Starting phenix.real_space_refine on Tue Sep 15 08:14:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ezm_4160/09_2026/6ezm_4160.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ezm_4160/09_2026/6ezm_4160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ezm_4160/09_2026/6ezm_4160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ezm_4160/09_2026/6ezm_4160.map" model { file = "/net/cci-nas-00/data/ceres_data/6ezm_4160/09_2026/6ezm_4160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ezm_4160/09_2026/6ezm_4160.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ezm_4160/09_2026/6ezm_4160.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ezm_4160/09_2026/6ezm_4160.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 sd= 0.048 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: 6 Type Number sf(0) Gaussians Mn 48 7.51 5 P 24 5.49 5 S 144 5.16 5 C 24000 2.51 5 N 6960 2.21 5 O 7224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38400 Number of models: 1 Model: "" Number of chains: 38 Chain: "U" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "J" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "K" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "L" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "M" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "N" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "O" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "P" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "Q" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "S" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "T" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "V" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "W" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "X" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "U" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Residues with excluded nonbonded symmetry interactions: 48 residue: pdb="MN MN U 302 " occ=0.50 residue: pdb=" C3 5LD U 303 " occ=0.30 ... (11 atoms not shown) pdb=" P9 5LD U 303 " occ=0.30 residue: pdb="MN MN U 305 " occ=0.50 residue: pdb=" C3 5LD U 306 " occ=0.30 ... (11 atoms not shown) pdb=" P9 5LD U 306 " occ=0.30 residue: pdb="MN MN A 401 " occ=0.50 residue: pdb=" C3 5LD A 402 " occ=0.30 ... (11 atoms not shown) pdb=" P9 5LD A 402 " occ=0.30 residue: pdb="MN MN A 405 " occ=0.50 residue: pdb=" C3 5LD A 406 " occ=0.30 ... (11 atoms not shown) pdb=" P9 5LD A 406 " occ=0.30 residue: pdb="MN MN B 302 " occ=0.50 residue: pdb=" C3 5LD B 303 " occ=0.30 ... (11 atoms not shown) pdb=" P9 5LD B 303 " occ=0.30 residue: pdb="MN MN B 304 " occ=0.50 residue: pdb=" C3 5LD B 305 " occ=0.30 ... (11 atoms not shown) pdb=" P9 5LD B 305 " occ=0.30 ... (remaining 36 not shown) Time building chain proxies: 9.53, per 1000 atoms: 0.25 Number of scatterers: 38400 At special positions: 0 Unit cell: (145.905, 145.905, 145.905, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 48 24.99 S 144 16.00 P 24 15.00 O 7224 8.00 N 6960 7.00 C 24000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9360 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 48 sheets defined 32.5% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'U' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS U 72 " --> pdb=" O ALA U 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 108 removed outlier: 3.660A pdb=" N ASP U 95 " --> pdb=" O HIS U 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS U 96 " --> pdb=" O THR U 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU U 100 " --> pdb=" O CYS U 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU U 108 " --> pdb=" O PHE U 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 158 through 172 removed outlier: 3.619A pdb=" N HIS U 162 " --> pdb=" O GLU U 158 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU U 164 " --> pdb=" O ILE U 160 " (cutoff:3.500A) Processing helix chain 'U' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA U 192 " --> pdb=" O ARG U 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 72 removed outlier: 3.569A pdb=" N HIS A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP A 95 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 100 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 204 removed outlier: 3.655A pdb=" N ALA A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP B 95 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 100 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS B 162 " --> pdb=" O GLU B 158 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP C 95 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU C 100 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 108 " --> pdb=" O PHE C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 164 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA C 192 " --> pdb=" O ARG C 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 72 removed outlier: 3.569A pdb=" N HIS D 72 " --> pdb=" O ALA D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP D 95 " --> pdb=" O HIS D 91 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU D 100 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 108 " --> pdb=" O PHE D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 72 removed outlier: 3.569A pdb=" N HIS E 72 " --> pdb=" O ALA E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 108 removed outlier: 3.660A pdb=" N ASP E 95 " --> pdb=" O HIS E 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU E 100 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 108 " --> pdb=" O PHE E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS E 162 " --> pdb=" O GLU E 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 164 " --> pdb=" O ILE E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 204 removed outlier: 3.655A pdb=" N ALA E 192 " --> pdb=" O ARG E 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS F 72 " --> pdb=" O ALA F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP F 95 " --> pdb=" O HIS F 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS F 96 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU F 100 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 108 " --> pdb=" O PHE F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 172 removed outlier: 3.619A pdb=" N HIS F 162 " --> pdb=" O GLU F 158 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU F 164 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 108 removed outlier: 3.660A pdb=" N ASP G 95 " --> pdb=" O HIS G 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS G 96 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU G 100 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU G 108 " --> pdb=" O PHE G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 172 removed outlier: 3.621A pdb=" N HIS G 162 " --> pdb=" O GLU G 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU G 164 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 204 removed outlier: 3.655A pdb=" N ALA G 192 " --> pdb=" O ARG G 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP H 95 " --> pdb=" O HIS H 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS H 96 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU H 100 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU H 108 " --> pdb=" O PHE H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS H 162 " --> pdb=" O GLU H 158 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU H 164 " --> pdb=" O ILE H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA H 192 " --> pdb=" O ARG H 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 72 removed outlier: 3.569A pdb=" N HIS I 72 " --> pdb=" O ALA I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP I 95 " --> pdb=" O HIS I 91 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS I 96 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU I 100 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU I 108 " --> pdb=" O PHE I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS I 162 " --> pdb=" O GLU I 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU I 164 " --> pdb=" O ILE I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA I 192 " --> pdb=" O ARG I 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 72 removed outlier: 3.569A pdb=" N HIS J 72 " --> pdb=" O ALA J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP J 95 " --> pdb=" O HIS J 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS J 96 " --> pdb=" O THR J 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU J 100 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU J 108 " --> pdb=" O PHE J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS J 162 " --> pdb=" O GLU J 158 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU J 164 " --> pdb=" O ILE J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA J 192 " --> pdb=" O