Starting phenix.real_space_refine on Wed Mar 20 10:37:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ofh_12874/03_2024/7ofh_12874_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ofh_12874/03_2024/7ofh_12874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ofh_12874/03_2024/7ofh_12874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ofh_12874/03_2024/7ofh_12874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ofh_12874/03_2024/7ofh_12874_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ofh_12874/03_2024/7ofh_12874_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 17235 2.51 5 N 4455 2.21 5 O 5400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "C PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "D PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D GLU 390": "OE1" <-> "OE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E ARG 337": "NH1" <-> "NH2" Residue "E GLU 390": "OE1" <-> "OE2" Residue "F PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "F ARG 337": "NH1" <-> "NH2" Residue "F GLU 390": "OE1" <-> "OE2" Residue "G PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G ARG 337": "NH1" <-> "NH2" Residue "G GLU 390": "OE1" <-> "OE2" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 185": "OE1" <-> "OE2" Residue "H ARG 337": "NH1" <-> "NH2" Residue "H GLU 390": "OE1" <-> "OE2" Residue "I PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 185": "OE1" <-> "OE2" Residue "I ARG 337": "NH1" <-> "NH2" Residue "I GLU 390": "OE1" <-> "OE2" Residue "J PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 185": "OE1" <-> "OE2" Residue "J ARG 337": "NH1" <-> "NH2" Residue "J GLU 390": "OE1" <-> "OE2" Residue "K PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 185": "OE1" <-> "OE2" Residue "K ARG 337": "NH1" <-> "NH2" Residue "K GLU 390": "OE1" <-> "OE2" Residue "L PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 185": "OE1" <-> "OE2" Residue "L ARG 337": "NH1" <-> "NH2" Residue "L GLU 390": "OE1" <-> "OE2" Residue "M PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 185": "OE1" <-> "OE2" Residue "M ARG 337": "NH1" <-> "NH2" Residue "M GLU 390": "OE1" <-> "OE2" Residue "N PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 185": "OE1" <-> "OE2" Residue "N ARG 337": "NH1" <-> "NH2" Residue "N GLU 390": "OE1" <-> "OE2" Residue "O PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 185": "OE1" <-> "OE2" Residue "O ARG 337": "NH1" <-> "NH2" Residue "O GLU 390": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27135 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 13.90, per 1000 atoms: 0.51 Number of scatterers: 27135 At special positions: 0 Unit cell: (144.72, 144.72, 113.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 5400 8.00 N 4455 7.00 C 17235 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.57 Conformation dependent library (CDL) restraints added in 4.9 seconds 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6510 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 60 sheets defined 6.5% alpha, 44.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.90 Creating SS restraints... Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 159 through 166 Proline residue: A 164 - end of helix Processing helix chain 'B' and resid 126 through 132 Processing helix chain 'B' and resid 159 through 166 Proline residue: B 164 - end of helix Processing helix chain 'C' and resid 126 through 132 Processing helix chain 'C' and resid 159 through 166 Proline residue: C 164 - end of helix Processing helix chain 'D' and resid 126 through 132 Processing helix chain 'D' and resid 159 through 166 Proline residue: D 164 - end of helix Processing helix chain 'E' and resid 126 through 132 Processing helix chain 'E' and resid 159 through 166 Proline residue: E 164 - end of helix Processing helix chain 'F' and resid 126 through 132 Processing helix chain 'F' and resid 159 through 166 Proline residue: F 164 - end of helix Processing helix chain 'G' and resid 126 through 132 Processing helix chain 'G' and resid 159 through 166 Proline residue: G 164 - end of helix Processing helix chain 'H' and resid 126 through 132 Processing helix chain 'H' and resid 159 through 166 Proline residue: H 164 - end of helix Processing helix chain 'I' and resid 126 through 132 Processing helix chain 'I' and resid 159 through 166 Proline residue: I 164 - end of helix Processing helix chain 'J' and resid 126 through 132 Processing helix chain 'J' and resid 159 through 166 Proline residue: J 164 - end of helix Processing helix chain 'K' and resid 126 through 132 Processing helix chain 'K' and resid 159 through 166 Proline residue: K 164 - end of helix Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 159 through 166 Proline residue: L 164 - end of helix Processing helix chain 'M' and resid 126 through 132 Processing helix chain 'M' and resid 159 through 166 Proline residue: M 164 - end of helix Processing helix chain 'N' and resid 126 through 132 Processing helix chain 'N' and resid 159 through 166 Proline residue: N 164 - end of helix Processing helix chain 'O' and resid 126 through 132 Processing helix chain 'O' and resid 159 through 166 Proline residue: O 164 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 109 through 115 Processing sheet with id= B, first strand: chain 'A' and resid 253 through 257 removed outlier: 7.013A pdb=" N VAL A 397 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU A 352 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA A 399 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR A 350 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N ILE A 401 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLY A 348 " --> pdb=" O ILE A 401 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= D, first strand: chain 'A' and resid 261 through 272 Processing sheet with id= E, first strand: chain 'B' and resid 109 through 115 Processing sheet with id= F, first strand: chain 'B' and resid 253 through 257 removed outlier: 7.004A pdb=" N VAL B 397 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU B 352 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA B 399 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR B 350 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ILE B 401 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY B 348 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 183 through 186 Processing sheet with id= H, first strand: chain 'B' and resid 261 through 272 Processing sheet with id= I, first strand: chain 'C' and resid 109 through 115 Processing sheet with id= J, first strand: chain 'C' and resid 253 through 257 removed outlier: 6.993A pdb=" N VAL C 397 " --> pdb=" O LEU C 352 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU C 352 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ALA C 399 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR C 350 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ILE C 401 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLY C 348 " --> pdb=" O ILE C 401 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 183 through 186 Processing sheet with id= L, first strand: chain 'C' and resid 261 through 272 Processing sheet with id= M, first strand: chain 'D' and resid 109 through 115 Processing sheet with id= N, first strand: chain 'D' and resid 253 through 257 removed outlier: 7.004A pdb=" N VAL D 397 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU D 352 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ALA D 399 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR D 350 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ILE D 401 " --> pdb=" O GLY D 348 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY D 348 " --> pdb=" O ILE D 401 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 183 through 186 Processing sheet with id= P, first strand: chain 