.113 2661 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.70 % Allowed : 10.29 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.17), residues: 2100 helix: 2.33 (0.26), residues: 363 sheet: -0.22 (0.19), residues: 576 loop : -0.14 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.005 0.001 HIS B 72 PHE 0.017 0.002 PHE K 14 TYR 0.013 0.001 TYR C 232 ARG 0.005 0.001 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 286 time to evaluate : 2.714 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: 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: E 79 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7721 (tt) REVERT: D 120 GLU cc_start: 0.9355 (mt-10) cc_final: 0.9080 (mm-30) REVERT: J 14 PHE cc_start: 0.7449 (p90) cc_final: 0.6453 (p90) REVERT: J 17 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: J 36 TYR cc_start: 0.8255 (m-80) cc_final: 0.7941 (m-80) REVERT: A 17 MET cc_start: 0.3512 (ttm) cc_final: 0.2698 (ttm) REVERT: A 132 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7589 (mp0) REVERT: F 17 TYR cc_start: 0.5678 (p90) cc_final: 0.5280 (p90) REVERT: B 27 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8463 (pp30) REVERT: B 120 GLU cc_start: 0.9281 (mt-10) cc_final: 0.9015 (mm-30) REVERT: B 158 ASP cc_start: 0.8642 (t0) cc_final: 0.8302 (t0) outliers start: 31 outliers final: 25 residues processed: 300 average time/residue: 0.7192 time to fit residues: 310.3118 Evaluate side-chains 293 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 266 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 156 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 ASN F 183 HIS ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 17241 Z= 0.440 Angle : 0.672 5.792 23361 Z= 0.368 Chirality : 0.044 0.182 2565 Planarity : 0.005 0.062 2991 Dihedral : 5.846 53.160 2661 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.85 % Allowed : 10.78 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.56 (0.17), residues: 2100 helix: 1.47 (0.25), residues: 366 sheet: -0.61 (0.20), residues: 570 loop : -0.81 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 35 HIS 0.010 0.002 HIS D 26 PHE 0.020 0.003 PHE E 121 TYR 0.018 0.002 TYR A 110 ARG 0.010 0.001 ARG I 100E *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 258 time to evaluate : 3.544 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: 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: E 79 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7775 (tt) REVERT: D 17 MET cc_start: 0.3157 (ttm) cc_final: 0.2397 (ttm) REVERT: D 120 GLU cc_start: 0.9344 (mt-10) cc_final: 0.9109 (mm-30) REVERT: D 149 MET cc_start: 0.7585 (mtt) cc_final: 0.7284 (ptt) REVERT: J 14 PHE cc_start: 0.7608 (p90) cc_final: 0.6510 (p90) REVERT: J 17 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7812 (m-30) REVERT: J 50 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8156 (m-30) REVERT: F 17 TYR cc_start: 0.5825 (p90) cc_final: 0.5470 (p90) REVERT: B 120 GLU cc_start: 0.9356 (mt-10) cc_final: 0.9044 (mm-30) outliers start: 52 outliers final: 36 residues processed: 285 average time/residue: 0.7036 time to fit residues: 295.4750 Evaluate side-chains 281 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 242 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 156 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.4980 chunk 182 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 168 optimal weight: 0.1980 chunk 94 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.003 0.048 17241 Z= 0.163 Angle : 0.534 5.639 23361 Z= 0.290 Chirality : 0.042 0.146 2565 Planarity : 0.004 0.032 2991 Dihedral : 5.361 51.112 2661 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.92 % Allowed : 11.99 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.05 (0.17), residues: 2100 helix: 2.32 (0.26), residues: 348 sheet: -0.42 (0.20), residues: 540 loop : -0.51 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS B 72 PHE 0.027 0.002 PHE F 147 TYR 0.016 0.002 TYR G 79 ARG 0.003 0.000 ARG J 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 279 time to evaluate : 2.737 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7725 (tt) REVERT: D 17 MET cc_start: 0.3140 (ttm) cc_final: 0.2447 (ttm) REVERT: D 120 GLU cc_start: 0.9336 (mt-10) cc_final: 0.9077 (mm-30) REVERT: J 14 PHE cc_start: 0.7629 (p90) cc_final: 0.6643 (p90) REVERT: J 17 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7939 (m-30) REVERT: K 17 ASP cc_start: 0.7981 (m-30) cc_final: 0.7687 (m-30) REVERT: B 120 GLU cc_start: 0.9349 (mt-10) cc_final: 0.9052 (mm-30) outliers start: 35 outliers final: 30 residues processed: 296 average time/residue: 0.6902 time to fit residues: 298.9984 Evaluate side-chains 294 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 262 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 148 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17241 Z= 0.263 Angle : 0.548 6.000 23361 Z= 0.299 Chirality : 0.041 0.147 2565 Planarity : 0.004 0.035 2991 Dihedral : 5.303 52.869 2661 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.46 % Allowed : 12.10 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.17), residues: 2100 helix: 2.06 (0.26), residues: 363 sheet: -0.50 (0.21), residues: 540 loop : -0.74 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 21 HIS 0.004 0.001 HIS B 72 PHE 0.026 0.002 PHE L 14 TYR 0.013 0.002 TYR E 105 ARG 0.004 0.001 ARG I 100E *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 260 time to evaluate : 2.875 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7737 (tt) REVERT: L 17 ASP cc_start: 0.7888 (m-30) cc_final: 0.7412 (m-30) REVERT: D 17 MET cc_start: 0.3191 (ttm) cc_final: 0.2547 (ttm) REVERT: D 120 GLU cc_start: 0.9339 (mt-10) cc_final: 0.9083 (mm-30) REVERT: J 17 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: K 17 ASP cc_start: 0.8004 (m-30) cc_final: 0.7754 (m-30) REVERT: B 120 GLU cc_start: 0.9361 (mt-10) cc_final: 0.9069 (mm-30) outliers start: 45 outliers final: 40 residues processed: 285 average time/residue: 0.7077 time to fit residues: 296.5970 Evaluate side-chains 298 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 256 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 156 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17241 Z= 0.236 Angle : 0.538 6.949 23361 Z= 0.293 Chirality : 0.041 0.145 2565 Planarity : 0.004 0.037 2991 Dihedral : 5.214 52.525 2661 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.41 % Allowed : 12.48 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.33 (0.17), residues: 2100 helix: 2.10 (0.26), residues: 363 sheet: -0.53 (0.21), residues: 540 loop : -0.79 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 21 HIS 0.004 0.001 HIS B 72 PHE 0.024 0.002 PHE L 14 TYR 0.012 0.002 TYR H 59 ARG 0.005 0.001 ARG F 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 258 time to evaluate : 2.942 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7722 (tt) REVERT: L 17 ASP cc_start: 0.7884 (m-30) cc_final: 0.7413 (m-30) REVERT: D 17 MET cc_start: 0.3275 (ttm) cc_final: 0.2635 (ttm) REVERT: D 120 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9073 (mm-30) REVERT: J 17 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7973 (m-30) REVERT: K 17 ASP cc_start: 0.8042 (m-30) cc_final: 0.7824 (m-30) REVERT: B 120 GLU cc_start: 0.9403 (mt-10) cc_final: 0.9078 (mm-30) outliers start: 44 outliers final: 41 residues processed: 283 average time/residue: 0.6914 time to fit residues: 283.4232 Evaluate side-chains 295 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 252 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 156 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17241 Z= 0.172 Angle : 0.511 6.745 23361 Z= 0.277 Chirality : 0.041 0.143 2565 Planarity : 0.004 0.035 2991 Dihedral : 5.007 52.711 2661 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.03 % Allowed : 12.75 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.24 (0.17), residues: 2100 helix: 2.15 (0.26), residues: 369 sheet: -0.48 (0.21), residues: 552 loop : -0.73 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 47 HIS 0.004 0.001 HIS B 72 PHE 0.024 0.002 PHE L 14 TYR 0.019 0.001 TYR C 105 ARG 0.005 0.000 ARG F 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 273 time to evaluate : 2.922 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7714 (tt) REVERT: L 17 ASP cc_start: 0.7896 (m-30) cc_final: 0.7390 (m-30) REVERT: D 17 MET cc_start: 0.3441 (ttm) cc_final: 0.2779 (ttm) REVERT: D 120 GLU cc_start: 0.9356 (mt-10) cc_final: 0.9059 (mm-30) REVERT: J 17 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: K 17 ASP cc_start: 0.8053 (m-30) cc_final: 0.7822 (m-30) REVERT: B 120 GLU cc_start: 0.9413 (mt-10) cc_final: 0.9083 (mm-30) outliers start: 37 outliers final: 34 residues processed: 294 average time/residue: 0.7066 time to fit residues: 303.4653 Evaluate side-chains 299 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 263 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 156 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 17241 Z= 0.424 Angle : 0.627 7.205 23361 Z= 0.344 Chirality : 0.043 0.144 2565 Planarity : 0.005 0.057 2991 Dihedral : 5.487 53.565 2661 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.24 % Allowed : 13.03 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.85 (0.17), residues: 2100 helix: 1.62 (0.25), residues: 369 sheet: -0.75 (0.21), residues: 540 loop : -1.19 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 35 HIS 0.008 0.002 HIS E 130 PHE 0.021 0.002 PHE L 14 TYR 0.015 0.002 TYR D 110 ARG 0.012 0.001 ARG I 100E ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 242 time to evaluate : 3.009 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: 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: E 79 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7817 (tt) REVERT: L 17 ASP cc_start: 0.7993 (m-30) cc_final: 0.7525 (m-30) REVERT: D 17 MET cc_start: 0.3592 (ttm) cc_final: 0.2934 (ttm) REVERT: D 120 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9065 (mm-30) REVERT: J 17 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: K 17 ASP cc_start: 0.8082 (m-30) cc_final: 0.7853 (m-30) REVERT: B 120 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9104 (mm-30) outliers start: 41 outliers final: 37 residues processed: 266 average time/residue: 0.7172 time to fit residues: 278.9209 Evaluate side-chains 276 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 237 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 156 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.136444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.111605 restraints weight = 93962.598| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.99 r_work: 0.3839 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17241 Z= 0.160 Angle : 0.523 7.111 23361 Z= 0.284 Chirality : 0.041 0.149 2565 Planarity : 0.004 0.039 2991 Dihedral : 5.095 52.032 2661 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.81 % Allowed : 13.74 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.51 (0.17), residues: 2100 helix: 1.99 (0.26), residues: 369 sheet: -0.64 (0.21), residues: 552 loop : -0.94 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 21 HIS 0.004 0.001 HIS B 72 PHE 0.024 0.002 PHE F 147 TYR 0.022 0.002 TYR C 105 ARG 0.005 0.000 ARG C 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8066.01 seconds wall clock time: 143 minutes 48.78 seconds (8628.78 seconds total)