ARG J 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS K 72 " --> pdb=" O ALA K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP K 95 " --> pdb=" O HIS K 91 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N CYS K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU K 100 " --> pdb=" O CYS K 96 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU K 108 " --> pdb=" O PHE K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS K 162 " --> pdb=" O GLU K 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU K 164 " --> pdb=" O ILE K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA K 192 " --> pdb=" O ARG K 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS L 72 " --> pdb=" O ALA L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP L 95 " --> pdb=" O HIS L 91 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N CYS L 96 " --> pdb=" O THR L 92 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU L 100 " --> pdb=" O CYS L 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU L 108 " --> pdb=" O PHE L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 172 removed outlier: 3.619A pdb=" N HIS L 162 " --> pdb=" O GLU L 158 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU L 164 " --> pdb=" O ILE L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 204 removed outlier: 3.655A pdb=" N ALA L 192 " --> pdb=" O ARG L 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS M 72 " --> pdb=" O ALA M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 108 removed outlier: 3.645A pdb=" N ASP M 95 " --> pdb=" O HIS M 91 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS M 96 " --> pdb=" O THR M 92 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU M 108 " --> pdb=" O PHE M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS M 162 " --> pdb=" O GLU M 158 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU M 164 " --> pdb=" O ILE M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA M 192 " --> pdb=" O ARG M 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS N 72 " --> pdb=" O ALA N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 108 removed outlier: 3.644A pdb=" N ASP N 95 " --> pdb=" O HIS N 91 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS N 96 " --> pdb=" O THR N 92 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU N 108 " --> pdb=" O PHE N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS N 162 " --> pdb=" O GLU N 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU N 164 " --> pdb=" O ILE N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA N 192 " --> pdb=" O ARG N 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS O 72 " --> pdb=" O ALA O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 108 removed outlier: 3.649A pdb=" N ASP O 95 " --> pdb=" O HIS O 91 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS O 96 " --> pdb=" O THR O 92 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU O 108 " --> pdb=" O PHE O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS O 162 " --> pdb=" O GLU O 158 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU O 164 " --> pdb=" O ILE O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA O 192 " --> pdb=" O ARG O 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS P 72 " --> pdb=" O ALA P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP P 95 " --> pdb=" O HIS P 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS P 96 " --> pdb=" O THR P 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU P 100 " --> pdb=" O CYS P 96 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU P 108 " --> pdb=" O PHE P 104 " (cutoff:3.500A) Processing helix chain 'P' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS P 162 " --> pdb=" O GLU P 158 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU P 164 " --> pdb=" O ILE P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA P 192 " --> pdb=" O ARG P 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP Q 95 " --> pdb=" O HIS Q 91 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS Q 96 " --> pdb=" O THR Q 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU Q 100 " --> pdb=" O CYS Q 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU Q 108 " --> pdb=" O PHE Q 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 158 through 172 removed outlier: 3.619A pdb=" N HIS Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU Q 164 " --> pdb=" O ILE Q 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA Q 192 " --> pdb=" O ARG Q 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 72 removed outlier: 3.571A pdb=" N HIS R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP R 95 " --> pdb=" O HIS R 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS R 96 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU R 100 " --> pdb=" O CYS R 96 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS R 162 " --> pdb=" O GLU R 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU R 164 " --> pdb=" O ILE R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA R 192 " --> pdb=" O ARG R 188 " (cutoff:3.500A) Processing helix chain 'S' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS S 72 " --> pdb=" O ALA S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP S 95 " --> pdb=" O HIS S 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS S 96 " --> pdb=" O THR S 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU S 100 " --> pdb=" O CYS S 96 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU S 108 " --> pdb=" O PHE S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS S 162 " --> pdb=" O GLU S 158 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU S 164 " --> pdb=" O ILE S 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 184 through 204 removed outlier: 3.655A pdb=" N ALA S 192 " --> pdb=" O ARG S 188 " (cutoff:3.500A) Processing helix chain 'T' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP T 95 " --> pdb=" O HIS T 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS T 96 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU T 100 " --> pdb=" O CYS T 96 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU T 108 " --> pdb=" O PHE T 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS T 162 " --> pdb=" O GLU T 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU T 164 " --> pdb=" O ILE T 160 " (cutoff:3.500A) Processing helix chain 'T' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA T 192 " --> pdb=" O ARG T 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 72 removed outlier: 3.569A pdb=" N HIS V 72 " --> pdb=" O ALA V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP V 95 " --> pdb=" O HIS V 91 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS V 96 " --> pdb=" O THR V 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU V 100 " --> pdb=" O CYS V 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU V 108 " --> pdb=" O PHE V 104 " (cutoff:3.500A) Processing helix chain 'V' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS V 162 " --> pdb=" O GLU V 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU V 164 " --> pdb=" O ILE V 160 " (cutoff:3.500A) Processing helix chain 'V' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA V 192 " --> pdb=" O ARG V 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS W 72 " --> pdb=" O ALA W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 90 through 108 removed outlier: 3.661A pdb=" N ASP W 95 " --> pdb=" O HIS W 91 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS W 96 " --> pdb=" O THR W 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU W 100 " --> pdb=" O CYS W 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU W 108 " --> pdb=" O PHE W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 172 removed outlier: 3.619A pdb=" N HIS W 162 " --> pdb=" O GLU W 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU W 164 " --> pdb=" O ILE W 160 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA W 192 " --> pdb=" O ARG W 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 72 removed outlier: 3.570A pdb=" N HIS X 72 " --> pdb=" O ALA X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 90 through 108 removed outlier: 3.660A pdb=" N ASP X 95 " --> pdb=" O HIS X 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS X 96 " --> pdb=" O THR X 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU X 100 " --> pdb=" O CYS X 96 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU X 108 " --> pdb=" O PHE X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 172 removed outlier: 3.620A pdb=" N HIS X 162 " --> pdb=" O GLU X 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU X 164 " --> pdb=" O ILE X 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 184 through 204 removed outlier: 3.656A pdb=" N ALA X 192 " --> pdb=" O ARG X 