'D' and resid 261 through 272 Processing sheet with id= Q, first strand: chain 'E' and resid 109 through 115 Processing sheet with id= R, first strand: chain 'E' and resid 253 through 257 removed outlier: 6.992A pdb=" N VAL E 397 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU E 352 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ALA E 399 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR E 350 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ILE E 401 " --> pdb=" O GLY E 348 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLY E 348 " --> pdb=" O ILE E 401 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 183 through 186 Processing sheet with id= T, first strand: chain 'E' and resid 261 through 272 Processing sheet with id= U, first strand: chain 'F' and resid 109 through 115 Processing sheet with id= V, first strand: chain 'F' and resid 253 through 257 removed outlier: 6.987A pdb=" N VAL F 397 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU F 352 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA F 399 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR F 350 " --> pdb=" O ALA F 399 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ILE F 401 " --> pdb=" O GLY F 348 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLY F 348 " --> pdb=" O ILE F 401 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 183 through 186 Processing sheet with id= X, first strand: chain 'F' and resid 261 through 272 Processing sheet with id= Y, first strand: chain 'G' and resid 109 through 115 Processing sheet with id= Z, first strand: chain 'G' and resid 253 through 257 removed outlier: 7.004A pdb=" N VAL G 397 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU G 352 " --> pdb=" O VAL G 397 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ALA G 399 " --> pdb=" O THR G 350 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR G 350 " --> pdb=" O ALA G 399 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ILE G 401 " --> pdb=" O GLY G 348 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLY G 348 " --> pdb=" O ILE G 401 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 183 through 186 Processing sheet with id= AB, first strand: chain 'G' and resid 261 through 272 Processing sheet with id= AC, first strand: chain 'H' and resid 109 through 115 Processing sheet with id= AD, first strand: chain 'H' and resid 253 through 257 removed outlier: 7.006A pdb=" N VAL H 397 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU H 352 " --> pdb=" O VAL H 397 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA H 399 " --> pdb=" O THR H 350 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR H 350 " --> pdb=" O ALA H 399 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ILE H 401 " --> pdb=" O GLY H 348 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLY H 348 " --> pdb=" O ILE H 401 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 183 through 186 Processing sheet with id= AF, first strand: chain 'H' and resid 261 through 272 Processing sheet with id= AG, first strand: chain 'I' and resid 109 through 115 Processing sheet with id= AH, first strand: chain 'I' and resid 253 through 257 removed outlier: 7.002A pdb=" N VAL I 397 " --> pdb=" O LEU I 352 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU I 352 " --> pdb=" O VAL I 397 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ALA I 399 " --> pdb=" O THR I 350 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR I 350 " --> pdb=" O ALA I 399 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ILE I 401 " --> pdb=" O GLY I 348 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLY I 348 " --> pdb=" O ILE I 401 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 183 through 186 Processing sheet with id= AJ, first strand: chain 'I' and resid 261 through 272 Processing sheet with id= AK, first strand: chain 'J' and resid 109 through 115 Processing sheet with id= AL, first strand: chain 'J' and resid 253 through 257 removed outlier: 6.994A pdb=" N VAL J 397 " --> pdb=" O LEU J 352 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU J 352 " --> pdb=" O VAL J 397 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ALA J 399 " --> pdb=" O THR J 350 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR J 350 " --> pdb=" O ALA J 399 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ILE J 401 " --> pdb=" O GLY J 348 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLY J 348 " --> pdb=" O ILE J 401 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'J' and resid 183 through 186 Processing sheet with id= AN, first strand: chain 'J' and resid 261 through 272 Processing sheet with id= AO, first strand: chain 'K' and resid 109 through 115 Processing sheet with id= AP, first strand: chain 'K' and resid 253 through 257 removed outlier: 7.003A pdb=" N VAL K 397 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU K 352 " --> pdb=" O VAL K 397 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA K 399 " --> pdb=" O THR K 350 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR K 350 " --> pdb=" O ALA K 399 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ILE K 401 " --> pdb=" O GLY K 348 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N GLY K 348 " --> pdb=" O ILE K 401 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'K' and resid 183 through 186 Processing sheet with id= AR, first strand: chain 'K' and resid 261 through 272 Processing sheet with id= AS, first strand: chain 'L' and resid 109 through 115 Processing sheet with id= AT, first strand: chain 'L' and resid 253 through 257 removed outlier: 7.001A pdb=" N VAL L 397 " --> pdb=" O LEU L 352 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU L 352 " --> pdb=" O VAL L 397 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA L 399 " --> pdb=" O THR L 350 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR L 350 " --> pdb=" O ALA L 399 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ILE L 401 " --> pdb=" O GLY L 348 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY L 348 " --> pdb=" O ILE L 401 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'L' and resid 183 through 186 Processing sheet with id= AV, first strand: chain 'L' and resid 261 through 272 Processing sheet with id= AW, first strand: chain 'M' and resid 109 through 115 Processing sheet with id= AX, first strand: chain 'M' and resid 253 through 257 removed outlier: 7.005A pdb=" N VAL M 397 " --> pdb=" O LEU M 352 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU M 352 " --> pdb=" O VAL M 397 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ALA M 399 " --> pdb=" O THR M 350 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR M 350 " --> pdb=" O ALA M 399 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ILE M 401 " --> pdb=" O GLY M 348 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N GLY M 348 " --> pdb=" O ILE M 401 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'M' and resid 183 through 186 Processing sheet with id= AZ, first strand: chain 'M' and resid 261 through 272 Processing sheet with id= BA, first strand: chain 'N' and resid 109 through 115 Processing sheet with id= BB, first strand: chain 'N' and resid 253 through 257 removed outlier: 7.004A pdb=" N VAL N 397 " --> pdb=" O LEU N 352 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU N 352 " --> pdb=" O VAL N 397 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA N 399 " --> pdb=" O THR N 350 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR N 350 " --> pdb=" O ALA N 399 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N ILE N 401 " --> pdb=" O GLY N 348 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLY N 348 " --> pdb=" O ILE N 401 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'N' and resid 183 through 186 Processing sheet with id= BD, first strand: chain 'N' and resid 261 through 272 Processing sheet with id= BE, first strand: chain 'O' and resid 109 through 115 Processing sheet with id= BF, first strand: chain 'O' and resid 253 through 257 removed outlier: 7.011A pdb=" N VAL O 397 " --> pdb=" O LEU O 352 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU O 352 " --> pdb=" O VAL O 397 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA O 399 " --> pdb=" O THR O 350 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR O 350 " --> pdb=" O ALA O 399 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ILE O 401 " --> pdb=" O GLY O 348 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLY O 348 " --> pdb=" O ILE O 401 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'O' and resid 183 through 186 Processing sheet with id= BH, first strand: chain 'O' and resid 261 through 272 1020 hydrogen bonds defined for protein. 