Starting phenix.real_space_refine on Fri Jun 28 02:50:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un7_42394/06_2024/8un7_42394.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un7_42394/06_2024/8un7_42394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un7_42394/06_2024/8un7_42394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un7_42394/06_2024/8un7_42394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un7_42394/06_2024/8un7_42394.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un7_42394/06_2024/8un7_42394.pdb" } resolution = 3.55 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= 0.002 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 Ca 8 9.91 5 S 56 5.16 5 C 9160 2.51 5 N 2344 2.21 5 O 2728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 42": "OD1" <-> "OD2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A ASP 159": "OD1" <-> "OD2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D ASP 159": "OD1" <-> "OD2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 42": "OD1" <-> "OD2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ASP 191": "OD1" <-> "OD2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "E ASP 43": "OD1" <-> "OD2" Residue "E TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "E ASP 159": "OD1" <-> "OD2" Residue "E ASP 193": "OD1" <-> "OD2" Residue "E PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C GLU 157": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ASP 191": "OD1" <-> "OD2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "C PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 71": "OD1" <-> "OD2" Residue "F PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F GLU 136": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F ASP 159": "OD1" <-> "OD2" Residue "F ASP 193": "OD1" <-> "OD2" Residue "F PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 42": "OD1" <-> "OD2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "G PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G ASP 159": "OD1" <-> "OD2" Residue "G GLU 169": "OE1" <-> "OE2" Residue "G ASP 191": "OD1" <-> "OD2" Residue "G ASP 193": "OD1" <-> "OD2" Residue "G PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 249": "OE1" <-> "OE2" Residue "H ASP 43": "OD1" <-> "OD2" Residue "H TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "H GLU 158": "OE1" <-> "OE2" Residue "H ASP 159": "OD1" <-> "OD2" Residue "H ASP 193": "OD1" <-> "OD2" Residue "H PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 14296 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "D" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "B" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "E" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "C" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "F" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "G" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "H" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.43, per 1000 atoms: 0.59 Number of scatterers: 14296 At special positions: 0 Unit cell: (110.295, 110.295, 108.585, 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) Ca 8 19.99 S 56 16.00 O 2728 8.00 N 2344 7.00 C 9160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 70 " distance=2.03 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 70 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 70 " distance=2.03 Simple disulfide: pdb=" SG CYS E 199 " - pdb=" SG CYS E 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 70 " distance=2.03 Simple disulfide: pdb=" SG CYS C 199 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 70 " distance=2.03 Simple disulfide: pdb=" SG CYS F 199 " - pdb=" SG CYS F 212 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 70 " distance=2.03 Simple disulfide: pdb=" SG CYS G 199 " - pdb=" SG CYS G 212 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 70 " distance=2.03 Simple disulfide: pdb=" SG CYS H 199 " - pdb=" SG CYS H 212 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 301 " - " ASN A 87 " " NAG A 302 " - " ASN A 137 " " NAG B 301 " - " ASN B 87 " " NAG B 302 " - " ASN B 137 " " NAG C 301 " - " ASN C 87 " " NAG C 302 " - " ASN C 137 " " NAG D 301 " - " ASN D 87 " " NAG D 302 " - " ASN D 137 " " NAG E 301 " - " ASN E 87 " " NAG E 302 " - " ASN E 137 " " NAG F 301 " - " ASN F 87 " " NAG F 302 " - " ASN F 137 " " NAG G 301 " - " ASN G 87 " " NAG G 302 " - " ASN G 137 " " NAG H 301 " - " ASN H 87 " " NAG H 302 " - " ASN H 137 " Time building additional restraints: 5.57 Conformation dependent library (CDL) restraints added in 2.7 seconds 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 20 sheets defined 18.0% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 40 through 46 removed outlier: 3.547A pdb=" N ILE A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 113 through 124 removed outlier: 3.980A pdb=" N LYS A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 193 through 199 removed outlier: 3.555A pdb=" N GLN A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 46 removed outlier: 3.827A pdb=" N ALA D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 113 through 124 removed outlier: 3.806A pdb=" N LYS D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 194 through 199 removed outlier: 3.603A pdb=" N ASN D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 46 removed outlier: 3.547A pdb=" N ILE B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 113 through 124 removed outlier: 3.980A pdb=" N LYS B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 193 through 199 removed outlier: 3.555A pdb=" N GLN B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 46 removed outlier: 3.827A pdb=" N ALA E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 102 Processing helix chain 'E' and resid 113 through 124 removed outlier: 3.806A pdb=" N LYS E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 160 Processing helix chain 'E' and resid 194 through 199 removed outlier: 3.603A pdb=" N ASN E 198 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 46 removed outlier: 3.547A pdb=" N ILE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 113 through 124 removed outlier: 3.980A pdb=" N LYS C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 193 through 199 removed outlier: 3.555A pdb=" N GLN C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 