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'U' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'U' and resid 118 through 124 removed outlier: 6.462A pdb=" N LEU U 128 " --> pdb=" O LEU U 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS U 179 " --> pdb=" O GLU U 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 5 through 8 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 124 removed outlier: 6.463A pdb=" N LEU A 128 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS A 179 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 8 Processing sheet with id=AA6, first strand: chain 'B' and resid 118 through 124 removed outlier: 6.461A pdb=" N LEU B 128 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS B 179 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AA8, first strand: chain 'C' and resid 118 through 124 removed outlier: 6.461A pdb=" N LEU C 128 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS C 179 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 5 through 8 Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 124 removed outlier: 6.462A pdb=" N LEU D 128 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS D 179 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AB3, first strand: chain 'E' and resid 118 through 124 removed outlier: 6.461A pdb=" N LEU E 128 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS E 179 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 5 through 8 Processing sheet with id=AB5, first strand: chain 'F' and resid 118 through 124 removed outlier: 6.462A pdb=" N LEU F 128 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS F 179 " --> pdb=" O GLU F 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 5 through 8 Processing sheet with id=AB7, first strand: chain 'G' and resid 118 through 124 removed outlier: 6.461A pdb=" N LEU G 128 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS G 179 " --> pdb=" O GLU G 144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 5 through 8 Processing sheet with id=AB9, first strand: chain 'H' and resid 118 through 124 removed outlier: 6.462A pdb=" N LEU H 128 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS H 179 " --> pdb=" O GLU H 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 5 through 8 Processing sheet with id=AC2, first strand: chain 'I' and resid 118 through 124 removed outlier: 6.462A pdb=" N LEU I 128 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS I 179 " --> pdb=" O GLU I 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 5 through 8 Processing sheet with id=AC4, first strand: chain 'J' and resid 118 through 124 removed outlier: 6.462A pdb=" N LEU J 128 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS J 179 " --> pdb=" O GLU J 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 5 through 8 Processing sheet with id=AC6, first strand: chain 'K' and resid 118 through 124 removed outlier: 6.462A pdb=" N LEU K 128 " --> pdb=" O LEU K 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS K 179 " --> pdb=" O GLU K 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AC8, first strand: chain 'L' and resid 118 through 124 removed outlier: 6.461A pdb=" N LEU L 128 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS L 179 " --> pdb=" O GLU L 144 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 5 through 8 Processing sheet with id=AD1, first strand: chain 'M' and resid 118 through 124 removed outlier: 6.462A pdb=" N LEU M 128 " --> pdb=" O LEU M 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS M 179 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 5 through 8 Processing sheet with id=AD3, first strand: chain 'N' and resid 118 through 124 removed outlier: 6.461A pdb=" N LEU N 128 " --> pdb=" O LEU N 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS N 179 " --> pdb=" O GLU N 144 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 5 through 8 Processing sheet with id=AD5, first strand: chain 'O' and resid 118 through 124 removed outlier: 6.461A pdb=" N LEU O 128 " --> pdb=" O LEU O 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS O 179 " --> pdb=" O GLU O 144 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 5 through 8 Processing sheet with id=AD7, first strand: chain 'P' and resid 118 through 124 removed outlier: 6.460A pdb=" N LEU P 128 " --> pdb=" O LEU P 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS P 179 " --> pdb=" O GLU P 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 5 through 8 Processing sheet with id=AD9, first strand: chain 'Q' and resid 118 through 124 removed outlier: 6.461A pdb=" N LEU Q 128 " --> pdb=" O LEU Q 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS Q 179 " --> pdb=" O GLU Q 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 5 through 8 Processing sheet with id=AE2, first strand: chain 'R' and resid 118 through 124 removed outlier: 6.461A pdb=" N LEU R 128 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS R 179 " --> pdb=" O GLU R 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 5 through 8 Processing sheet with id=AE4, first strand: chain 'S' and resid 118 through 124 removed outlier: 6.462A pdb=" N LEU S 128 " --> pdb=" O LEU S 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS S 179 " --> pdb=" O GLU S 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 5 through 8 Processing sheet with id=AE6, first strand: chain 'T' and resid 118 through 124 removed outlier: 6.461A pdb=" N LEU T 128 " --> pdb=" O LEU T 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS T 179 " --> pdb=" O GLU T 144 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 5 through 8 Processing sheet with id=AE8, first strand: chain 'V' and resid 118 through 124 removed outlier: 6.461A pdb=" N LEU V 128 " --> pdb=" O LEU V 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS V 179 " --> pdb=" O GLU V 144 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 5 through 8 Processing sheet with id=AF1, first strand: chain 'W' and resid 118 through 124 removed outlier: 6.461A pdb=" N LEU W 128 " --> pdb=" O LEU W 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS W 179 " --> pdb=" O GLU W 144 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 5 through 8 Processing sheet with id=AF3, first strand: chain 'X' and resid 118 through 124 removed outlier: 6.462A pdb=" N LEU X 128 " --> pdb=" O LEU X 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS X 179 " --> pdb=" O GLU X 144 " (cutoff:3.500A) 1947 hydrogen bonds defined for protein. 5625 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.23 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9370 1.33 - 1.45: 7371 1.45 - 1.57: 22043 1.57 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 39000 Sorted by residual: bond pdb=" O12 5LD U 306 " pdb=" P9 5LD U 306 " ideal model delta sigma weight residual 1.561 1.488 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" O12 5LD E 402 " pdb=" P9 5LD E 402 " ideal model delta sigma weight residual 1.561 1.488 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O12 5LD O 305 " pdb=" P9 5LD O 305 " ideal model delta sigma weight residual 1.561 1.488 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O12 5LD H 302 " pdb=" P9 5LD H 302 " ideal model delta sigma weight residual 1.561 1.488 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" O12 5LD B 305 " pdb=" P9 5LD B 305 " ideal model delta sigma weight residual 1.561 1.488 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 38995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 50914 2.84 - 5.69: 1438 5.69 - 8.53: 350 8.53 - 11.37: 74 11.37 - 14.22: 24 Bond angle restraints: 52800 Sorted by residual: angle pdb=" CG ARG X 138 " pdb=" CD ARG X 138 " pdb=" NE ARG X 138 " ideal model delta sigma weight residual 112.00 100.92 11.08 2.20e+00 2.07e-01 2.54e+01 angle pdb=" CG ARG T 138 " pdb=" CD ARG T 138 " pdb=" NE ARG T 138 " ideal model delta sigma weight residual 112.00 100.93 11.07 2.20e+00 2.07e-01 2.53e+01 angle pdb=" CG ARG G 138 " pdb=" CD ARG G 138 " pdb=" NE ARG G 138 " ideal model delta sigma weight residual 112.00 100.94 11.06 2.20e+00 2.07e-01 2.53e+01 angle pdb=" CG ARG K 138 " pdb=" CD ARG K 138 " pdb=" NE ARG K 138 " ideal model delta sigma weight residual 112.00 100.94 11.06 2.20e+00 2.07e-01 2.53e+01 angle pdb=" CG ARG L 138 " pdb=" CD ARG L 138 " pdb=" NE ARG L 138 " ideal model delta sigma weight residual 112.00 100.94 11.06 2.20e+00 2.07e-01 2.53e+01 ... (remaining 52795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.30: 20887 12.30 - 24.60: 1878 24.60 - 36.90: 315 36.90 - 49.20: 100 49.20 - 61.50: 52 Dihedral angle restraints: 23232 sinusoidal: 8808 harmonic: 14424 Sorted by residual: dihedral pdb=" CA THR F 48 " pdb=" C THR F 48 " pdb=" N GLN F 49 " pdb=" CA GLN F 49 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA THR V 48 " pdb=" C THR V 48 " pdb=" N