2880 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: 8.63 Time building geometry restraints manager: 10.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5066 1.32 - 1.44: 5815 1.44 - 1.56: 16359 1.56 - 1.68: 105 1.68 - 1.80: 75 Bond restraints: 27420 Sorted by residual: bond pdb=" CA SER B 154 " pdb=" CB SER B 154 " ideal model delta sigma weight residual 1.530 1.478 0.052 1.50e-02 4.44e+03 1.21e+01 bond pdb=" CA SER C 258 " pdb=" CB SER C 258 " ideal model delta sigma weight residual 1.530 1.476 0.055 1.57e-02 4.06e+03 1.21e+01 bond pdb=" CA SER L 154 " pdb=" CB SER L 154 " ideal model delta sigma weight residual 1.530 1.480 0.051 1.50e-02 4.44e+03 1.15e+01 bond pdb=" CA SER A 154 " pdb=" CB SER A 154 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.50e-02 4.44e+03 1.11e+01 bond pdb=" CA SER D 301 " pdb=" CB SER D 301 " ideal model delta sigma weight residual 1.530 1.482 0.047 1.43e-02 4.89e+03 1.09e+01 ... (remaining 27415 not shown) Histogram of bond angle deviations from ideal: 97.68 - 104.61: 575 104.61 - 111.55: 12206 111.55 - 118.48: 10932 118.48 - 125.42: 13478 125.42 - 132.35: 204 Bond angle restraints: 37395 Sorted by residual: angle pdb=" N PRO D 156 " pdb=" CA PRO D 156 " pdb=" CB PRO D 156 " ideal model delta sigma weight residual 103.32 97.68 5.64 8.40e-01 1.42e+00 4.52e+01 angle pdb=" N PRO G 156 " pdb=" CA PRO G 156 " pdb=" CB PRO G 156 " ideal model delta sigma weight residual 103.32 97.82 5.50 8.40e-01 1.42e+00 4.29e+01 angle pdb=" N PRO A 156 " pdb=" CA PRO A 156 " pdb=" CB PRO A 156 " ideal model delta sigma weight residual 103.32 97.83 5.49 8.40e-01 1.42e+00 4.27e+01 angle pdb=" N PRO O 156 " pdb=" CA PRO O 156 " pdb=" CB PRO O 156 " ideal model delta sigma weight residual 103.32 97.85 5.47 8.40e-01 1.42e+00 4.23e+01 angle pdb=" N PRO F 156 " pdb=" CA PRO F 156 " pdb=" CB PRO F 156 " ideal model delta sigma weight residual 103.32 97.91 5.41 8.40e-01 1.42e+00 4.15e+01 ... (remaining 37390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 16935 21.18 - 42.36: 1012 42.36 - 63.54: 353 63.54 - 84.73: 30 84.73 - 105.91: 15 Dihedral angle restraints: 18345 sinusoidal: 8430 harmonic: 9915 Sorted by residual: dihedral pdb=" C ARG M 293 " pdb=" N ARG M 293 " pdb=" CA ARG M 293 " pdb=" CB ARG M 293 " ideal model delta harmonic sigma weight residual -122.60 -110.31 -12.29 0 2.50e+00 1.60e-01 2.42e+01 dihedral pdb=" C ARG K 293 " pdb=" N ARG K 293 " pdb=" CA ARG K 293 " pdb=" CB ARG K 293 " ideal model delta harmonic sigma weight residual -122.60 -110.35 -12.25 0 2.50e+00 1.60e-01 2.40e+01 dihedral pdb=" C TYR F 359 " pdb=" N TYR F 359 " pdb=" CA TYR F 359 " pdb=" CB TYR F 359 " ideal model delta harmonic sigma weight residual -122.60 -110.44 -12.16 0 2.50e+00 1.60e-01 2.37e+01 ... (remaining 18342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2293 0.069 - 0.138: 1683 0.138 - 0.206: 756 0.206 - 0.275: 139 0.275 - 0.344: 49 Chirality restraints: 4920 Sorted by residual: chirality pdb=" C9 CPS K 501 " pdb=" C20 CPS K 501 " pdb=" C5 CPS K 501 " pdb=" C8 CPS K 501 " both_signs ideal model delta sigma weight residual False 2.63 2.29 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" C9 CPS J 501 " pdb=" C20 CPS J 501 " pdb=" C5 CPS J 501 " pdb=" C8 CPS J 501 " both_signs ideal model delta sigma weight residual False 2.63 2.29 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C9 CPS H 501 " pdb=" C20 CPS H 501 " pdb=" C5 CPS H 501 " pdb=" C8 CPS H 501 " both_signs ideal model delta sigma weight residual False 2.63 2.29 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 4917 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C23 CPS I 501 " -0.008 2.00e-02 2.50e+03 4.01e-02 2.01e+01 pdb=" C24 CPS I 501 " -0.012 2.00e-02 2.50e+03 pdb=" C25 CPS I 501 " 0.046 2.00e-02 2.50e+03 pdb=" N1 CPS I 501 " -0.065 2.00e-02 2.50e+03 pdb=" O1 CPS I 501 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 CPS M 501 " -0.008 2.00e-02 2.50e+03 3.96e-02 1.96e+01 pdb=" C24 CPS M 501 " -0.011 2.00e-02 2.50e+03 pdb=" C25 CPS M 501 " 0.046 2.00e-02 2.50e+03 pdb=" N1 CPS M 501 " -0.065 2.00e-02 2.50e+03 pdb=" O1 CPS M 501 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 CPS G 501 " 0.008 2.00e-02 2.50e+03 3.94e-02 1.94e+01 pdb=" C24 CPS G 501 " 0.011 2.00e-02 2.50e+03 pdb=" C25 CPS G 501 " -0.045 2.00e-02 2.50e+03 pdb=" N1 CPS G 501 " 0.064 2.00e-02 2.50e+03 pdb=" O1 CPS G 501 " -0.038 2.00e-02 2.50e+03 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4580 2.77 - 3.30: 23126 3.30 - 3.83: 41227 3.83 - 4.37: 52342 4.37 - 4.90: 90832 Nonbonded interactions: 212107 Sorted by model distance: nonbonded pdb=" O SER E 385 " pdb=" OD1 ASP E 386 " model vdw 2.236 3.040 nonbonded pdb=" O SER M 385 " pdb=" OD1 ASP M 386 " model vdw 2.236 3.040 nonbonded pdb=" O SER B 385 " pdb=" OD1 ASP B 386 " model vdw 2.237 3.040 nonbonded pdb=" O SER I 385 " pdb=" OD1 ASP I 386 " model vdw 2.238 3.040 nonbonded pdb=" O SER A 385 " pdb=" OD1 ASP A 386 " model vdw 2.238 3.040 ... (remaining 212102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'B' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'C' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'D' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'E' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'F' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'G' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'H' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'I' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'J' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'K' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'L' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'M' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'N' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'O' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.000 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 68.770 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 0.063 27420 Z= 0.686 Angle : 1.597 7.963 37395 Z= 1.016 Chirality : 0.106 0.344 4920 Planarity : 0.007 0.040 4530 Dihedral : 15.397 105.907 11835 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.27 % Favored : 87.61 % Rotamer: Outliers : 3.90 % Allowed : 11.48 % Favored : 84.62 % Cbeta Deviations : 0.