46 removed outlier: 3.827A pdb=" N ALA F 46 " --> pdb=" O ASP F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 102 Processing helix chain 'F' and resid 113 through 124 removed outlier: 3.806A pdb=" N LYS F 123 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 160 Processing helix chain 'F' and resid 194 through 199 removed outlier: 3.603A pdb=" N ASN F 198 " --> pdb=" O LEU F 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 46 removed outlier: 3.547A pdb=" N ILE G 44 " --> pdb=" O ASP G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 102 Processing helix chain 'G' and resid 113 through 124 removed outlier: 3.980A pdb=" N LYS G 123 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 160 Processing helix chain 'G' and resid 193 through 199 removed outlier: 3.555A pdb=" N GLN G 197 " --> pdb=" O ASP G 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 46 removed outlier: 3.827A pdb=" N ALA H 46 " --> pdb=" O ASP H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 102 Processing helix chain 'H' and resid 113 through 124 removed outlier: 3.806A pdb=" N LYS H 123 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 160 Processing helix chain 'H' and resid 194 through 199 removed outlier: 3.603A pdb=" N ASN H 198 " --> pdb=" O LEU H 194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 57 removed outlier: 3.926A pdb=" N GLY A 53 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A 70 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 104 removed outlier: 3.754A pdb=" N TYR A 110 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 84 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET A 250 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS A 84 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR A 248 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY A 167 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE A 147 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL A 165 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 149 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU A 163 " --> pdb=" O ILE A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY D 53 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS D 70 " --> pdb=" O GLY D 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN D 83 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE D 69 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 81 " --> pdb=" O PHE D 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS D 84 " --> pdb=" O TYR D 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR D 110 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY D 53 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS D 70 " --> pdb=" O GLY D 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN D 83 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE D 69 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 81 " --> pdb=" O PHE D 69 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET D 250 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS D 84 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR D 248 " --> pdb=" O LYS D 84 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 247 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU D 133 " --> pdb=" O ARG D 247 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D 249 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY D 167 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N PHE D 147 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL D 165 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE D 149 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU D 163 " --> pdb=" O ILE D 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 185 through 186 removed outlier: 3.621A pdb=" N SER D 186 " --> pdb=" O PHE D 207 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE D 207 " --> pdb=" O SER D 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 57 removed outlier: 3.926A pdb=" N GLY B 53 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 70 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 104 removed outlier: 3.754A pdb=" N TYR B 110 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 84 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET B 250 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS B 84 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR B 248 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY B 167 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE B 147 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL B 165 " --> pdb=" O PHE B 147 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 149 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU B 163 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY E 53 " --> pdb=" O CYS E 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS E 70 " --> pdb=" O GLY E 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN E 83 " --> pdb=" O PRO E 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE E 69 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL E 81 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS E 84 " --> pdb=" O TYR E 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR E 110 " --> pdb=" O LYS E 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY E 53 " --> pdb=" O CYS E 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS E 70 " --> pdb=" O GLY E 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN E 83 " --> pdb=" O PRO E 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE E 69 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL E 81 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET E 250 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS E 84 " --> pdb=" O THR E 248 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR E 248 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG E 247 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 133 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 249 " --> pdb=" O ASP E 131 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY E 167 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N PHE E 147 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL E 165 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE E 149 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU E 163 " --> pdb=" O ILE E 