GLN V 49 " pdb=" CA GLN V 49 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA THR T 48 " pdb=" C THR T 48 " pdb=" N GLN T 49 " pdb=" CA GLN T 49 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 23229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4446 0.061 - 0.123: 1462 0.123 - 0.184: 214 0.184 - 0.246: 40 0.246 - 0.307: 6 Chirality restraints: 6168 Sorted by residual: chirality pdb=" CA ILE B 82 " pdb=" N ILE B 82 " pdb=" C ILE B 82 " pdb=" CB ILE B 82 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA ILE K 82 " pdb=" N ILE K 82 " pdb=" C ILE K 82 " pdb=" CB ILE K 82 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ILE J 82 " pdb=" N ILE J 82 " pdb=" C ILE J 82 " pdb=" CB ILE J 82 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 6165 not shown) Planarity restraints: 6840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU N 94 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C GLU N 94 " 0.059 2.00e-02 2.50e+03 pdb=" O GLU N 94 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP N 95 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU M 94 " 0.016 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C GLU M 94 " -0.058 2.00e-02 2.50e+03 pdb=" O GLU M 94 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP M 95 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG P 116 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C ARG P 116 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG P 116 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE P 117 " 0.015 2.00e-02 2.50e+03 ... (remaining 6837 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 411 2.51 - 3.11: 25765 3.11 - 3.71: 59354 3.71 - 4.30: 88670 4.30 - 4.90: 153643 Nonbonded interactions: 327843 Sorted by model distance: nonbonded pdb="MN MN M 405 " pdb=" O13 5LD M 406 " model vdw 1.913 2.320 nonbonded pdb="MN MN K 304 " pdb=" O13 5LD K 305 " model vdw 1.927 2.320 nonbonded pdb="MN MN U 305 " pdb=" O13 5LD U 306 " model vdw 1.928 2.320 nonbonded pdb="MN MN O 304 " pdb=" O13 5LD O 305 " model vdw 1.928 2.320 nonbonded pdb="MN MN C 304 " pdb=" O13 5LD C 305 " model vdw 1.929 2.320 ... (remaining 327838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 219) selection = (chain 'B' and resid 3 through 219) selection = (chain 'C' and resid 3 through 219) selection = (chain 'D' and resid 3 through 219) selection = (chain 'E' and resid 3 through 219) selection = (chain 'F' and resid 3 through 219) selection = (chain 'G' and resid 3 through 219) selection = (chain 'H' and resid 3 through 219) selection = (chain 'I' and resid 3 through 219) selection = (chain 'J' and resid 3 through 219) selection = (chain 'K' and resid 3 through 219) selection = chain 'L' selection = (chain 'M' and resid 3 through 219) selection = chain 'N' selection = (chain 'O' and resid 3 through 219) selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = (chain 'U' and resid 3 through 219) selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 0.060 Extract box with map and model: 0.650 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 37.630 Find NCS groups from input model: 1.360 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: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.010 0.073 39000 Z= 0.442 Angle : 1.278 14.218 52800 Z= 0.643 Chirality : 0.062 0.307 6168 Planarity : 0.008 0.051 6840 Dihedral : 10.272 61.498 13872 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 0.10 % Allowed : 3.64 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.97 (0.08), residues: 4992 helix: -3.98 (0.07), residues: 1584 sheet: -1.94 (0.12), residues: 1392 loop : -3.55 (0.09), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG H 130 TYR 0.024 0.007 TYR X 140 PHE 0.019 0.004 PHE C 117 TRP 0.006 0.002 TRP L 75 HIS 0.019 0.006 HIS T 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00975 / 0.44 (39000) covalent geometry : angle 1.27812 / 0.64 (52800) hydrogen bonds : bond 0.24911 / 16.87 ( 1947) hydrogen bonds : angle 8.39962 / 5.80 ( 5625) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1375 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1371 time to evaluate : 1.425 Fit side-chains REVERT: U 94 GLU cc_start: 0.7944 (tt0) cc_final: 0.7725 (tt0) REVERT: U 188 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8410 (mtp180) REVERT: A 94 GLU cc_start: 0.7985 (tt0) cc_final: 0.7734 (tt0) REVERT: A 185 ASP cc_start: 0.8164 (m-30) cc_final: 0.7923 (m-30) REVERT: A 188 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.8434 (mtp180) REVERT: B 94 GLU cc_start: 0.7974 (tt0) cc_final: 0.7729 (tt0) REVERT: B 188 ARG cc_start: 0.8645 (ttm-80) cc_final: 0.8379 (mtp180) REVERT: D 63 ASP cc_start: 0.7652 (m-30) cc_final: 0.7444 (m-30) REVERT: E 63 ASP cc_start: 0.7624 (m-30) cc_final: 0.7385 (m-30) REVERT: E 185 ASP cc_start: 0.8176 (m-30) cc_final: 0.7945 (m-30) REVERT: E 188 ARG cc_start: 0.8680 (ttm-80) cc_final: 0.8423 (mtp180) REVERT: F 188 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8404 (mtp180) REVERT: G 55 VAL cc_start: 0.8999 (m) cc_final: 0.8760 (t) REVERT: G 80 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7837 (mt-10) REVERT: H 61 PHE cc_start: 0.8785 (t80) cc_final: 0.8302 (t80) REVERT: H 63 ASP cc_start: 0.7599 (m-30) cc_final: 0.7394 (m-30) REVERT: I 181 ARG cc_start: 0.8598 (ptp-170) cc_final: 0.8071 (ptp90) REVERT: J 80 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7704 (mt-10) REVERT: K 94 GLU cc_start: 0.7994 (tt0) cc_final: 0.7727 (tt0) REVERT: K 185 ASP cc_start: 0.8168 (m-30) cc_final: 0.7937 (m-30) REVERT: K 188 ARG cc_start: 0.8732 (ttm-80) cc_final: 0.8484 (mtp180) REVERT: L 188 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8419 (mtp180) REVERT: M 94 GLU cc_start: 0.7950 (tt0) cc_final: 0.7706 (tt0) REVERT: M 181 ARG cc_start: 0.8573 (ptp-170) cc_final: 0.8082 (ptp90) REVERT: M 188 ARG cc_start: 0.8698 (ttm-80) cc_final: 0.8437 (mtp180) REVERT: N 94 GLU cc_start: 0.7993 (tt0) cc_final: 0.7755 (tt0) REVERT: N 169 GLU cc_start: 0.6853 (tt0) cc_final: 0.6583 (tt0) REVERT: N 188 ARG cc_start: 0.8666 (ttm-80) cc_final: 0.8430 (mtp180) REVERT: O 94 GLU cc_start: 0.8022 (tt0) cc_final: 0.7760 (tt0) REVERT: O 185 ASP cc_start: 0.8168 (m-30) cc_final: 0.7936 (m-30) REVERT: O 188 ARG cc_start: 0.8742 (ttm-80) cc_final: 0.8480 (mtp180) REVERT: P 61 PHE cc_start: 0.8791 (t80) cc_final: 0.8281 (t80) REVERT: P 169 GLU cc_start: 0.6867 (tt0) cc_final: 0.6642 (tt0) REVERT: P 181 ARG cc_start: 0.8520 (ptp-170) cc_final: 0.8091 (ptp90) REVERT: Q 181 ARG cc_start: 0.8606 (ptp-170) cc_final: 0.8138 (ptp90) REVERT: Q 188 ARG cc_start: 0.8725 (ttm-80) cc_final: 0.8464 (mtp180) REVERT: R 63 ASP cc_start: 0.7603 (m-30) cc_final: 0.7401 (m-30) REVERT: R 94 GLU cc_start: 0.7914 (tt0) cc_final: 0.7613 (tt0) REVERT: R 188 ARG cc_start: 0.8708 (ttm-80) cc_final: 0.8447 (mtp180) REVERT: S 94 GLU cc_start: 0.7910 (tt0) cc_final: 0.7675 (tt0) REVERT: S 181 ARG cc_start: 0.8608 (ptp-170) cc_final: 0.8075 (ptp90) REVERT: T 63 ASP cc_start: 0.7613 (m-30) cc_final: 0.7405 (m-30) REVERT: T 94 GLU cc_start: 0.7902 (tt0) cc_final: 0.7640 (tt0) REVERT: T 181 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8013 (ptp90) REVERT: V 63 ASP cc_start: 0.7669 (m-30) cc_final: 0.7463 (m-30) REVERT: V 188 ARG cc_start: 0.8719 (ttm-80) cc_final: 0.8448 (mtp180) REVERT: W 188 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8421 (mtp180) REVERT: X 181 ARG cc_start: 0.8641 (ptp-170) cc_final: 0.8371 (ptp90) REVERT: X 188 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.8434 (mtp180) outliers start: 4 outliers final: 4 residues processed: 1375 average time/residue: 0.2851 time to fit residues: 592.3474 Evaluate side-chains 937 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 933 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 96 CYS Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain O residue 96 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 494 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 13 ASN U 54 ASN U 67 HIS U 176 HIS U 207 ASN A 13 ASN A 54 ASN A 67 HIS A 176 HIS A 207 ASN A 210 ASN B 13 ASN B 54 ASN B 67 HIS B 176 HIS B 207 ASN B 210 ASN C 13 ASN C 18 GLN C 67 HIS C 207 ASN C 210 ASN D 13 ASN D 54 ASN D 67 HIS D 207 ASN D 210 ASN E 13 ASN E 54 ASN E 67 HIS E 207 ASN E 210 ASN F 13 ASN F 18 GLN F 54 ASN F 67 HIS F 176 HIS F 207 ASN F 210 ASN G 13 ASN G 54 ASN G 67 HIS G 207 ASN H 13 ASN H 54 ASN H 67 HIS H 207 ASN H 210 ASN I 13 ASN I 18 GLN I 54 ASN I 67 HIS I 207 ASN I 210 ASN J 13 ASN J 18 GLN J 67 HIS J 176 HIS J 207 ASN J 210 ASN K 13 ASN K 67 HIS K 176 HIS K 207 ASN K 210 ASN L 13 ASN L 54 ASN L 67 HIS L 176 HIS L 207 ASN L 210 ASN M 13 ASN M 67 HIS M 207 ASN M 210 ASN N 13 ASN N 54 ASN N 67 HIS N 176 HIS N 207 ASN N 210 ASN O 13 ASN O 67 HIS O 176 HIS O 207 ASN O 210 ASN P 13 ASN P 54 ASN P 67 