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.12), residues: 3285 helix: -3.73 (0.17), residues: 270 sheet: -2.61 (0.09), residues: 2355 loop : -2.55 (0.18), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 245 PHE 0.021 0.006 PHE N 166 TYR 0.048 0.014 TYR F 394 ARG 0.006 0.001 ARG M 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 906 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.9102 (mttt) cc_final: 0.8797 (mtmt) REVERT: A 122 LYS cc_start: 0.8874 (tttt) cc_final: 0.8660 (ptpp) REVERT: A 126 ARG cc_start: 0.8776 (mtt180) cc_final: 0.8493 (mmt180) REVERT: A 153 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8522 (t) REVERT: A 156 PRO cc_start: 0.8806 (OUTLIER) cc_final: 0.8502 (Cg_exo) REVERT: A 180 GLU cc_start: 0.8324 (tt0) cc_final: 0.8079 (mt-10) REVERT: A 261 LYS cc_start: 0.9046 (mttp) cc_final: 0.8704 (mmmt) REVERT: B 115 LYS cc_start: 0.9021 (mttt) cc_final: 0.8716 (mtmm) REVERT: B 122 LYS cc_start: 0.8744 (tttt) cc_final: 0.8519 (ptpp) REVERT: B 153 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8491 (t) REVERT: B 156 PRO cc_start: 0.8900 (OUTLIER) cc_final: 0.8622 (Cg_exo) REVERT: B 180 GLU cc_start: 0.8254 (tt0) cc_final: 0.7901 (mt-10) REVERT: B 346 ARG cc_start: 0.8290 (mtt180) cc_final: 0.8072 (ttm110) REVERT: C 115 LYS cc_start: 0.9086 (mttt) cc_final: 0.8785 (mtmm) REVERT: C 156 PRO cc_start: 0.8843 (OUTLIER) cc_final: 0.8535 (Cg_exo) REVERT: C 180 GLU cc_start: 0.8333 (tt0) cc_final: 0.8124 (mt-10) REVERT: C 360 LYS cc_start: 0.7863 (tttt) cc_final: 0.7645 (mtpp) REVERT: C 364 GLN cc_start: 0.7516 (tt0) cc_final: 0.6860 (tm-30) REVERT: C 390 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7834 (pt0) REVERT: D 126 ARG cc_start: 0.8557 (mtt180) cc_final: 0.8342 (mmt180) REVERT: D 133 LYS cc_start: 0.7553 (tttt) cc_final: 0.7278 (ttmm) REVERT: D 153 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8563 (t) REVERT: D 180 GLU cc_start: 0.8172 (tt0) cc_final: 0.7774 (mt-10) REVERT: D 248 ILE cc_start: 0.9003 (mm) cc_final: 0.8700 (mm) REVERT: D 261 LYS cc_start: 0.9174 (mttp) cc_final: 0.8874 (mmmt) REVERT: D 400 THR cc_start: 0.8852 (m) cc_final: 0.8384 (p) REVERT: E 115 LYS cc_start: 0.9137 (mttt) cc_final: 0.8850 (mtmt) REVERT: E 133 LYS cc_start: 0.7460 (tttt) cc_final: 0.6865 (tppt) REVERT: E 261 LYS cc_start: 0.9213 (mttp) cc_final: 0.8972 (mmmt) REVERT: F 122 LYS cc_start: 0.8776 (tttt) cc_final: 0.8524 (ptpp) REVERT: F 180 GLU cc_start: 0.8150 (tt0) cc_final: 0.7891 (mt-10) REVERT: F 245 HIS cc_start: 0.8290 (t70) cc_final: 0.7988 (t70) REVERT: F 261 LYS cc_start: 0.9127 (mttp) cc_final: 0.8873 (mmmt) REVERT: F 400 THR cc_start: 0.8912 (m) cc_final: 0.8593 (p) REVERT: G 126 ARG cc_start: 0.8690 (mtt180) cc_final: 0.8405 (mmt180) REVERT: G 180 GLU cc_start: 0.8225 (tt0) cc_final: 0.7845 (mt-10) REVERT: G 346 ARG cc_start: 0.8494 (mtt180) cc_final: 0.8286 (ttm110) REVERT: G 400 THR cc_start: 0.8821 (m) cc_final: 0.8523 (p) REVERT: H 122 LYS cc_start: 0.8689 (tttt) cc_final: 0.8463 (ptpp) REVERT: H 133 LYS cc_start: 0.7775 (tttt) cc_final: 0.7464 (ttmm) REVERT: H 161 ASP cc_start: 0.8155 (m-30) cc_final: 0.7817 (m-30) REVERT: H 180 GLU cc_start: 0.8099 (tt0) cc_final: 0.7727 (mt-10) REVERT: H 300 MET cc_start: 0.9190 (ttp) cc_final: 0.8964 (ttm) REVERT: H 337 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8425 (mtm110) REVERT: H 390 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7779 (pt0) REVERT: H 400 THR cc_start: 0.8763 (m) cc_final: 0.8450 (p) REVERT: I 115 LYS cc_start: 0.8943 (mttt) cc_final: 0.8688 (mtmm) REVERT: I 122 LYS cc_start: 0.8795 (tttt) cc_final: 0.8552 (ptpp) REVERT: I 133 LYS cc_start: 0.7622 (tttt) cc_final: 0.7039 (tppt) REVERT: I 180 GLU cc_start: 0.8194 (tt0) cc_final: 0.7827 (mt-10) REVERT: I 400 THR cc_start: 0.8751 (m) cc_final: 0.8437 (p) REVERT: J 133 LYS cc_start: 0.7547 (tttt) cc_final: 0.7316 (ttmm) REVERT: J 141 ASN cc_start: 0.8503 (m-40) cc_final: 0.8125 (m-40) REVERT: J 180 GLU cc_start: 0.8272 (tt0) cc_final: 0.7801 (mt-10) REVERT: J 300 MET cc_start: 0.9174 (ttp) cc_final: 0.8891 (ttm) REVERT: J 337 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8426 (mtm110) REVERT: J 390 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7864 (pt0) REVERT: J 400 THR cc_start: 0.8765 (m) cc_final: 0.8428 (p) REVERT: K 115 LYS cc_start: 0.9139 (mttt) cc_final: 0.8849 (mtmm) REVERT: K 180 GLU cc_start: 0.8246 (tt0) cc_final: 0.7809 (mt-10) REVERT: K 346 ARG cc_start: 0.8390 (mtt180) cc_final: 0.8129 (ttm110) REVERT: K 400 THR cc_start: 0.8742 (m) cc_final: 0.8223 (p) REVERT: L 180 GLU cc_start: 0.8246 (tt0) cc_final: 0.7947 (mt-10) REVERT: L 238 ARG cc_start: 0.7497 (mtt90) cc_final: 0.7293 (mpt180) REVERT: L 346 ARG cc_start: 0.8289 (mtt180) cc_final: 0.8015 (ttm110) REVERT: M 115 LYS cc_start: 0.9138 (mttt) cc_final: 0.8872 (mtmm) REVERT: M 120 ARG cc_start: 0.8996 (mtm180) cc_final: 0.8687 (mtm-85) REVERT: M 141 ASN cc_start: 0.8625 (m-40) cc_final: 0.8424 (m-40) REVERT: M 156 PRO cc_start: 0.8793 (OUTLIER) cc_final: 0.8505 (Cg_exo) REVERT: M 238 ARG cc_start: 0.7382 (mtt90) cc_final: 0.7110 (mpt180) REVERT: M 248 ILE cc_start: 0.9025 (mm) cc_final: 0.8767 (mm) REVERT: M 300 MET cc_start: 0.9232 (ttp) cc_final: 0.8785 (ttm) REVERT: M 390 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7643 (pt0) REVERT: M 400 THR cc_start: 0.8572 (m) cc_final: 0.8001 (p) REVERT: N 115 LYS cc_start: 0.9101 (mttt) cc_final: 0.8900 (mtmt) REVERT: N 122 LYS cc_start: 0.8912 (tttt) cc_final: 0.8705 (ptpp) REVERT: N 126 ARG cc_start: 0.8651 (mtt180) cc_final: 0.8444 (mmt180) REVERT: N 180 GLU cc_start: 0.8223 (tt0) cc_final: 0.7938 (mt-10) REVERT: N 242 THR cc_start: 0.7946 (m) cc_final: 0.7588 (p) REVERT: N 300 MET cc_start: 0.9209 (ttp) cc_final: 0.8881 (ttm) REVERT: N 400 THR cc_start: 0.8811 (m) cc_final: 0.8231 (p) REVERT: O 122 LYS cc_start: 0.8860 (tttt) cc_final: 0.8607 (ptpp) REVERT: O 133 LYS cc_start: 0.7650 (tttt) cc_final: 0.7399 (ttmm) REVERT: O 180 GLU cc_start: 0.8323 (tt0) cc_final: 0.7846 (mt-10) REVERT: O 261 LYS cc_start: 0.8967 (mttp) cc_final: 0.8734 (mmtt) REVERT: O 300 MET cc_start: 0.9232 (ttp) cc_final: 0.8966 (ttp) REVERT: O 389 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7456 (tm-30) outliers start: 120 outliers final: 19 residues processed: 987 average time/residue: 1.2464 time to fit residues: 1439.3075 Evaluate side-chains 627 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 599 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 156 PRO Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 156 PRO Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 156 PRO Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 156 PRO Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain E residue 156 PRO Chi-restraints excluded: chain F residue 156 PRO Chi-restraints excluded: chain F residue 365 ASP Chi-restraints excluded: chain G residue 156 PRO Chi-restraints excluded: chain H residue 156 PRO Chi-restraints excluded: chain H residue 332 VAL Chi-restraints excluded: chain H residue 337 ARG Chi-restraints excluded: chain H residue 365 ASP Chi-restraints excluded: chain I residue 156 PRO Chi-restraints excluded: chain J residue 156 PRO Chi-restraints excluded: chain J residue 337 ARG Chi-restraints excluded: chain K residue 156 PRO Chi-restraints excluded: chain L residue 156 PRO Chi-restraints excluded: chain M residue 156 PRO Chi-restraints excluded: chain N residue 156 PRO Chi-restraints excluded: chain N residue 332 VAL Chi-restraints excluded: chain N residue 388 ASN Chi-restraints excluded: chain O residue 156 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 313 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 361 ASN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN C 112 GLN C 187 GLN C 336 GLN C 361 ASN D 112 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN E 187 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 ASN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 361 ASN H 112 GLN H 187 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 GLN H 361 ASN H 388 ASN ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 ASN J 336 GLN J 361 ASN K 187 GLN K 328 GLN K 336 GLN K 349 GLN K 388 ASN L 112 GLN L 187 GLN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 GLN L 388 ASN M 349 GLN M 361 ASN N 187 GLN N 336 GLN N 361 ASN O 112 GLN O 336 GLN O 361 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27420 Z= 0.288 Angle : 0.661 7.918 37395 Z= 0.338 Chirality : 0.050 0.245 4920 Planarity : 0.005 0.046 4530 Dihedral : 9.565 114.792 5858 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.20 % Allowed : 16.23 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.14), residues: 3285 helix: -1.66 (0.26), residues: 345 sheet: -1.69 (0.10), residues: 2130 loop : -0.97 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 245 PHE 0.022 0.002 PHE H 194 TYR 0.022 0.003 TYR N 359 ARG 0.007 0.001 ARG N 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 527 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.9114 (mttt) cc_final: 0.8857 (mtmt) REVERT: A 122 LYS cc_start: 0.8996 (tttt) cc_final: 0.8793 (ptpp) REVERT: A 161 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: A 180 GLU cc_start: 0.8308 (tt0) cc_final: 0.8036 (mt-10) REVERT: A 261 LYS cc_start: 0.9151 (mttp) cc_final: 0.8803 (mmmt) REVERT: A 307 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7706 (mmt) REVERT: A 364 GLN cc_start: 0.7364 (tt0) cc_final: 0.6890 (tm-30) REVERT: B 180 GLU cc_start: 0.8285 (tt0) cc_final: 0.8012 (mt-10) REVERT: B 253 ARG cc_start: 0.8723 (mtp180) cc_final: 0.7998 (mtp85) REVERT: B 364 GLN cc_start: 0.7577 (tt0) cc_final: 0.6946 (tm-30) REVERT: C 115 LYS cc_start: 0.9142 (mttt) cc_final: 0.8848 (mtmm) REVERT: C 180 GLU cc_start: 0.8403 (tt0) cc_final: 0.8171 (mt-10) REVERT: C 364 GLN cc_start: 0.7410 (tt0) cc_final: 0.6825 (tm-30) REVERT: D 126 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8318 (mmt180) REVERT: D 180 GLU cc_start: 0.8198 (tt0) cc_final: 0.7832 (mt-10) REVERT: D 261 LYS cc_start: 0.9085 (mttp) cc_final: 0.8720 (mmmt) REVERT: D 360 LYS cc_start: 0.7991 (tttt) cc_final: 0.7559 (mttm) REVERT: D 364 GLN cc_start: 0.7659 (tt0) cc_final: 0.7081 (tm-30) REVERT: D 398 LYS cc_start: 0.9091 (tttm) cc_final: 0.8868 (ttpp) REVERT: E 133 LYS cc_start: 0.7551 (tttt) cc_final: 0.6973 (tppt) REVERT: E 261 LYS cc_start: 0.9200 (mttp) cc_final: 0.8944 (mmmt) REVERT: E 360 LYS cc_start: 0.8095 (tttt) cc_final: 0.7859 (tttt) REVERT: F 180 GLU cc_start: 0.8180 (tt0) cc_final: 0.7931 (mt-10) REVERT: F 261 LYS cc_start: 0.9082 (mttp) cc_final: 0.8777 (mmmt) REVERT: F 360 LYS cc_start: 0.8144 (tttt) cc_final: 0.7854 (ttmt) REVERT: F 364 GLN cc_start: 0.7636 (tt0) cc_final: 0.6920 (tm-30) REVERT: F 394 TYR cc_start: 0.9160 (m-80) cc_final: 0.8923 (m-80) REVERT: G 126 ARG cc_start: 0.8570 (mtt180) cc_final: 0.8287 (mmt180) REVERT: G 180 GLU cc_start: 0.8346 (tt0) cc_final: 0.7987 (mt-10) REVERT: G 261 LYS cc_start: 0.9251 (mmtm) cc_final: 0.9010 (mmtt) REVERT: G 346 ARG cc_start: 0.8155 (mtt180) cc_final: 0.7886 (ttm110) REVERT: G 364 GLN cc_start: 0.7531 (tt0) cc_final: 0.6734 (tm-30) REVERT: G 398 LYS cc_start: 0.9153 (tttm) cc_final: 0.8874 (ttpp) REVERT: H 133 LYS cc_start: 0.7675 (tttt) cc_final: 0.7412 (ttmm) REVERT: H 180 GLU cc_start: 0.8313 (tt0) cc_final: 0.7978 (mt-10) REVERT: H 360 LYS cc_start: 0.8211 (tttt) cc_final: 0.7910 (mttt) REVERT: H 364 GLN cc_start: 0.7661 (tt0) cc_final: 0.6921 (tm-30) REVERT: I 115 LYS cc_start: 0.8986 (mttt) cc_final: 0.8725 (mtmm) REVERT: I 122 LYS cc_start: 0.8889 (tttt) cc_final: 0.8661 (ptpp) REVERT: I 133 LYS cc_start: 0.7449 (tttt) cc_final: 0.6890 (tppt) REVERT: I 180 GLU cc_start: 0.8368 (tt0) cc_final: 0.8091 (mt-10) REVERT: I 261 LYS cc_start: 0.9248 (mmtm) cc_final: 0.8964 (mmtp) REVERT: I 360 LYS cc_start: 0.8121 (tttt) cc_final: 0.7859 (ttmm) REVERT: I 364 GLN cc_start: 0.7403 (tt0) cc_final: 0.6785 (tm-30) REVERT: J 133 LYS cc_start: 0.7496 (tttt) cc_final: 0.6834 (tppt) REVERT: J 180 GLU cc_start: 0.8326 (tt0) cc_final: 0.7913 (mt-10) REVERT: J 261 LYS cc_start: 0.9285 (mmmt) cc_final: 0.9012 (mmmt) REVERT: J 319 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8740 (mtpt) REVERT: J 364 GLN cc_start: 0.7474 (tt0) cc_final: 0.6743 (tm-30) REVERT: K 115 LYS cc_start: 0.9068 (mttt) cc_final: 0.8766 (mtmm) REVERT: K 180 GLU cc_start: 0.8383 (tt0) cc_final: 0.7955 (mt-10) REVERT: K 261 LYS cc_start: 0.9155 (mttm) cc_final: 0.8923 (mmmt) REVERT: K 364 GLN cc_start: 0.7565 (tt0) cc_final: 0.7060 (tm-30) REVERT: K 398 LYS cc_start: 0.9131 (tttm) cc_final: 0.8810 (tttt) REVERT: L 180 GLU cc_start: 0.8423 (tt0) cc_final: 0.8123 (mt-10) REVERT: L 344 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8607 (t0) REVERT: L 364 GLN cc_start: 0.7597 (tt0) cc_final: 0.7003 (tm-30) REVERT: M 115 LYS cc_start: 0.9112 (mttt) cc_final: 0.8817 (mtmm) REVERT: M 238 ARG cc_start: 0.7355 (mtt90) cc_final: 0.7139 (mpt180) REVERT: M 253 ARG cc_start: 0.8646 (mtp180) cc_final: 0.8031 (mtt90) REVERT: M 300 MET cc_start: 0.9191 (ttp) cc_final: 0.8723 (ttm) REVERT: N 115 LYS cc_start: 0.9096 (mttt) cc_final: 0.8868 (mtmt) REVERT: N 180 GLU cc_start: 0.8288 (tt0) cc_final: 0.7958 (mt-10) REVERT: N 300 MET cc_start: 0.9162 (ttp) cc_final: 0.8902 (ttm) REVERT: N 328 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8334 (tt0) REVERT: N 364 GLN cc_start: 0.7432 (tt0) cc_final: 0.6883 (tm-30) REVERT: N 398 LYS cc_start: 0.9134 (tttm) cc_final: 0.8930 (ttpp) REVERT: O 133 LYS cc_start: 0.7637 (tttt) cc_final: 0.7083 (tppt) REVERT: O 161 ASP cc_start: 0.7956 (m-30) cc_final: 0.7719 (m-30) REVERT: O 180 GLU cc_start: 0.8345 (tt0) cc_final: 0.8001 (mt-10) REVERT: O 261 LYS cc_start: 0.9131 (mttp) cc_final: 0.8902 (mmtt) REVERT: O 292 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8305 (pp20) REVERT: O 311 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8592 (m110) REVERT: O 364 GLN cc_start: 0.7532 (tt0) cc_final: 0.6894 (tm-30) REVERT: O 389 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7711 (mt-10) outliers start: 129 outliers final: 46 residues processed: 617 average time/residue: 1.5579 time to fit residues: 1091.6672 Evaluate side-chains 540 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 488 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 307 MET Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 311 ASN Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 165 GLN Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain I residue 148 SER Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 386 ASP Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 319 LYS Chi-restraints excluded: chain J residue 325 SER Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 344 ASN Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 325 SER Chi-restraints excluded: chain M residue 386 ASP Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 328 GLN Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 307 MET Chi-restraints excluded: chain O residue 311 ASN Chi-restraints excluded: chain O residue 386 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 chunk 260 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 313 optimal weight: 2.9990 chunk 339 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 251 optimal weight: 10.0000 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 328 GLN C 336 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN F 336 GLN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 GLN I 328 GLN ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 336 GLN K 187 GLN K 336 GLN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 344 ASN N 187 GLN N 336 GLN O 328 GLN O 336 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 27420 Z= 0.291 Angle : 0.600 7.684 37395 Z= 0.306 Chirality : 0.048 0.218 4920 Planarity : 0.005 0.043 4530 Dihedral : 8.710 113.621 5790 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.23 % Allowed : 18.99 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3285 helix: -1.03 (0.29), residues: 345 sheet: -1.09 (0.11), residues: 2145 loop : -0.70 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 245 PHE 0.017 0.002 PHE H 194 TYR 0.016 0.003 TYR I 359 ARG 0.004 0.001 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 466 time to evaluate : 3.