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 185 through 186 removed outlier: 3.621A pdb=" N SER E 186 " --> pdb=" O PHE E 207 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE E 207 " --> pdb=" O SER E 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 57 removed outlier: 3.926A pdb=" N GLY C 53 " --> pdb=" O CYS C 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS C 70 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 104 removed outlier: 3.754A pdb=" N TYR C 110 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 84 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET C 250 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS C 84 " --> pdb=" O THR C 248 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 248 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY C 167 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE C 147 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL C 165 " --> pdb=" O PHE C 147 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE C 149 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU C 163 " --> pdb=" O ILE C 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY F 53 " --> pdb=" O CYS F 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS F 70 " --> pdb=" O GLY F 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN F 83 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE F 69 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL F 81 " --> pdb=" O PHE F 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS F 84 " --> pdb=" O TYR F 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR F 110 " --> pdb=" O LYS F 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY F 53 " --> pdb=" O CYS F 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS F 70 " --> pdb=" O GLY F 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN F 83 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE F 69 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL F 81 " --> pdb=" O PHE F 69 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET F 250 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS F 84 " --> pdb=" O THR F 248 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR F 248 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG F 247 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU F 133 " --> pdb=" O ARG F 247 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU F 249 " --> pdb=" O ASP F 131 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY F 167 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N PHE F 147 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL F 165 " --> pdb=" O PHE F 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE F 149 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU F 163 " --> pdb=" O ILE F 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 185 through 186 removed outlier: 3.621A pdb=" N SER F 186 " --> pdb=" O PHE F 207 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE F 207 " --> pdb=" O SER F 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 53 through 57 removed outlier: 3.926A pdb=" N GLY G 53 " --> pdb=" O CYS G 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS G 70 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 103 through 104 removed outlier: 3.754A pdb=" N TYR G 110 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS G 84 " --> pdb=" O TYR G 110 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET G 250 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS G 84 " --> pdb=" O THR G 248 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR G 248 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY G 167 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE G 147 " --> pdb=" O VAL G 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL G 165 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE G 149 " --> pdb=" O LEU G 163 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU G 163 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY H 53 " --> pdb=" O CYS H 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS H 70 " --> pdb=" O GLY H 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN H 83 " --> pdb=" O PRO H 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE H 69 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL H 81 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS H 84 " --> pdb=" O TYR H 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR H 110 " --> pdb=" O LYS H 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY H 53 " --> pdb=" O CYS H 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS H 70 " --> pdb=" O GLY H 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN H 83 " --> pdb=" O PRO H 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE H 69 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL H 81 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET H 250 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS H 84 " --> pdb=" O THR H 248 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR H 248 " --> pdb=" O LYS H 84 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG H 247 " --> pdb=" O GLU H 133 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU H 133 " --> pdb=" O ARG H 247 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU H 249 " --> pdb=" O ASP H 131 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY H 167 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N PHE H 147 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL H 165 " --> pdb=" O PHE H 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE H 149 " --> pdb=" O LEU H 163 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU H 163 " --> pdb=" O ILE H 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 185 through 186 removed outlier: 3.621A pdb=" N SER H 186 " --> pdb=" O PHE H 207 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE H 207 " --> pdb=" O SER H 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 336 hydrogen bonds defined for protein. 888 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: 3.92 Time building geometry restraints manager: 6.