HIS P 176 HIS P 207 ASN P 210 ASN Q 13 ASN Q 67 HIS Q 176 HIS Q 207 ASN R 13 ASN R 54 ASN R 67 HIS R 176 HIS R 207 ASN R 210 ASN S 13 ASN S 54 ASN S 67 HIS S 176 HIS S 207 ASN S 210 ASN T 13 ASN T 18 GLN T 54 ASN T 67 HIS T 176 HIS T 207 ASN T 210 ASN V 13 ASN V 54 ASN V 67 HIS V 176 HIS V 207 ASN V 210 ASN W 13 ASN W 18 GLN W 67 HIS W 176 HIS W 207 ASN W 210 ASN X 13 ASN X 18 GLN X 54 ASN X 67 HIS X 176 HIS X 207 ASN X 210 ASN Total number of N/Q/H flips: 134 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.144657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.123557 restraints weight = 49716.389| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.53 r_work: 0.3225 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 39000 Z= 0.169 Angle : 0.695 8.578 52800 Z= 0.357 Chirality : 0.046 0.167 6168 Planarity : 0.008 0.088 6840 Dihedral : 7.530 55.995 5356 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.24 % Allowed : 8.48 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.10), residues: 4992 helix: -1.25 (0.11), residues: 1608 sheet: -1.60 (0.13), residues: 1296 loop : -3.38 (0.10), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 138 TYR 0.014 0.003 TYR H 140 PHE 0.013 0.002 PHE L 35 TRP 0.004 0.001 TRP G 75 HIS 0.006 0.002 HIS V 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (39000) covalent geometry : angle 0.69500 / 0.36 (52800) hydrogen bonds : bond 0.03550 / 2.40 ( 1947) hydrogen bonds : angle 4.38097 / 3.06 ( 5625) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1225 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 1057 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 80 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8141 (mt-10) REVERT: U 183 LYS cc_start: 0.8029 (pttp) cc_final: 0.7753 (pttp) REVERT: B 80 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8245 (mt-10) REVERT: B 183 LYS cc_start: 0.8118 (pttp) cc_final: 0.7822 (pttp) REVERT: C 183 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7713 (pttp) REVERT: E 183 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7730 (pttp) REVERT: G 55 VAL cc_start: 0.8966 (m) cc_final: 0.8610 (t) REVERT: G 86 HIS cc_start: 0.7452 (t-90) cc_final: 0.7125 (p-80) REVERT: G 172 ARG cc_start: 0.8948 (mmm160) cc_final: 0.8652 (mtp-110) REVERT: I 183 LYS cc_start: 0.7955 (pttp) cc_final: 0.7664 (pttp) REVERT: J 80 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8220 (mt-10) REVERT: J 183 LYS cc_start: 0.8063 (pttp) cc_final: 0.7851 (pttp) REVERT: K 149 ARG cc_start: 0.8300 (mtp180) cc_final: 0.8045 (mtp180) REVERT: L 95 ASP cc_start: 0.8015 (m-30) cc_final: 0.7599 (m-30) REVERT: L 183 LYS cc_start: 0.8036 (pttp) cc_final: 0.7785 (pttp) REVERT: L 212 VAL cc_start: 0.7526 (OUTLIER) cc_final: 0.7320 (p) REVERT: M 80 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8373 (mt-10) REVERT: N 183 LYS cc_start: 0.8088 (pttp) cc_final: 0.7820 (pttp) REVERT: O 80 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8320 (mt-10) REVERT: Q 10 ARG cc_start: 0.8511 (ttt-90) cc_final: 0.8302 (ttt-90) REVERT: R 150 GLU cc_start: 0.7900 (tt0) cc_final: 0.7539 (tt0) REVERT: R 183 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7766 (pttp) REVERT: T 10 ARG cc_start: 0.8618 (ttt-90) cc_final: 0.8403 (ttt-90) REVERT: V 150 GLU cc_start: 0.7954 (tt0) cc_final: 0.7705 (tt0) REVERT: V 183 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7721 (pttp) REVERT: W 183 LYS cc_start: 0.8026 (pttp) cc_final: 0.7761 (pttp) outliers start: 168 outliers final: 112 residues processed: 1119 average time/residue: 0.2793 time to fit residues: 478.0012 Evaluate side-chains 1028 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 911 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 16 LYS Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 183 LYS Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 215 THR Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain O residue 183 LYS Chi-restraints excluded: chain O residue 215 THR Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 96 CYS Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 183 LYS Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 96 CYS Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 183 LYS Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 96 CYS Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 96 CYS Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 96 CYS Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 23 optimal weight: 0.0030 chunk 332 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 399 optimal weight: 20.0000 chunk 445 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 129 optimal weight: 40.0000 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 13 ASN A 13 ASN A 54 ASN B 13 ASN C 13 ASN C 54 ASN D 13 ASN D 54 ASN D 176 HIS E 13 ASN E 54 ASN E 210 ASN F 13 ASN ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN G 13 ASN H 13 ASN H 54 ASN H 176 HIS H 210 ASN I 13 ASN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 ASN I 176 HIS J 13 ASN K 13 ASN K 210 ASN L 13 ASN M 13 ASN M 176 HIS M 210 ASN N 13 ASN N 210 ASN O 13 ASN O 210 ASN P 13 ASN P 54 ASN P 210 ASN Q 13 ASN R 13 ASN R 54 ASN S 13 ASN T 13 ASN T 54 ASN V 13 ASN V 54 ASN V 210 ASN W 13 ASN ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 54 ASN W 210 ASN X 13 ASN ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.137732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.116912 restraints weight = 49937.509| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.47 r_work: 0.3111 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 39000 Z= 0.174 Angle : 0.637 9.106 52800 Z= 0.329 Chirality : 0.046 0.158 6168 Planarity : 0.006 0.069 6840 Dihedral : 7.032 49.674 5352 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.65 % Allowed : 10.10 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.11), residues: 4992 helix: 0.23 (0.12), residues: 1632 sheet: -1.21 (0.14), residues: 1272 loop : -3.26 (0.11), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG V 172 TYR 0.013 0.003 TYR C 140 PHE 0.008 0.002 PHE G 193 TRP 0.002 0.000 TRP G 75 HIS 0.007 0.002 HIS K 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (39000) covalent geometry : angle 0.63719 / 0.33 (52800) hydrogen bonds : bond 0.03330 / 2.25 ( 1947) hydrogen bonds : angle 3.95754 / 2.76 ( 5625) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 955 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 149 ARG cc_start: 0.8513 (mtp180) cc_final: 0.8236 (mtp180) REVERT: B 80 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8329 (mt-10) REVERT: C 10 ARG cc_start: 0.8667 (ttt-90) cc_final: 0.8411 (ttt-90) REVERT: D 149 ARG cc_start: 0.8496 (mtp180) cc_final: 0.8284 (mtp180) REVERT: E 178 ASP cc_start: 0.8394 (m-30) cc_final: 0.7804 (m-30) REVERT: F 10 ARG cc_start: 0.8585 (ttt-90) cc_final: 0.8374 (ttt-90) REVERT: F 149 ARG cc_start: 0.8512 (mtp180) cc_final: 0.8261 (mtp180) REVERT: G 86 HIS cc_start: 0.7500 (t-90) cc_final: 0.7165 (p-80) REVERT: G 172 ARG cc_start: 0.8963 (mmm160) cc_final: 0.8519 (mtp-110) REVERT: H 65 MET cc_start: 0.8803 (mmp) cc_final: 0.8600 (mmp) REVERT: H 149 ARG cc_start: 0.8438 (mtp180) cc_final: 0.8223 (mtp180) REVERT: I 149 ARG cc_start: 0.8403 (mtp180) cc_final: 0.8170 (mtp180) REVERT: J 149 ARG cc_start: 0.8493 (mtp180) cc_final: 0.7939 (mtp180) REVERT: J 150 GLU cc_start: 0.8357 (tt0) cc_final: 0.8143 (tt0) REVERT: L 149 ARG cc_start: 0.8464 (mtp180) cc_final: 0.7910 (mtp180) REVERT: N 149 ARG cc_start: 0.8475 (mtp180) cc_final: 0.7930 (mtp180) REVERT: N 183 LYS cc_start: 0.8012 (pttp) cc_final: 0.7807 (pttp) REVERT: O 80 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8315 (mt-10) REVERT: O 149 ARG cc_start: 0.8510 (mtp180) cc_final: 0.7985 (mtp180) REVERT: R 149 ARG cc_start: 0.8378 (mtp180) cc_final: 0.7822 (mtp180) REVERT: R 183 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7795 (pttp) REVERT: S 10 ARG cc_start: 0.8661 (ttt-90) cc_final: 0.8455 (ttt-90) REVERT: S 149 ARG cc_start: 0.8499 (mtp180) cc_final: 0.8244 (mtp180) REVERT: S 181 ARG cc_start: 0.8679 (ptp90) cc_final: 0.8451 (ptp-170) REVERT: T 65 MET cc_start: 0.8905 (mmp) cc_final: 0.8705 (mmp) REVERT: X 183 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7775 (pttm) outliers start: 184 outliers final: 132 residues processed: 1032 average time/residue: 0.2662 time to fit residues: 422.6132 Evaluate side-chains 969 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 835 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 96 CYS Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 96 CYS Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 183 LYS Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 215 THR Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain O residue 183 LYS Chi-restraints excluded: chain