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.9140 (mttt) cc_final: 0.8886 (mtmt) REVERT: A 122 LYS cc_start: 0.9105 (tttt) cc_final: 0.8878 (ptpp) REVERT: A 180 GLU cc_start: 0.8300 (tt0) cc_final: 0.7986 (mt-10) REVERT: A 261 LYS cc_start: 0.9106 (mttp) cc_final: 0.8702 (mmtt) REVERT: A 307 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7824 (mmt) REVERT: B 133 LYS cc_start: 0.7570 (tttt) cc_final: 0.7293 (tttp) REVERT: B 180 GLU cc_start: 0.8359 (tt0) cc_final: 0.8058 (mt-10) REVERT: B 253 ARG cc_start: 0.8733 (mtp180) cc_final: 0.8030 (mtp85) REVERT: B 364 GLN cc_start: 0.7542 (tt0) cc_final: 0.6927 (tm-30) REVERT: C 126 ARG cc_start: 0.8515 (mmt180) cc_final: 0.8151 (mtp-110) REVERT: C 180 GLU cc_start: 0.8432 (tt0) cc_final: 0.8190 (mt-10) REVERT: C 248 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8764 (mm) REVERT: C 307 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.6744 (mmp) REVERT: C 360 LYS cc_start: 0.7818 (tttt) cc_final: 0.7593 (mtpt) REVERT: C 364 GLN cc_start: 0.7535 (tt0) cc_final: 0.6942 (tm-30) REVERT: D 126 ARG cc_start: 0.8630 (mtt180) cc_final: 0.8382 (mmt180) REVERT: D 180 GLU cc_start: 0.8211 (tt0) cc_final: 0.7778 (mt-10) REVERT: D 364 GLN cc_start: 0.7542 (tt0) cc_final: 0.6905 (tm-30) REVERT: D 398 LYS cc_start: 0.9051 (tttm) cc_final: 0.8830 (tttp) REVERT: E 133 LYS cc_start: 0.7492 (tttt) cc_final: 0.7001 (tppt) REVERT: E 253 ARG cc_start: 0.8758 (mtm180) cc_final: 0.8041 (mtt90) REVERT: E 261 LYS cc_start: 0.9189 (mttp) cc_final: 0.8875 (mmmt) REVERT: F 180 GLU cc_start: 0.8299 (tt0) cc_final: 0.8018 (mt-10) REVERT: F 360 LYS cc_start: 0.8056 (tttt) cc_final: 0.7734 (ttmt) REVERT: F 394 TYR cc_start: 0.9153 (m-80) cc_final: 0.8916 (m-80) REVERT: G 126 ARG cc_start: 0.8594 (mtt180) cc_final: 0.8327 (mmt180) REVERT: G 180 GLU cc_start: 0.8317 (tt0) cc_final: 0.8012 (mt-10) REVERT: G 261 LYS cc_start: 0.9209 (mmtm) cc_final: 0.8974 (mmtt) REVERT: G 346 ARG cc_start: 0.8297 (mtt180) cc_final: 0.8026 (ttm110) REVERT: G 364 GLN cc_start: 0.7530 (tt0) cc_final: 0.6774 (tm-30) REVERT: G 398 LYS cc_start: 0.9134 (tttm) cc_final: 0.8872 (ttpp) REVERT: H 133 LYS cc_start: 0.7609 (tttt) cc_final: 0.7337 (ttmm) REVERT: H 180 GLU cc_start: 0.8566 (tt0) cc_final: 0.8215 (mt-10) REVERT: H 248 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8791 (mm) REVERT: H 360 LYS cc_start: 0.8177 (tttt) cc_final: 0.7953 (tttt) REVERT: H 364 GLN cc_start: 0.7582 (tt0) cc_final: 0.6846 (tm-30) REVERT: I 115 LYS cc_start: 0.9047 (mttt) cc_final: 0.8787 (mtmm) REVERT: I 122 LYS cc_start: 0.8841 (tttt) cc_final: 0.8639 (ptpp) REVERT: I 180 GLU cc_start: 0.8424 (tt0) cc_final: 0.8152 (mt-10) REVERT: I 248 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8691 (mm) REVERT: I 261 LYS cc_start: 0.9255 (mmtm) cc_final: 0.8953 (mmtp) REVERT: I 360 LYS cc_start: 0.8189 (tttt) cc_final: 0.7875 (ttmt) REVERT: I 364 GLN cc_start: 0.7538 (tt0) cc_final: 0.6895 (tm-30) REVERT: J 133 LYS cc_start: 0.7512 (tttt) cc_final: 0.6920 (tppt) REVERT: J 180 GLU cc_start: 0.8198 (tt0) cc_final: 0.7824 (mt-10) REVERT: J 261 LYS cc_start: 0.9278 (mmmt) cc_final: 0.9043 (mmmt) REVERT: J 364 GLN cc_start: 0.7483 (tt0) cc_final: 0.6781 (tm-30) REVERT: K 115 LYS cc_start: 0.9110 (mttt) cc_final: 0.8795 (mtmm) REVERT: K 133 LYS cc_start: 0.7886 (ttpp) cc_final: 0.7532 (ttmm) REVERT: K 180 GLU cc_start: 0.8435 (tt0) cc_final: 0.8015 (mt-10) REVERT: K 300 MET cc_start: 0.9145 (ttp) cc_final: 0.8914 (ttm) REVERT: K 364 GLN cc_start: 0.7602 (tt0) cc_final: 0.7122 (tm-30) REVERT: K 398 LYS cc_start: 0.9121 (tttm) cc_final: 0.8740 (tttt) REVERT: L 180 GLU cc_start: 0.8523 (tt0) cc_final: 0.8200 (mt-10) REVERT: L 307 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7761 (mtt) REVERT: L 344 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8574 (t0) REVERT: L 364 GLN cc_start: 0.7601 (tt0) cc_final: 0.7018 (tm-30) REVERT: M 115 LYS cc_start: 0.9096 (mttt) cc_final: 0.8852 (mttp) REVERT: M 253 ARG cc_start: 0.8682 (mtp180) cc_final: 0.8074 (mtt90) REVERT: M 300 MET cc_start: 0.9166 (ttp) cc_final: 0.8681 (ttm) REVERT: N 180 GLU cc_start: 0.8273 (tt0) cc_final: 0.7898 (mt-10) REVERT: N 261 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8866 (mmtm) REVERT: N 364 GLN cc_start: 0.7500 (tt0) cc_final: 0.6938 (tm-30) REVERT: O 133 LYS cc_start: 0.7635 (tttt) cc_final: 0.7117 (tppt) REVERT: O 180 GLU cc_start: 0.8500 (tt0) cc_final: 0.8083 (mt-10) REVERT: O 261 LYS cc_start: 0.9108 (mttp) cc_final: 0.8875 (mmtt) REVERT: O 292 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8365 (pp20) REVERT: O 300 MET cc_start: 0.9118 (ttp) cc_final: 0.8821 (ttp) REVERT: O 311 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8593 (m110) REVERT: O 358 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8356 (m-30) REVERT: O 364 GLN cc_start: 0.7532 (tt0) cc_final: 0.6856 (tm-30) outliers start: 130 outliers final: 66 residues processed: 563 average time/residue: 1.6039 time to fit residues: 1023.3783 Evaluate side-chains 525 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 450 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 307 MET Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 141 ASN Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 311 ASN Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 165 GLN Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain I residue 148 SER Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 301 SER Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 325 SER Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 256 THR Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 344 ASN Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 325 SER Chi-restraints excluded: chain M residue 386 ASP Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 148 SER Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 307 MET Chi-restraints excluded: chain O residue 311 ASN Chi-restraints excluded: chain O residue 358 ASP Chi-restraints excluded: chain O residue 386 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 314 optimal weight: 6.9990 chunk 333 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 141 ASN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN D 336 GLN E 336 GLN F 141 ASN F 336 GLN G 336 GLN H 336 GLN I 336 GLN J 141 ASN J 336 GLN ** K 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 GLN N 336 GLN O 336 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27420 Z= 0.352 Angle : 0.613 7.660 37395 Z= 0.312 Chirality : 0.048 0.189 4920 Planarity : 0.005 0.045 4530 Dihedral : 8.681 110.833 5790 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.33 % Allowed : 19.61 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3285 helix: -0.89 (0.29), residues: 345 sheet: -0.78 (0.11), residues: 2145 loop : -0.65 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 245 PHE 0.014 0.002 PHE H 194 TYR 0.018 0.003 TYR L 394 ARG 0.005 0.001 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 453 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9073 (tttt) cc_final: 0.8845 (ptpp) REVERT: A 180 GLU cc_start: 0.8238 (tt0) cc_final: 0.7940 (mt-10) REVERT: A 261 LYS cc_start: 0.9110 (mttp) cc_final: 0.8757 (mmmt) REVERT: A 387 SER cc_start: 0.7753 (t) cc_final: 0.7465 (m) REVERT: B 133 LYS cc_start: 0.7478 (tttt) cc_final: 0.7193 (tttp) REVERT: B 180 GLU cc_start: 0.8360 (tt0) cc_final: 0.8036 (mt-10) REVERT: B 253 ARG cc_start: 0.8788 (mtp180) cc_final: 0.8052 (mtp85) REVERT: B 364 GLN cc_start: 0.7507 (tt0) cc_final: 0.6843 (tm-30) REVERT: C 122 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8851 (ptpp) REVERT: C 180 GLU cc_start: 0.8413 (tt0) cc_final: 0.8183 (mt-10) REVERT: C 307 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.6773 (mmt) REVERT: C 364 GLN cc_start: 0.7470 (tt0) cc_final: 0.6834 (tm-30) REVERT: D 180 GLU cc_start: 0.8366 (tt0) cc_final: 0.8002 (mt-10) REVERT: D 364 GLN cc_start: 0.7507 (tt0) cc_final: 0.6858 (tm-30) REVERT: D 398 LYS cc_start: 0.9043 (tttm) cc_final: 0.8829 (tttp) REVERT: E 133 LYS