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4360 1.33 - 1.46: 3252 1.46 - 1.58: 7028 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 14720 Sorted by residual: bond pdb=" C1 NAG B 302 " pdb=" O5 NAG B 302 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 NAG G 302 " pdb=" O5 NAG G 302 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 NAG C 302 " pdb=" O5 NAG C 302 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" CD GLU C 136 " pdb=" OE1 GLU C 136 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.27e+00 ... (remaining 14715 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.97: 328 106.97 - 113.75: 7300 113.75 - 120.54: 6036 120.54 - 127.32: 6084 127.32 - 134.11: 172 Bond angle restraints: 19920 Sorted by residual: angle pdb=" CA GLU B 136 " pdb=" CB GLU B 136 " pdb=" CG GLU B 136 " ideal model delta sigma weight residual 114.10 126.38 -12.28 2.00e+00 2.50e-01 3.77e+01 angle pdb=" CA GLU C 136 " pdb=" CB GLU C 136 " pdb=" CG GLU C 136 " ideal model delta sigma weight residual 114.10 126.38 -12.28 2.00e+00 2.50e-01 3.77e+01 angle pdb=" CA GLU A 136 " pdb=" CB GLU A 136 " pdb=" CG GLU A 136 " ideal model delta sigma weight residual 114.10 126.38 -12.28 2.00e+00 2.50e-01 3.77e+01 angle pdb=" CA GLU G 136 " pdb=" CB GLU G 136 " pdb=" CG GLU G 136 " ideal model delta sigma weight residual 114.10 126.38 -12.28 2.00e+00 2.50e-01 3.77e+01 angle pdb=" C GLU G 136 " pdb=" CA GLU G 136 " pdb=" CB GLU G 136 " ideal model delta sigma weight residual 110.42 100.19 10.23 1.99e+00 2.53e-01 2.65e+01 ... (remaining 19915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 7180 17.13 - 34.26: 944 34.26 - 51.39: 340 51.39 - 68.52: 56 68.52 - 85.65: 24 Dihedral angle restraints: 8544 sinusoidal: 3544 harmonic: 5000 Sorted by residual: dihedral pdb=" CA ARG B 190 " pdb=" C ARG B 190 " pdb=" N ASP B 191 " pdb=" CA ASP B 191 " ideal model delta harmonic sigma weight residual -180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ARG A 190 " pdb=" C ARG A 190 " pdb=" N ASP A 191 " pdb=" CA ASP A 191 " ideal model delta harmonic sigma weight residual -180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ARG C 190 " pdb=" C ARG C 190 " pdb=" N ASP C 191 " pdb=" CA ASP C 191 " ideal model delta harmonic sigma weight residual 180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 8541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1332 0.039 - 0.077: 432 0.077 - 0.115: 152 0.115 - 0.154: 48 0.154 - 0.192: 12 Chirality restraints: 1976 Sorted by residual: chirality pdb=" C1 NAG G 302 " pdb=" ND2 ASN G 137 " pdb=" C2 NAG G 302 " pdb=" O5 NAG G 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 137 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" C1 NAG C 302 " pdb=" ND2 ASN C 137 " pdb=" C2 NAG C 302 " pdb=" O5 NAG C 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 1973 not shown) Planarity restraints: 2608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 136 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" CD GLU B 136 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU B 136 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 136 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 136 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" CD GLU C 136 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU C 136 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU C 136 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 136 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" CD GLU G 136 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU G 136 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU G 136 " -0.014 2.00e-02 2.50e+03 ... (remaining 2605 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 16 2.28 - 2.94: 6524 2.94 - 3.59: 17416 3.59 - 4.25: 31200 4.25 - 4.90: 55740 Nonbonded interactions: 110896 Sorted by model distance: nonbonded pdb=" NE2 GLN D 192 " pdb="CA CA D 303 " model vdw 1.628 2.590 nonbonded pdb=" NE2 GLN H 192 " pdb="CA CA H 303 " model vdw 1.628 2.590 nonbonded pdb=" NE2 GLN F 192 " pdb="CA CA F 303 " model vdw 1.628 2.590 nonbonded pdb=" NE2 GLN E 192 " pdb="CA CA E 303 " model vdw 1.628 2.590 nonbonded pdb=" CB ASP A 191 " pdb="CA CA A 303 " model vdw 1.905 2.910 ... (remaining 110891 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.910 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 40.110 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.004 0.037 14720 Z= 0.239 Angle : 0.747 12.278 19920 Z= 0.416 Chirality : 0.047 0.192 1976 Planarity : 0.004 0.033 2592 Dihedral : 18.144 85.653 5360 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.92 % Allowed : 12.67 % Favored : 86.41 % Rotamer: Outliers : 4.72 % Allowed : 29.44 % Favored : 65.83 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.15), residues: 1736 helix: -2.11 (0.28), residues: 240 sheet: -1.45 (0.28), residues: 320 loop : -4.10 (0.11), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 235 HIS 0.003 0.001 HIS B 118 PHE 0.018 0.001 PHE A 82 TYR 0.011 0.001 TYR E 45 ARG 0.003 0.000 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 200 time to evaluate : 1.629 Fit side-chains REVERT: A 50 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.5976 (mp-120) REVERT: A 193 ASP cc_start: 0.6914 (m-30) cc_final: 0.6449 (m-30) REVERT: A 197 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7318 (mp10) REVERT: D 135 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6329 (t80) REVERT: D 213 HIS cc_start: 0.6549 (OUTLIER) cc_final: 0.6326 (m-70) REVERT: B 50 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.5973 (mp-120) REVERT: B 193 ASP cc_start: 0.6922 (m-30) cc_final: 0.6452 (m-30) REVERT: B 197 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: E 135 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6330 (t80) REVERT: E 213 HIS cc_start: 0.6556 (OUTLIER) cc_final: 0.6332 (m-70) REVERT: C 50 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.5979 (mp-120) REVERT: C 193 ASP cc_start: 0.6924 (m-30) cc_final: 0.6457 (m-30) REVERT: C 197 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7322 (mp10) REVERT: F 135 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.6334 (t80) REVERT: F 213 HIS cc_start: 0.6511 (OUTLIER) cc_final: 0.6288 (m-70) REVERT: G 50 GLN cc_start: 0.6413 (OUTLIER) cc_final: 0.5977 (mp-120) REVERT: G 193 ASP cc_start: 0.6919 (m-30) cc_final: 0.6453 (m-30) REVERT: G 197 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7315 (mp10) REVERT: H 135 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6333 (t80) REVERT: H 213 HIS cc_start: 0.6517 (OUTLIER) cc_final: 0.6290 (m-70) outliers start: 68 outliers final: 36 residues processed: 256 average time/residue: 0.2904 time to fit residues: 104.3630 Evaluate side-chains 248 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 196 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 213 HIS Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 213 HIS Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 213 HIS Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 213 HIS Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.0470 chunk 127 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 152 optimal weight: 0.6980 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14720 Z= 0.184 Angle : 0.557 5.922 19920 Z= 0.301 Chirality : 0.044 0.198 1976 Planarity : 0.003 0.032 2592 Dihedral : 8.023 52.824 2364 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.40 % Favored : 85.37 % Rotamer: Outliers : 5.42 % Allowed : 25.14 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.15), residues: 1736 helix: -1.38 (0.27), residues: 288 sheet: -1.31 (0.27), residues: 320 loop : -4.20 (0.12), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 235 HIS 0.002 0.001 HIS F 180 PHE 0.021 0.001 PHE B 82 TYR 0.010 0.001 TYR E 110 ARG 0.002 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 202 time to evaluate : 1.569 Fit side-chains REVERT: A 193 ASP cc_start: 0.6845 (m-30) cc_final: 0.6331 (m-30) REVERT: A 197 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: D 157 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: B 193 ASP cc_start: 0.6846 (m-30) cc_final: 0.6329 (m-30) REVERT: B 197 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7485 (mp10) REVERT: E 157 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8064 (tt0) REVERT: C 193 ASP cc_start: 0.6853 (m-30) cc_final: 0.6334 (m-30) REVERT: C 197 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: F 157 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8064 (tt0) REVERT: G 193 ASP cc_start: 0.6849 (m-30) cc_final: 0.6328 (m-30) REVERT: G 197 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: H 157 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8061 (tt0) outliers start: 78 outliers final: 36 residues processed: 262 average time/residue: 0.2944 time to fit residues: 107.3298 Evaluate side-chains 246 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 202 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 199 CYS Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 198 ASN Chi-restraints excluded: chain F residue 199 CYS Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 199 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 14720 Z= 0.482 Angle : 0.754 5.012 19920 Z= 0.409 Chirality : 0.053 0.215 1976 Planarity : 0.006 0.070 2592 Dihedral : 8.026 55.590 2308 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.69 % Allowed : 16.36 % Favored : 82.95 % Rotamer: Outliers : 8.06 % Allowed : 22.78 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.66 (0.16), residues: 1736 helix: -1.58 (0.27), residues: 296 sheet: -1.77 (0.28), residues: 344 loop : -4.28 (0.12), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 235 HIS 0.007 0.002 HIS H 180 PHE 0.029 0.002 PHE E 82 TYR 0.024 0.003 TYR H 110 ARG 0.008 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 200 time to evaluate : 1.608 Fit side-chains REVERT: A 83 GLN cc_start: 0.9391 (OUTLIER) cc_final: 0.8608 (tp40) REVERT: A 133 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: A 197 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7417 (mp10) REVERT: D 157 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: D 247 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7567 (mtm180) REVERT: B 83 GLN cc_start: 0.9395 (OUTLIER) cc_final: 0.8613 (tp40) REVERT: B 133 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: B 197 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7421 (mp10) REVERT: E 157 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: E 247 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7568 (mtm180) REVERT: C 83 GLN cc_start: 0.9393 (OUTLIER) cc_final: 0.8610 (tp40) REVERT: C 133 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: C 197 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7416 (mp10) REVERT: F 157 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: F 247 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7566 (mtm180) REVERT: G 83 GLN cc_start: 0.9391 (OUTLIER) cc_final: 0.8611 (tp40) REVERT: G 133 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: G 197 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: H 157 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: H 247 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7572 (mtm180) outliers start: 116 outliers final: 60 residues processed: 292 average time/residue: 0.2832 time to fit residues: 116.5053 Evaluate side-chains 276 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 196 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 207 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 207 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 250 MET Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 244 SER Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 162 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 14720 Z= 0.259 Angle : 0.609 5.014 19920 Z= 0.331 Chirality : 0.047 0.219 1976 Planarity : 0.004 0.045 2592 Dihedral : 7.359 53.792 2308 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.69 % Allowed : 14.75 % Favored : 84.56 % Rotamer: Outliers : 7.71 % Allowed : 23.40 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.16), residues: 1736 helix: -1.28 (0.28), residues: 296 sheet: -1.76 (0.28), residues: 344 loop : -4.25 (0.12), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 235 HIS 0.003 0.001 HIS D 180 PHE 0.023 0.002 PHE C 82 TYR 0.014 0.001 TYR D 110 ARG 0.003 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 187 time to evaluate : 1.585 Fit side-chains REVERT: A 50 GLN cc_start: 0.6350 (OUTLIER) cc_final: 0.5846 (mp-120) REVERT: A 83 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.8594 (tp40) REVERT: A 133 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: A 159 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.5821 (m-30) REVERT: A 197 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7438 (mp10) REVERT: D 157 