O residue 215 THR Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 96 CYS Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 183 LYS Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 96 CYS Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 183 LYS Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 96 CYS Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 96 CYS Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 96 CYS Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain X residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 169 optimal weight: 6.9990 chunk 369 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 448 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 336 optimal weight: 20.0000 chunk 178 optimal weight: 6.9990 chunk 379 optimal weight: 4.9990 chunk 498 optimal weight: 1.9990 chunk 360 optimal weight: 30.0000 chunk 445 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 13 ASN U 54 ASN A 13 ASN A 54 ASN B 13 ASN B 54 ASN C 13 ASN C 54 ASN D 13 ASN D 54 ASN E 13 ASN E 176 HIS F 13 ASN F 54 ASN G 54 ASN G 176 HIS H 13 ASN I 13 ASN J 54 ASN K 13 ASN K 54 ASN L 54 ASN M 13 ASN M 54 ASN N 13 ASN N 54 ASN O 13 ASN O 54 ASN P 13 ASN P 54 ASN Q 13 ASN Q 54 ASN R 13 ASN R 54 ASN S 54 ASN T 13 ASN W 13 ASN W 54 ASN X 13 ASN ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 54 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.113294 restraints weight = 49668.023| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.46 r_work: 0.3070 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 39000 Z= 0.242 Angle : 0.686 9.046 52800 Z= 0.352 Chirality : 0.048 0.151 6168 Planarity : 0.007 0.077 6840 Dihedral : 7.218 49.858 5352 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 6.49 % Allowed : 8.61 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.11), residues: 4992 helix: 0.65 (0.12), residues: 1680 sheet: -1.30 (0.13), residues: 1416 loop : -3.22 (0.11), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 172 TYR 0.011 0.002 TYR Q 140 PHE 0.011 0.002 PHE Q 117 TRP 0.002 0.001 TRP X 75 HIS 0.007 0.002 HIS O 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (39000) covalent geometry : angle 0.68607 / 0.35 (52800) hydrogen bonds : bond 0.03452 / 2.33 ( 1947) hydrogen bonds : angle 3.92343 / 2.74 ( 5625) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 257 poor density : 861 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 183 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7771 (pttp) REVERT: E 150 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: E 178 ASP cc_start: 0.8396 (m-30) cc_final: 0.7889 (m-30) REVERT: F 149 ARG cc_start: 0.8595 (mtp180) cc_final: 0.8366 (mtm180) REVERT: G 86 HIS cc_start: 0.7618 (t-90) cc_final: 0.7274 (p-80) REVERT: J 149 ARG cc_start: 0.8614 (mtp180) cc_final: 0.8390 (mtm180) REVERT: K 5 LYS cc_start: 0.9213 (mttp) cc_final: 0.8889 (mttt) REVERT: M 10 ARG cc_start: 0.8651 (ttt-90) cc_final: 0.8438 (ttt-90) REVERT: N 10 ARG cc_start: 0.8526 (ttt-90) cc_final: 0.8299 (ttt-90) REVERT: N 183 LYS cc_start: 0.8098 (pttp) cc_final: 0.7828 (pttp) REVERT: O 183 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7866 (pttp) REVERT: Q 10 ARG cc_start: 0.8617 (ttt-90) cc_final: 0.8098 (ttt-90) REVERT: R 54 ASN cc_start: 0.8817 (t0) cc_final: 0.8612 (t0) REVERT: R 183 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7857 (pttp) REVERT: S 10 ARG cc_start: 0.8489 (ttt-90) cc_final: 0.8276 (ttt-90) REVERT: S 149 ARG cc_start: 0.8540 (mtp180) cc_final: 0.8296 (mtm180) REVERT: T 149 ARG cc_start: 0.8478 (mtp180) cc_final: 0.8232 (mtp180) REVERT: V 5 LYS cc_start: 0.9144 (mttp) cc_final: 0.8809 (mttt) REVERT: V 183 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7838 (pttp) outliers start: 257 outliers final: 184 residues processed: 996 average time/residue: 0.2554 time to fit residues: 397.9576 Evaluate side-chains 996 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 807 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 13 ASN Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 13 ASN Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 16 LYS Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 183 LYS Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 215 THR Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain O residue 183 LYS Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 13 ASN Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 12 THR Chi-restraints excluded: chain R residue 13 ASN Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain S residue 183 LYS Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 13 ASN Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 183 LYS Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 160 ILE Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 13 ASN Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 92 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 13 ASN Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain X residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 328 optimal weight: 4.9990 chunk 234 optimal weight: 40.0000 chunk 367 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 256 optimal weight: 5.9990 chunk 190 optimal weight: 0.6980 chunk 427 optimal weight: 9.9990 chunk 390 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 471 optimal weight: 9.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 13 ASN U 86 HIS A 13 ASN A 54 ASN B 13 ASN C 13 ASN C 176 HIS D 13 ASN D 54 ASN E 13 ASN F 13 ASN F 54 ASN H 13 ASN I 13 ASN K 13 ASN K 54 ASN M 13 ASN M 54 ASN N 13 ASN O 13 ASN O 54 ASN P 54 ASN Q 13 ASN Q 54 ASN Q 86 HIS R 13 ASN S 54 ASN T 13 ASN W 13 ASN W 54 ASN X 13 ASN ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 54 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.133351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.111841 restraints weight = 49689.188| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.46 r_work: 0.3043 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 39000 Z= 0.235 Angle : 0.678 9.184 52800 Z= 0.347 Chirality : 0.048 0.162 6168 Planarity : 0.006 0.066 6840 Dihedral : 7.114 49.217 5352 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 6.46 % Allowed : 8.56 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.11), residues: 4992 helix: 0.89 (0.12), residues: 1680 sheet: -1.11 (0.13), residues: 1416 loop : -3.24 (0.11), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 138 TYR 0.010 0.002 TYR T 140 PHE 0.010 0.002 PHE Q 117 TRP 0.002 0.001 TRP X 75 HIS 0.007 0.002 HIS F 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.24 (39000) covalent geometry : angle 0.67782 / 0.35 (52800) hydrogen bonds : bond 0.03331 / 2.24 ( 1947) hydrogen bonds : angle 3.89899 / 2.73 ( 5625) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 832 time to evaluate : 1.363 Fit side-chains REVERT: B 80 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8334 (mt-10) REVERT: C 183 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7785 (pttp) REVERT: E 150 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: F 5 LYS cc_start: 0.9214 (mttp) cc_final: 0.8990 (mttt) REVERT: K 5 LYS cc_start: 0.9241 (mttp) cc_final: 0.8920 (mttt) REVERT: N 10 ARG cc_start: 0.8531 (ttt-90) cc_final: 0.8271 (ttt-90) REVERT: N 183 LYS cc_start: 0.8171 (pttp) cc_final: 0.7877 (pttp) REVERT: Q 10 ARG cc_start: 0.8662 (ttt-90) cc_final: 0.8368 (ttt-90) REVERT: Q 183 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7725 (pttp) REVERT: R 183 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7848 (pttp) REVERT: S 10 ARG cc_start: 0.8510 (ttt-90) cc_final: 0.8309 (ttt-90) REVERT: S 149 ARG cc_start: 0.8466 (mtp180) cc_final: 0.8265 (mtm180) REVERT: V 5 LYS cc_start: 0.9159 (mttp) cc_final: 0.8819 (mttt) REVERT: V 183 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7849 (pttp) outliers start: 256 outliers final: 180 residues processed: 966 average time/residue: 0.2613 time to fit residues: 393.6308 Evaluate side-chains 978 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 793 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 16 LYS Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 183 LYS Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain O residue 183 LYS Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 160 ILE Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 12 THR Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain S residue 183 LYS Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 183 LYS Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 160 ILE Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 92 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 160 ILE Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain X residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 69 optimal weight: 20.0000 chunk 456 optimal weight: 0.9980 chunk 433 optimal weight: 4.9990 chunk 429 optimal weight: 10.0000 chunk 458 optimal weight: 7.9990 chunk 493 optimal weight: 9.9990 chunk 352 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 366 optimal weight: 5.