cc_start: 0.7498 (tttt) cc_final: 0.7013 (tppt) REVERT: E 148 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8419 (t) REVERT: E 261 LYS cc_start: 0.9173 (mttp) cc_final: 0.8921 (mmmt) REVERT: F 129 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8325 (mt-10) REVERT: F 141 ASN cc_start: 0.8705 (m-40) cc_final: 0.8469 (m110) REVERT: F 180 GLU cc_start: 0.8330 (tt0) cc_final: 0.8031 (mt-10) REVERT: F 264 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8670 (tt) REVERT: F 394 TYR cc_start: 0.9168 (m-80) cc_final: 0.8914 (m-80) REVERT: G 126 ARG cc_start: 0.8590 (mtt180) cc_final: 0.8318 (mmt180) REVERT: G 180 GLU cc_start: 0.8363 (tt0) cc_final: 0.8053 (mt-10) REVERT: G 261 LYS cc_start: 0.9212 (mmtm) cc_final: 0.8979 (mmtt) REVERT: G 346 ARG cc_start: 0.8266 (mtt180) cc_final: 0.8028 (ttm110) REVERT: G 364 GLN cc_start: 0.7712 (tt0) cc_final: 0.6879 (tm-30) REVERT: G 392 THR cc_start: 0.9164 (t) cc_final: 0.8882 (m) REVERT: G 398 LYS cc_start: 0.9132 (tttm) cc_final: 0.8870 (ttpp) REVERT: H 180 GLU cc_start: 0.8544 (tt0) cc_final: 0.8185 (mt-10) REVERT: H 364 GLN cc_start: 0.7609 (tt0) cc_final: 0.6841 (tm-30) REVERT: H 389 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7954 (mt-10) REVERT: I 115 LYS cc_start: 0.9080 (mttt) cc_final: 0.8803 (mtmm) REVERT: I 122 LYS cc_start: 0.8848 (tttt) cc_final: 0.8615 (ptpp) REVERT: I 180 GLU cc_start: 0.8426 (tt0) cc_final: 0.8152 (mt-10) REVERT: I 261 LYS cc_start: 0.9261 (mmtm) cc_final: 0.9013 (mmtp) REVERT: I 360 LYS cc_start: 0.8213 (tttt) cc_final: 0.7888 (ttmt) REVERT: I 364 GLN cc_start: 0.7522 (tt0) cc_final: 0.6920 (tm-30) REVERT: J 133 LYS cc_start: 0.7438 (tttt) cc_final: 0.6945 (tppt) REVERT: J 180 GLU cc_start: 0.8246 (tt0) cc_final: 0.7876 (mt-10) REVERT: J 261 LYS cc_start: 0.9247 (mmmt) cc_final: 0.9012 (mmmt) REVERT: J 364 GLN cc_start: 0.7529 (tt0) cc_final: 0.6839 (tm-30) REVERT: K 115 LYS cc_start: 0.9079 (mttt) cc_final: 0.8781 (mtmm) REVERT: K 180 GLU cc_start: 0.8456 (tt0) cc_final: 0.8026 (mt-10) REVERT: K 364 GLN cc_start: 0.7678 (tt0) cc_final: 0.7149 (tm-30) REVERT: K 398 LYS cc_start: 0.9142 (tttm) cc_final: 0.8777 (ttpp) REVERT: L 133 LYS cc_start: 0.7655 (tttm) cc_final: 0.7153 (tppt) REVERT: L 180 GLU cc_start: 0.8503 (tt0) cc_final: 0.8200 (mt-10) REVERT: L 364 GLN cc_start: 0.7628 (tt0) cc_final: 0.7040 (tm-30) REVERT: M 115 LYS cc_start: 0.9072 (mttt) cc_final: 0.8827 (mttp) REVERT: M 253 ARG cc_start: 0.8701 (mtp180) cc_final: 0.8069 (mtt90) REVERT: M 300 MET cc_start: 0.9143 (ttp) cc_final: 0.8664 (ttm) REVERT: N 180 GLU cc_start: 0.8238 (tt0) cc_final: 0.7883 (mt-10) REVERT: N 261 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8910 (mmtm) REVERT: N 264 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8622 (tt) REVERT: N 364 GLN cc_start: 0.7447 (tt0) cc_final: 0.6916 (tm-30) REVERT: O 133 LYS cc_start: 0.7679 (tttt) cc_final: 0.7173 (tppt) REVERT: O 180 GLU cc_start: 0.8489 (tt0) cc_final: 0.8029 (mt-10) REVERT: O 261 LYS cc_start: 0.9066 (mttp) cc_final: 0.8824 (mmtt) REVERT: O 292 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8366 (pp20) REVERT: O 311 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8551 (m110) REVERT: O 358 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8360 (m-30) REVERT: O 360 LYS cc_start: 0.7973 (tttt) cc_final: 0.7748 (tttt) REVERT: O 364 GLN cc_start: 0.7572 (tt0) cc_final: 0.6852 (tm-30) outliers start: 164 outliers final: 75 residues processed: 579 average time/residue: 1.6763 time to fit residues: 1096.0430 Evaluate side-chains 532 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 449 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 307 MET Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 311 ASN Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain G residue 336 GLN Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 165 GLN Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 301 SER Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 301 SER Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 383 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 256 THR Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 325 SER Chi-restraints excluded: chain M residue 386 ASP Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 264 ILE Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 148 SER Chi-restraints excluded: chain O residue 159 ILE Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 307 MET Chi-restraints excluded: chain O residue 311 ASN Chi-restraints excluded: chain O residue 358 ASP Chi-restraints excluded: chain O residue 386 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 0.3980 chunk 189 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 299 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 141 ASN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN F 336 GLN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 GLN I 336 GLN J 141 ASN J 336 GLN K 141 ASN K 336 GLN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 243 ASN N 141 ASN N 336 GLN O 336 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27420 Z= 0.218 Angle : 0.515 7.851 37395 Z= 0.263 Chirality : 0.046 0.190 4920 Planarity : 0.005 0.042 4530 Dihedral : 8.029 106.576 5790 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.33 % Allowed : 21.24 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3285 helix: -0.51 (0.29), residues: 345 sheet: -0.58 (0.11), residues: 2130 loop : -0.61 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 245 PHE 0.011 0.001 PHE J 194 TYR 0.015 0.002 TYR L 394 ARG 0.003 0.000 ARG J 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 449 time to evaluate : 3.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9069 (tttt) cc_final: 0.8846 (ptpp) REVERT: A 180 GLU cc_start: 0.8333 (tt0) cc_final: 0.8046 (mt-10) REVERT: A 261 LYS cc_start: 0.9127 (mttp) cc_final: 0.8734 (mmtt) REVERT: B 133 LYS cc_start: 0.7405 (tttt) cc_final: 0.6885 (tppt) REVERT: B 180 GLU cc_start: 0.8342 (tt0) cc_final: 0.8059 (mt-10) REVERT: B 253 ARG cc_start: 0.8764 (mtp180) cc_final: 0.8054 (mtp85) REVERT: B 364 GLN cc_start: 0.7474 (tt0) cc_final: 0.6832 (tm-30) REVERT: C 122 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8874 (ptpp) REVERT: C 307 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.6709 (mmp) REVERT: C 364 GLN cc_start: 0.7447 (tt0) cc_final: 0.6809 (tm-30) REVERT: D 180 GLU cc_start: 0.8397 (tt0) cc_final: 0.8019 (mt-10) REVERT: D 364 GLN cc_start: 0.7465 (tt0) cc_final: 0.6846 (tm-30) REVERT: D 398 LYS cc_start: 0.9049 (tttm) cc_final: 0.8813 (tttp) REVERT: E 126 ARG cc_start: 0.8946 (mmm-85) cc_final: 0.8685 (mtp-110) REVERT: E 133 LYS cc_start: 0.7453 (tttt) cc_final: 0.7023 (tppt) REVERT: E 261 LYS cc_start: 0.9154 (mttp) cc_final: 0.8857 (mmmt) REVERT: F 129 GLU cc_start: 0.8580 (tp30) cc_final: 0.8371 (mt-10) REVERT: F 180 GLU cc_start: 0.8272 (tt0) cc_final: 0.8011 (mt-10) REVERT: F 261 LYS cc_start: 0.9125 (mmtm) cc_final: 0.8860 (mmmt) REVERT: F 394 TYR cc_start: 0.9146 (m-80) cc_final: 0.8909 (m-80) REVERT: G 180 GLU cc_start: 0.8374 (tt0) cc_final: 0.8064 (mt-10) REVERT: G 261 LYS cc_start: 0.9202 (mmtm) cc_final: 0.8978 (mmtt) REVERT: G 344 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8571 (m-40) REVERT: G 346 ARG cc_start: 0.8241 (mtt180) cc_final: 0.7981 (ttm110) REVERT: G 364 GLN cc_start: 0.7693 (tt0) cc_final: 0.6880 (tm-30) REVERT: G 392 THR cc_start: 0.9163 (t) cc_final: 0.8849 (m) REVERT: G 398 LYS cc_start: 0.9146 (tttm) cc_final: 0.8893 (ttpp) REVERT: H 180 GLU cc_start: 0.8552 (tt0) cc_final: 0.8203 (mt-10) REVERT: H 248 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8770 (mm) REVERT: H 364 GLN cc_start: 0.7600 (tt0) cc_final: 0.6852 (tm-30) REVERT: I 115 LYS cc_start: 0.9087 (mttt) cc_final: 0.8805 (mtmm) REVERT: I 180 GLU cc_start: 0.8498 (tt0) cc_final: 0.8191 (mt-10) REVERT: I 261 LYS