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: D 247 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7488 (mtm180) REVERT: B 50 GLN cc_start: 0.6349 (OUTLIER) cc_final: 0.5846 (mp-120) REVERT: B 83 GLN cc_start: 0.9366 (OUTLIER) cc_final: 0.8598 (tp40) REVERT: B 133 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: B 159 ASP cc_start: 0.6764 (OUTLIER) cc_final: 0.5818 (m-30) REVERT: B 197 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7440 (mp10) REVERT: E 157 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: E 247 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7484 (mtm180) REVERT: C 50 GLN cc_start: 0.6354 (OUTLIER) cc_final: 0.5836 (mp-120) REVERT: C 83 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.8595 (tp40) REVERT: C 133 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: C 159 ASP cc_start: 0.6769 (OUTLIER) cc_final: 0.5823 (m-30) REVERT: C 197 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: F 157 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: F 247 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7489 (mtm180) REVERT: G 50 GLN cc_start: 0.6354 (OUTLIER) cc_final: 0.5836 (mp-120) REVERT: G 83 GLN cc_start: 0.9364 (OUTLIER) cc_final: 0.8599 (tp40) REVERT: G 133 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: G 159 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.5821 (m-30) REVERT: G 197 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7438 (mp10) REVERT: H 157 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: H 247 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7493 (mtm180) outliers start: 111 outliers final: 59 residues processed: 278 average time/residue: 0.3037 time to fit residues: 119.3047 Evaluate side-chains 263 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 176 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 207 PHE Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 198 ASN Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 207 PHE Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 244 SER Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 ASN E 138 ASN F 138 ASN H 138 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 14720 Z= 0.235 Angle : 0.583 5.129 19920 Z= 0.316 Chirality : 0.046 0.217 1976 Planarity : 0.004 0.041 2592 Dihedral : 7.126 54.004 2308 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.38 % Favored : 83.93 % Rotamer: Outliers : 7.78 % Allowed : 24.03 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.16), residues: 1736 helix: -1.11 (0.29), residues: 296 sheet: -1.71 (0.28), residues: 344 loop : -4.26 (0.12), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 235 HIS 0.003 0.001 HIS E 180 PHE 0.023 0.002 PHE G 82 TYR 0.013 0.001 TYR H 110 ARG 0.003 0.000 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 188 time to evaluate : 1.672 Fit side-chains REVERT: A 50 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.5825 (mt0) REVERT: A 83 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.8589 (tp40) REVERT: A 133 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: A 159 ASP cc_start: 0.6750 (OUTLIER) cc_final: 0.5810 (m-30) REVERT: A 197 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7413 (mp10) REVERT: D 157 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: D 247 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7470 (mtm180) REVERT: B 50 GLN cc_start: 0.6261 (OUTLIER) cc_final: 0.5821 (mt0) REVERT: B 83 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.8586 (tp40) REVERT: B 133 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: B 159 ASP cc_start: 0.6746 (OUTLIER) cc_final: 0.5810 (m-30) REVERT: B 197 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: E 157 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: E 247 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7464 (mtm180) REVERT: C 50 GLN cc_start: 0.6263 (OUTLIER) cc_final: 0.5821 (mt0) REVERT: C 83 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.8585 (tp40) REVERT: C 133 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: C 159 ASP cc_start: 0.6749 (OUTLIER) cc_final: 0.5811 (m-30) REVERT: C 197 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7400 (mp10) REVERT: F 157 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: F 247 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7471 (mtm180) REVERT: G 50 GLN cc_start: 0.6268 (OUTLIER) cc_final: 0.5824 (mt0) REVERT: G 83 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.8587 (tp40) REVERT: G 133 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: G 159 ASP cc_start: 0.6750 (OUTLIER) cc_final: 0.5809 (m-30) REVERT: G 197 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7402 (mp10) REVERT: H 157 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: H 247 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7473 (mtm180) outliers start: 112 outliers final: 64 residues processed: 284 average time/residue: 0.2692 time to fit residues: 108.7238 Evaluate side-chains 264 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 172 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 198 ASN Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 32 optimal weight: 0.2980 chunk 95 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 14720 Z= 0.306 Angle : 0.632 5.948 19920 Z= 0.343 Chirality : 0.048 0.213 1976 Planarity : 0.005 0.051 2592 Dihedral : 7.429 55.148 2308 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.69 % Allowed : 16.13 % Favored : 83.18 % Rotamer: Outliers : 9.24 % Allowed : 23.26 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.16), residues: 1736 helix: -1.15 (0.29), residues: 296 sheet: -1.74 (0.28), residues: 344 loop : -4.27 (0.12), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 235 HIS 0.004 0.002 HIS F 180 PHE 0.025 0.002 PHE A 82 TYR 0.016 0.002 TYR E 110 ARG 0.004 0.000 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 178 time to evaluate : 1.483 Fit side-chains REVERT: A 50 GLN cc_start: 0.6317 (OUTLIER) cc_final: 0.5900 (mt0) REVERT: A 83 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8611 (tp40) REVERT: A 159 ASP cc_start: 0.6760 (OUTLIER) cc_final: 0.5811 (m-30) REVERT: A 197 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: D 157 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: D 247 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7500 (mtm180) REVERT: B 50 GLN cc_start: 0.6313 (OUTLIER) cc_final: 0.5897 (mt0) REVERT: B 83 GLN cc_start: 0.9378 (OUTLIER) cc_final: 0.8614 (tp40) REVERT: B 159 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.5812 (m-30) REVERT: B 197 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: E 157 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: E 247 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7496 (mtm180) REVERT: C 50 GLN cc_start: 0.6317 (OUTLIER) cc_final: 0.5899 (mt0) REVERT: C 83 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8610 (tp40) REVERT: C 159 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.5811 (m-30) REVERT: C 197 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7431 (mp10) REVERT: F 157 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: F 247 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7501 (mtm180) REVERT: G 50 GLN cc_start: 0.6313 (OUTLIER) cc_final: 0.5895 (mt0) REVERT: G 83 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8614 (tp40) REVERT: G 159 ASP cc_start: 0.6760 (OUTLIER) cc_final: 0.5810 (m-30) REVERT: G 197 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: H 157 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: H 247 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7505 (mtm180) outliers start: 133 outliers final: 74 residues processed: 287 average time/residue: 0.3020 time to fit residues: 120.0249 Evaluate side-chains 276 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 178 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 207 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 198 ASN Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 207 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 244 SER Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 14720 Z= 0.138 Angle : 0.528 6.958 19920 Z= 0.282 Chirality : 0.044 0.224 1976 Planarity : 0.003 0.025 2592 Dihedral : 6.601 55.307 2308 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.06 % Favored : 85.71 % Rotamer: Outliers : 6.11 % Allowed : 25.56 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.16), residues: 1736 helix: -1.05 (0.29), residues: 312 sheet: -1.60 (0.28), residues: 344 loop : -4.17 (0.12), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 235 HIS 0.003 0.001 HIS G 118 PHE 0.019 0.001 PHE G 82 TYR 0.008 0.001 TYR B 99 ARG 0.001 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 212 time to evaluate : 1.655 Fit side-chains REVERT: A 50 GLN cc_start: 0.6261 (OUTLIER) cc_final: 0.5668 (mt0) REVERT: A 78 LYS cc_start: 0.7756 (mptt) cc_final: 0.6996 (mmtt) REVERT: A 159 ASP cc_start: 0.6897 (OUTLIER) cc_final: 0.6024 (m-30) REVERT: A 197 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7361 (mp10) REVERT: D 72 MET cc_start: 0.7173 (mmt) cc_final: 0.6194 (mmt) REVERT: B 50 GLN cc_start: 0.6261 (OUTLIER) cc_final: 0.5668 (mt0) REVERT: B 78 LYS cc_start: 0.7763 (mptt) cc_final: 0.7002 (mmtt) REVERT: B 159 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6020 (m-30) REVERT: B 197 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: E 72 MET cc_start: 0.7303 (mmt) cc_final: 0.6387 (mmt) REVERT: C 50 GLN cc_start: 0.6263 (OUTLIER) cc_final: 0.5668 (mt0) REVERT: C 78 LYS cc_start: 0.7763 (mptt) cc_final: 0.7000 (mmtt) REVERT: C 159 ASP cc_start: 0.6899 (OUTLIER) cc_final: 0.6023 (m-30) REVERT: C 197 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: F 72 MET cc_start: 0.7177 (mmt) cc_final: 0.6198 (mmt) REVERT: G 50 GLN cc_start: 0.6267 (OUTLIER) cc_final: 0.5668 (mt0) REVERT: G 78 LYS cc_start: 0.7761 (mptt) cc_final: 0.6998 (mmtt) REVERT: G 159 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6017 (m-30) REVERT: G 197 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7361 (mp10) REVERT: H 72 MET cc_start: 0.7215 (mmt) cc_final: 0.6263 (mmt) outliers start: 88 outliers final: 53 residues processed: 292 average time/residue: 0.2897 time to fit residues: 119.5365 Evaluate side-chains 259 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 194 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 198 ASN Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 244 SER Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 14720 Z= 0.459 Angle : 0.724 6.676 19920 Z= 0.391 Chirality : 0.052 0.201 1976 Planarity : 0.006 0.067 2592 Dihedral : 7.870 59.975 2308 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.46 % Allowed : 17.45 % Favored : 82.09 % Rotamer: Outliers : 6.81 % Allowed : 25.28 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.16), residues: 1736 helix: -1.17 (0.29), residues: 296 sheet: -1.75 (0.28), residues: 344 loop : -4.32 (0.12), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 235 HIS 0.006 0.002 HIS H 180 PHE 0.029 0.002 PHE D 82 TYR 0.022 0.002 TYR D 110 ARG 0.005 0.001 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 189 time to evaluate : 1.470 Fit side-chains REVERT: A 83 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.8600 (tp40) REVERT: A 159 ASP cc_start: 0.6803 (OUTLIER) cc_final: 0.5828 (m-30) REVERT: A 197 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: D 157 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: D 247 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7540 (mtm180) REVERT: B 83 GLN cc_start: 0.9397 (OUTLIER) cc_final: 0.8605 (tp40) REVERT: B 159 ASP cc_start: 0.6799 (OUTLIER) cc_final: 0.5828 (m-30) REVERT: B 197 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7443 (mp10) REVERT: E 157 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: E 247 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7536 (mtm180) REVERT: C 83 GLN cc_start: 0.9396 (OUTLIER) cc_final: 0.8601 (tp40) REVERT: C 159 ASP cc_start: 0.6799 (OUTLIER) cc_final: 0.5826 (m-30) REVERT: C 197 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7440 (mp10) REVERT: F 157 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: F 247 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7541 (mtm180) REVERT: G 83 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.8603 (tp40) REVERT: G 159 ASP cc_start: 0.6802 (OUTLIER) cc_final: 0.5829 (m-30) REVERT: G 197 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7443 (mp10) REVERT: H 157 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: H 247 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7544 (mtm180) outliers start: 98 