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN D 13 ASN D 54 ASN F 56 HIS K 54 ASN M 54 ASN P 54 ASN Q 54 ASN R 54 ASN S 54 ASN W 13 ASN ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 56 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.112056 restraints weight = 49699.076| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.41 r_work: 0.3060 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 39000 Z= 0.249 Angle : 0.689 8.718 52800 Z= 0.354 Chirality : 0.048 0.161 6168 Planarity : 0.006 0.061 6840 Dihedral : 7.046 50.133 5352 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 5.45 % Allowed : 9.52 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.11), residues: 4992 helix: 1.13 (0.12), residues: 1680 sheet: -1.02 (0.13), residues: 1416 loop : -3.24 (0.11), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 172 TYR 0.009 0.003 TYR C 140 PHE 0.010 0.002 PHE Q 117 TRP 0.002 0.001 TRP K 75 HIS 0.007 0.002 HIS U 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.25 (39000) covalent geometry : angle 0.68852 / 0.35 (52800) hydrogen bonds : bond 0.03404 / 2.29 ( 1947) hydrogen bonds : angle 3.92640 / 2.74 ( 5625) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 825 time to evaluate : 1.219 Fit side-chains REVERT: E 150 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: F 5 LYS cc_start: 0.9206 (mttp) cc_final: 0.8993 (mttt) REVERT: H 56 HIS cc_start: 0.7381 (m-70) cc_final: 0.7084 (m-70) REVERT: K 5 LYS cc_start: 0.9248 (mttp) cc_final: 0.8919 (mttt) REVERT: N 183 LYS cc_start: 0.8164 (pttp) cc_final: 0.7866 (pttp) REVERT: R 183 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7886 (pttp) REVERT: S 10 ARG cc_start: 0.8532 (ttt-90) cc_final: 0.8326 (ttt-90) REVERT: V 183 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7885 (pttp) REVERT: X 56 HIS cc_start: 0.7450 (m-70) cc_final: 0.7114 (m-70) outliers start: 216 outliers final: 186 residues processed: 934 average time/residue: 0.2690 time to fit residues: 390.3962 Evaluate side-chains 971 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 782 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 16 LYS Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 183 LYS Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain O residue 183 LYS Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 160 ILE Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 12 THR Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain S residue 183 LYS Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 183 LYS Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 160 ILE Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 13 ASN Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 92 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 160 ILE Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 183 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 378 optimal weight: 20.0000 chunk 499 optimal weight: 8.9990 chunk 267 optimal weight: 1.9990 chunk 490 optimal weight: 9.9990 chunk 256 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 220 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 470 optimal weight: 3.9990 chunk 438 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS C 86 HIS D 13 ASN D 86 HIS F 56 HIS F 86 HIS J 86 HIS L 86 HIS P 56 HIS R 54 ASN W 56 HIS ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 54 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.133373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.112012 restraints weight = 49936.062| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.46 r_work: 0.3072 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 39000 Z= 0.185 Angle : 0.637 8.932 52800 Z= 0.328 Chirality : 0.046 0.155 6168 Planarity : 0.005 0.044 6840 Dihedral : 6.822 47.975 5352 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.17 % Allowed : 11.01 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.11), residues: 4992 helix: 1.54 (0.12), residues: 1680 sheet: -0.88 (0.13), residues: 1416 loop : -3.18 (0.12), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 172 TYR 0.008 0.002 TYR M 140 PHE 0.008 0.002 PHE U 61 TRP 0.002 0.001 TRP W 75 HIS 0.005 0.002 HIS U 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (39000) covalent geometry : angle 0.63663 / 0.33 (52800) hydrogen bonds : bond 0.03043 / 2.05 ( 1947) hydrogen bonds : angle 3.86053 / 2.69 ( 5625) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 834 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: C 56 HIS cc_start: 0.7453 (m-70) cc_final: 0.7164 (m-70) REVERT: E 150 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: F 5 LYS cc_start: 0.9217 (mttp) cc_final: 0.8997 (mttt) REVERT: K 5 LYS cc_start: 0.9270 (mttp) cc_final: 0.8945 (mttt) REVERT: O 62 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8988 (tp) REVERT: S 10 ARG cc_start: 0.8534 (ttt-90) cc_final: 0.8323 (ttt-90) REVERT: V 183 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7869 (pttp) REVERT: W 56 HIS cc_start: 0.7556 (m-70) cc_final: 0.7279 (m-70) outliers start: 165 outliers final: 137 residues processed: 917 average time/residue: 0.2639 time to fit residues: 374.8448 Evaluate side-chains 946 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 806 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 183 LYS Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain O residue 183 LYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 160 ILE Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain S residue 183 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 183 LYS Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 92 THR Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 160 ILE Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain X residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 150 optimal weight: 30.0000 chunk 500 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 429 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 459 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 227 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 394 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 86 HIS D 86 HIS F 56 HIS H 54 ASN H 56 HIS J 54 ASN J 56 HIS J 86 HIS L 86 HIS O 86 HIS P 56 HIS R 54 ASN R 86 HIS V 54 ASN V 56 HIS ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 56 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.111882 restraints weight = 50080.075| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.43 r_work: 0.3031 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 39000 Z= 0.229 Angle : 0.679 8.809 52800 Z= 0.350 Chirality : 0.048 0.160 6168 Planarity : 0.006 0.045 6840 Dihedral : 6.879 50.468 5352 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 4.42 % Allowed : 11.26 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.11), residues: 4992 helix: 1.47 (0.12), residues: 1680 sheet: -0.84 (0.13), residues: 1416 loop : -3.13 (0.12), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 172 TYR 0.007 0.002 TYR H 140 PHE 0.010 0.002 PHE U 61 TRP 0.002 0.001 TRP Q 75 HIS 0.006 0.002 HIS F 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (39000) covalent geometry : angle 0.67937 / 0.35 (52800) hydrogen bonds : bond 0.03275 / 2.20 ( 1947) hydrogen bonds : angle 3.91599 / 2.73 ( 5625) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 796 time to evaluate : 1.455 Fit side-chains REVERT: E 150 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: F 5 LYS cc_start: 0.9191 (mttp) cc_final: 0.8972 (mttt) REVERT: G 10 ARG cc_start: 0.8692 (ttt-90) cc_final: 0.8485 (ttt-90) REVERT: K 5 LYS cc_start: 0.9260 (mttp) cc_final: 0.8928 (mttt) REVERT: S 10 ARG cc_start: 0.8538 (ttt-90) cc_final: 0.8314 (ttt-90) REVERT: X 150 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7636 (tt0) outliers start: 175 outliers final: 155 residues processed: 912 average time/residue: 0.2658 time to fit residues: 376.7452 Evaluate side-chains 943 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 786 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 183 LYS Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain O residue 183 LYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 160 ILE Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain S residue 183 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 151 LYS Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 183 LYS Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 160 ILE Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 92 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 160 