outliers final: 66 residues processed: 271 average time/residue: 0.2919 time to fit residues: 110.5746 Evaluate side-chains 270 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 184 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 198 ASN Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 244 SER Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 150 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 0.0470 chunk 118 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14720 Z= 0.155 Angle : 0.558 8.402 19920 Z= 0.296 Chirality : 0.045 0.224 1976 Planarity : 0.003 0.024 2592 Dihedral : 6.343 56.191 2296 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.36 % Favored : 86.41 % Rotamer: Outliers : 4.86 % Allowed : 27.50 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.16), residues: 1736 helix: -1.11 (0.29), residues: 312 sheet: -1.66 (0.28), residues: 344 loop : -4.15 (0.12), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 235 HIS 0.002 0.001 HIS A 118 PHE 0.019 0.001 PHE C 82 TYR 0.008 0.001 TYR A 99 ARG 0.001 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 193 time to evaluate : 1.457 Fit side-chains REVERT: A 71 ASP cc_start: 0.7802 (t0) cc_final: 0.7601 (t0) REVERT: A 78 LYS cc_start: 0.7716 (mptt) cc_final: 0.6975 (mmtt) REVERT: A 159 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6053 (m-30) REVERT: A 197 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: D 72 MET cc_start: 0.7176 (mmt) cc_final: 0.6214 (mmt) REVERT: D 247 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7250 (mtm180) REVERT: B 71 ASP cc_start: 0.7801 (t0) cc_final: 0.7601 (t0) REVERT: B 78 LYS cc_start: 0.7722 (mptt) cc_final: 0.6978 (mmtt) REVERT: B 159 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6040 (m-30) REVERT: B 197 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: E 72 MET cc_start: 0.7321 (mmt) cc_final: 0.6356 (mmt) REVERT: E 247 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7248 (mtm180) REVERT: C 78 LYS cc_start: 0.7724 (mptt) cc_final: 0.6979 (mmtt) REVERT: C 159 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.6040 (m-30) REVERT: C 197 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: F 72 MET cc_start: 0.7182 (mmt) cc_final: 0.6222 (mmt) REVERT: F 247 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7250 (mtm180) REVERT: G 78 LYS cc_start: 0.7723 (mptt) cc_final: 0.6978 (mmtt) REVERT: G 159 ASP cc_start: 0.6913 (OUTLIER) cc_final: 0.6049 (m-30) REVERT: G 197 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7301 (mp10) REVERT: H 72 MET cc_start: 0.7235 (mmt) cc_final: 0.6268 (mmt) REVERT: H 247 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7258 (mtm180) outliers start: 70 outliers final: 49 residues processed: 251 average time/residue: 0.2942 time to fit residues: 102.8980 Evaluate side-chains 251 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 190 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 198 ASN Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 244 SER Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 14720 Z= 0.520 Angle : 0.787 8.542 19920 Z= 0.421 Chirality : 0.054 0.196 1976 Planarity : 0.006 0.071 2592 Dihedral : 7.648 55.140 2296 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.46 % Allowed : 16.82 % Favored : 82.72 % Rotamer: Outliers : 5.14 % Allowed : 27.99 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.16), residues: 1736 helix: -1.27 (0.29), residues: 296 sheet: -1.89 (0.27), residues: 344 loop : -4.34 (0.12), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 235 HIS 0.007 0.002 HIS D 180 PHE 0.031 0.002 PHE D 82 TYR 0.024 0.003 TYR F 110 ARG 0.006 0.001 ARG F 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 179 time to evaluate : 1.689 Fit side-chains REVERT: A 159 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.5829 (m-30) REVERT: A 197 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7290 (mp10) REVERT: D 72 MET cc_start: 0.7376 (mmt) cc_final: 0.6499 (mmt) REVERT: D 247 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7609 (mtm180) REVERT: B 159 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.5826 (m-30) REVERT: B 197 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7292 (mp10) REVERT: E 247 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7602 (mtm180) REVERT: C 159 ASP cc_start: 0.6800 (OUTLIER) cc_final: 0.5821 (m-30) REVERT: C 197 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7294 (mp10) REVERT: F 72 MET cc_start: 0.7382 (mmt) cc_final: 0.6505 (mmt) REVERT: F 247 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7611 (mtm180) REVERT: G 159 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.5826 (m-30) REVERT: G 197 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7290 (mp10) REVERT: H 72 MET cc_start: 0.7376 (mmt) cc_final: 0.6501 (mmt) REVERT: H 247 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7615 (mtm180) outliers start: 74 outliers final: 59 residues processed: 242 average time/residue: 0.2991 time to fit residues: 101.2391 Evaluate side-chains 246 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 175 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 198 ASN Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 244 SER Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 137 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.160709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.141110 restraints weight = 17742.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.142771 restraints weight = 14224.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.144056 restraints weight = 12159.738| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14720 Z= 0.153 Angle : 0.573 9.680 19920 Z= 0.304 Chirality : 0.044 0.224 1976 Planarity : 0.003 0.027 2592 Dihedral : 6.274 49.452 2296 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer: Outliers : 5.42 % Allowed : 27.43 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.16), residues: 1736 helix: -1.12 (0.29), residues: 312 sheet: -1.72 (0.27), residues: 344 loop : -4.18 (0.12), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 235 HIS 0.002 0.001 HIS E 226 PHE 0.020 0.001 PHE C 82 TYR 0.009 0.001 TYR A 99 ARG 0.001 0.000 ARG C 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2897.24 seconds wall clock time: 52 minutes 13.73 seconds (3133.73 seconds total)