ILE Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain X residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 30.0000 chunk 402 optimal weight: 30.0000 chunk 431 optimal weight: 10.0000 chunk 242 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 484 optimal weight: 3.9990 chunk 460 optimal weight: 0.9990 chunk 340 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 54 ASN B 56 HIS C 54 ASN C 56 HIS D 86 HIS F 56 HIS I 54 ASN I 86 HIS J 56 HIS J 86 HIS L 86 HIS M 56 HIS N 54 ASN N 56 HIS O 86 HIS P 56 HIS R 54 ASN R 86 HIS V 56 HIS W 54 ASN W 56 HIS X 56 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110189 restraints weight = 50451.216| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.51 r_work: 0.3015 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 39000 Z= 0.234 Angle : 0.686 8.763 52800 Z= 0.352 Chirality : 0.048 0.159 6168 Planarity : 0.006 0.043 6840 Dihedral : 6.891 50.368 5352 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.42 % Allowed : 11.21 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.12), residues: 4992 helix: 1.61 (0.13), residues: 1632 sheet: -0.79 (0.13), residues: 1416 loop : -3.10 (0.12), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 10 TYR 0.007 0.002 TYR K 140 PHE 0.010 0.002 PHE U 61 TRP 0.002 0.001 TRP Q 75 HIS 0.007 0.002 HIS F 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (39000) covalent geometry : angle 0.68558 / 0.35 (52800) hydrogen bonds : bond 0.03289 / 2.21 ( 1947) hydrogen bonds : angle 3.95053 / 2.76 ( 5625) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 794 time to evaluate : 1.130 Fit side-chains REVERT: E 150 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: F 5 LYS cc_start: 0.9200 (mttp) cc_final: 0.8985 (mttt) REVERT: H 56 HIS cc_start: 0.7719 (m-70) cc_final: 0.7246 (m170) REVERT: K 5 LYS cc_start: 0.9257 (mttp) cc_final: 0.8930 (mttt) REVERT: S 10 ARG cc_start: 0.8543 (ttt-90) cc_final: 0.8299 (ttt-90) REVERT: X 150 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7677 (tt0) outliers start: 175 outliers final: 160 residues processed: 906 average time/residue: 0.2646 time to fit residues: 372.2494 Evaluate side-chains 946 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 784 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 16 LYS Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 183 LYS Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain O residue 183 LYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 160 ILE Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain S residue 183 LYS Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 151 LYS Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 183 LYS Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 160 ILE Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 92 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 160 ILE Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain X residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 228 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 465 optimal weight: 8.9990 chunk 477 optimal weight: 0.9980 chunk 467 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 301 optimal weight: 0.9990 chunk 480 optimal weight: 9.9990 chunk 283 optimal weight: 0.9980 chunk 411 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 46 GLN C 56 HIS F 56 HIS G 56 HIS J 56 HIS L 86 HIS M 56 HIS N 56 HIS P 56 HIS R 54 ASN V 56 HIS W 56 HIS X 56 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.115550 restraints weight = 50196.596| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.42 r_work: 0.3115 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 39000 Z= 0.116 Angle : 0.586 8.708 52800 Z= 0.304 Chirality : 0.044 0.154 6168 Planarity : 0.005 0.041 6840 Dihedral : 6.355 42.343 5352 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.06 % Allowed : 12.55 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.12), residues: 4992 helix: 2.16 (0.13), residues: 1680 sheet: -0.68 (0.13), residues: 1416 loop : -3.06 (0.12), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 138 TYR 0.009 0.002 TYR M 140 PHE 0.007 0.001 PHE J 121 TRP 0.003 0.001 TRP G 75 HIS 0.005 0.001 HIS M 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (39000) covalent geometry : angle 0.58585 / 0.30 (52800) hydrogen bonds : bond 0.02652 / 1.79 ( 1947) hydrogen bonds : angle 3.72047 / 2.59 ( 5625) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 844 time to evaluate : 1.490 Fit side-chains REVERT: U 140 TYR cc_start: 0.8803 (t80) cc_final: 0.8526 (t80) REVERT: A 140 TYR cc_start: 0.8794 (t80) cc_final: 0.8546 (t80) REVERT: B 62 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8947 (tp) REVERT: B 140 TYR cc_start: 0.8774 (t80) cc_final: 0.8482 (t80) REVERT: B 172 ARG cc_start: 0.9038 (mmm160) cc_final: 0.8460 (mtp85) REVERT: C 140 TYR cc_start: 0.8666 (t80) cc_final: 0.8317 (t80) REVERT: C 178 ASP cc_start: 0.8420 (m-30) cc_final: 0.8098 (m-30) REVERT: D 140 TYR cc_start: 0.8712 (t80) cc_final: 0.8473 (t80) REVERT: E 140 TYR cc_start: 0.8745 (t80) cc_final: 0.8418 (t80) REVERT: E 150 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7613 (tp30) REVERT: F 140 TYR cc_start: 0.8746 (t80) cc_final: 0.8473 (t80) REVERT: G 62 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8879 (tp) REVERT: G 140 TYR cc_start: 0.8729 (t80) cc_final: 0.8451 (t80) REVERT: H 56 HIS cc_start: 0.7712 (m-70) cc_final: 0.7238 (m170) REVERT: H 140 TYR cc_start: 0.8700 (t80) cc_final: 0.8386 (t80) REVERT: I 140 TYR cc_start: 0.8707 (t80) cc_final: 0.8428 (t80) REVERT: J 140 TYR cc_start: 0.8734 (t80) cc_final: 0.8456 (t80) REVERT: K 5 LYS cc_start: 0.9211 (mttp) cc_final: 0.8892 (mttt) REVERT: K 62 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8910 (tp) REVERT: K 140 TYR cc_start: 0.8750 (t80) cc_final: 0.8423 (t80) REVERT: L 140 TYR cc_start: 0.8736 (t80) cc_final: 0.8346 (t80) REVERT: M 62 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8940 (tp) REVERT: M 140 TYR cc_start: 0.8759 (t80) cc_final: 0.8418 (t80) REVERT: N 140 TYR cc_start: 0.8768 (t80) cc_final: 0.8523 (t80) REVERT: O 140 TYR cc_start: 0.8791 (t80) cc_final: 0.8551 (t80) REVERT: P 140 TYR cc_start: 0.8729 (t80) cc_final: 0.8465 (t80) REVERT: Q 140 TYR cc_start: 0.8745 (t80) cc_final: 0.8415 (t80) REVERT: R 140 TYR cc_start: 0.8772 (t80) cc_final: 0.8555 (t80) REVERT: S 140 TYR cc_start: 0.8718 (t80) cc_final: 0.8501 (t80) REVERT: T 140 TYR cc_start: 0.8755 (t80) cc_final: 0.8428 (t80) REVERT: T 181 ARG cc_start: 0.8767 (ptp90) cc_final: 0.8559 (ptp-170) REVERT: V 140 TYR cc_start: 0.8763 (t80) cc_final: 0.8538 (t80) REVERT: W 140 TYR cc_start: 0.8743 (t80) cc_final: 0.8486 (t80) REVERT: X 140 TYR cc_start: 0.8771 (t80) cc_final: 0.8502 (t80) REVERT: X 150 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: X 181 ARG cc_start: 0.8999 (ptp-170) cc_final: 0.8787 (ptp-170) outliers start: 121 outliers final: 82 residues processed: 898 average time/residue: 0.2641 time to fit residues: 367.1361 Evaluate side-chains 906 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 818 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 92 THR Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain X residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 376 optimal weight: 2.9990 chunk 307 optimal weight: 9.9990 chunk 188 optimal weight: 30.0000 chunk 373 optimal weight: 10.0000 chunk 495 optimal weight: 4.9990 chunk 408 optimal weight: 10.0000 chunk 411 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 284 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 56 HIS C 56 HIS E 86 HIS F 56 HIS G 56 HIS J 56 HIS K 56 HIS L 86 HIS M 56 HIS N 56 HIS O 56 HIS P 56 HIS Q 54 ASN Q 56 HIS R 54 ASN R 86 HIS S 54 ASN S 56 HIS S 86 HIS V 56 HIS W 56 HIS X 56 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.111439 restraints weight = 50237.029| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.53 r_work: 0.3052 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 39000 Z= 0.194 Angle : 0.638 8.634 52800 Z= 0.331 Chirality : 0.047 0.156 6168 Planarity : 0.005 0.038 6840 Dihedral : 6.656 48.675 5352 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.45 % Allowed : 13.01 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.12), residues: 4992 helix: 2.03 (0.13), residues: 1680 sheet: -0.68 (0.13), residues: 1416 loop : -3.03 (0.12), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 10 TYR 0.007 0.002 TYR M 140 PHE 0.009 0.002 PHE U 61 TRP 0.002 0.001 TRP W 75 HIS 0.005 0.002 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (39000) covalent geometry : angle 0.63751 / 0.33 (52800) hydrogen bonds : bond 0.03024 / 2.04 ( 1947) hydrogen bonds : angle 3.82709 / 2.67 ( 5625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11245.45 seconds wall clock time: 193 minutes 8.32 seconds (11588.32 seconds total)