cc_start: 0.9202 (mmtm) cc_final: 0.8891 (mmtp) REVERT: I 364 GLN cc_start: 0.7552 (tt0) cc_final: 0.6928 (tm-30) REVERT: J 133 LYS cc_start: 0.7290 (tttt) cc_final: 0.6777 (tppt) REVERT: J 180 GLU cc_start: 0.8285 (tt0) cc_final: 0.7898 (mt-10) REVERT: J 261 LYS cc_start: 0.9252 (mmtt) cc_final: 0.8988 (mmmt) REVERT: J 319 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8747 (mtpt) REVERT: J 364 GLN cc_start: 0.7487 (tt0) cc_final: 0.6801 (tm-30) REVERT: K 115 LYS cc_start: 0.9093 (mttt) cc_final: 0.8790 (mtmm) REVERT: K 133 LYS cc_start: 0.7866 (ttpp) cc_final: 0.7498 (ttmm) REVERT: K 180 GLU cc_start: 0.8483 (tt0) cc_final: 0.8040 (mt-10) REVERT: K 364 GLN cc_start: 0.7645 (tt0) cc_final: 0.7106 (tm-30) REVERT: K 398 LYS cc_start: 0.9127 (tttm) cc_final: 0.8797 (ttpp) REVERT: L 133 LYS cc_start: 0.7623 (tttm) cc_final: 0.7131 (tppt) REVERT: L 180 GLU cc_start: 0.8547 (tt0) cc_final: 0.8234 (mt-10) REVERT: L 307 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7659 (mtt) REVERT: L 364 GLN cc_start: 0.7555 (tt0) cc_final: 0.6966 (tm-30) REVERT: M 115 LYS cc_start: 0.9085 (mttt) cc_final: 0.8837 (mttp) REVERT: M 253 ARG cc_start: 0.8648 (mtp180) cc_final: 0.8041 (mtt90) REVERT: M 300 MET cc_start: 0.9138 (ttp) cc_final: 0.8622 (ttm) REVERT: N 126 ARG cc_start: 0.8408 (mmp-170) cc_final: 0.8178 (mmm-85) REVERT: N 180 GLU cc_start: 0.8183 (tt0) cc_final: 0.7854 (mt-10) REVERT: N 182 LEU cc_start: 0.8397 (tt) cc_final: 0.8167 (tm) REVERT: N 261 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8883 (mmtm) REVERT: N 364 GLN cc_start: 0.7507 (tt0) cc_final: 0.6902 (tm-30) REVERT: O 133 LYS cc_start: 0.7723 (tttt) cc_final: 0.7257 (tppt) REVERT: O 180 GLU cc_start: 0.8491 (tt0) cc_final: 0.8051 (mt-10) REVERT: O 261 LYS cc_start: 0.9083 (mttp) cc_final: 0.8843 (mmtt) REVERT: O 292 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8394 (pp20) REVERT: O 300 MET cc_start: 0.9101 (ttp) cc_final: 0.8547 (ttp) REVERT: O 311 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8548 (m110) REVERT: O 364 GLN cc_start: 0.7537 (tt0) cc_final: 0.6831 (tm-30) outliers start: 133 outliers final: 60 residues processed: 550 average time/residue: 1.6632 time to fit residues: 1032.7057 Evaluate side-chains 506 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 439 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 307 MET Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 311 ASN Chi-restraints excluded: chain G residue 344 ASN Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 165 GLN Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain H residue 386 ASP Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 301 SER Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 319 LYS Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 336 GLN Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 256 THR Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 325 SER Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 148 SER Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 307 MET Chi-restraints excluded: chain O residue 311 ASN Chi-restraints excluded: chain O residue 386 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 0.0170 chunk 300 optimal weight: 0.0980 chunk 65 optimal weight: 8.9990 chunk 195 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 333 optimal weight: 0.2980 chunk 277 optimal weight: 0.0270 chunk 154 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN F 141 ASN F 336 GLN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 GLN J 141 ASN K 141 ASN ** K 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 ASN ** N 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 336 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 27420 Z= 0.102 Angle : 0.437 7.840 37395 Z= 0.221 Chirality : 0.045 0.205 4920 Planarity : 0.004 0.039 4530 Dihedral : 7.135 93.653 5790 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.86 % Allowed : 22.76 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.15), residues: 3285 helix: -0.08 (0.29), residues: 345 sheet: -0.31 (0.11), residues: 2235 loop : -0.46 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 245 PHE 0.008 0.001 PHE J 194 TYR 0.016 0.001 TYR L 394 ARG 0.004 0.000 ARG C 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 464 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9031 (tttt) cc_final: 0.8813 (ptpp) REVERT: A 123 ASP cc_start: 0.8554 (m-30) cc_final: 0.8317 (m-30) REVERT: A 133 LYS cc_start: 0.7488 (tttp) cc_final: 0.6975 (tppt) REVERT: A 180 GLU cc_start: 0.8396 (tt0) cc_final: 0.8139 (mt-10) REVERT: A 364 GLN cc_start: 0.7392 (tt0) cc_final: 0.6800 (tm-30) REVERT: B 133 LYS cc_start: 0.7282 (tttt) cc_final: 0.6782 (tppt) REVERT: B 180 GLU cc_start: 0.8335 (tt0) cc_final: 0.8105 (mt-10) REVERT: B 364 GLN cc_start: 0.7457 (tt0) cc_final: 0.6825 (tm-30) REVERT: C 364 GLN cc_start: 0.7376 (tt0) cc_final: 0.6787 (tm-30) REVERT: D 133 LYS cc_start: 0.7626 (ttpp) cc_final: 0.7218 (ttmm) REVERT: D 180 GLU cc_start: 0.8197 (tt0) cc_final: 0.7897 (mt-10) REVERT: D 364 GLN cc_start: 0.7388 (tt0) cc_final: 0.6775 (tm-30) REVERT: E 126 ARG cc_start: 0.8882 (mmm-85) cc_final: 0.8661 (mtp-110) REVERT: E 133 LYS cc_start: 0.7375 (tttt) cc_final: 0.6999 (tppt) REVERT: E 261 LYS cc_start: 0.9117 (mttp) cc_final: 0.8787 (mmmt) REVERT: F 126 ARG cc_start: 0.8802 (mmm-85) cc_final: 0.8586 (mtm180) REVERT: F 133 LYS cc_start: 0.7620 (tttp) cc_final: 0.7123 (tppt) REVERT: F 261 LYS cc_start: 0.9180 (mmtm) cc_final: 0.8894 (mmtt) REVERT: F 364 GLN cc_start: 0.7592 (tt0) cc_final: 0.6857 (tm-30) REVERT: G 133 LYS cc_start: 0.7906 (tttp) cc_final: 0.7285 (tppt) REVERT: G 180 GLU cc_start: 0.8425 (tt0) cc_final: 0.8128 (mt-10) REVERT: G 261 LYS cc_start: 0.9166 (mmtm) cc_final: 0.8925 (mmmt) REVERT: G 307 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7819 (mtt) REVERT: G 364 GLN cc_start: 0.7606 (tt0) cc_final: 0.6816 (tm-30) REVERT: G 392 THR cc_start: 0.9149 (t) cc_final: 0.8813 (m) REVERT: G 398 LYS cc_start: 0.9079 (tttm) cc_final: 0.8870 (tttp) REVERT: H 180 GLU cc_start: 0.8604 (tt0) cc_final: 0.8232 (mt-10) REVERT: H 364 GLN cc_start: 0.7535 (tt0) cc_final: 0.6798 (tm-30) REVERT: I 115 LYS cc_start: 0.8956 (mttt) cc_final: 0.8723 (mtmm) REVERT: I 180 GLU cc_start: 0.8523 (tt0) cc_final: 0.8238 (mt-10) REVERT: I 261 LYS cc_start: 0.9185 (mmtm) cc_final: 0.8887 (mmtp) REVERT: I 364 GLN cc_start: 0.7389 (tt0) cc_final: 0.6857 (tm-30) REVERT: J 133 LYS cc_start: 0.7206 (tttt) cc_final: 0.6772 (tppt) REVERT: J 180 GLU cc_start: 0.8132 (tt0) cc_final: 0.7911 (mt-10) REVERT: J 253 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8032 (mtt90) REVERT: J 261 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.9014 (mmmt) REVERT: J 364 GLN cc_start: 0.7441 (tt0) cc_final: 0.6787 (tm-30) REVERT: K 115 LYS cc_start: 0.9080 (mttt) cc_final: 0.8779 (mtmm) REVERT: K 133 LYS cc_start: 0.7890 (ttpp) cc_final: 0.7564 (ttmm) REVERT: K 180 GLU cc_start: 0.8433 (tt0) cc_final: 0.8118 (mt-10) REVERT: K 261 LYS cc_start: 0.9022 (mttm) cc_final: 0.8756 (mmmt) REVERT: K 364 GLN cc_start: 0.7553 (tt0) cc_final: 0.7073 (tm-30) REVERT: K 398 LYS cc_start: 0.9062 (tttm) cc_final: 0.8777 (ttpp) REVERT: L 133 LYS cc_start: 0.7594 (tttm) cc_final: 0.7159 (tppt) REVERT: L 180 GLU cc_start: 0.8545 (tt0) cc_final: 0.8231 (mt-10) REVERT: L 364 GLN cc_start: 0.7496 (tt0) cc_final: 0.6920 (tm-30) REVERT: M 253 ARG cc_start: 0.8419 (mtp180) cc_final: 0.7887 (mtt90) REVERT: M 300 MET cc_start: 0.9079 (ttp) cc_final: 0.8609 (ttm) REVERT: N 126 ARG cc_start: 0.8695 (mmp-170) cc_final: 0.8269 (mmm-85) REVERT: N 133 LYS cc_start: 0.7626 (tttm) cc_final: 0.7298 (tppt) REVERT: N 180 GLU cc_start: 0.8354 (tt0) cc_final: 0.8031 (mt-10) REVERT: N 182 LEU cc_start: 0.8306 (tt) cc_final: 0.8099 (tm) REVERT: N 261 LYS cc_start: 0.9058 (mmtt) cc_final: 0.8806 (mmtm) REVERT: N 364 GLN cc_start: 0.7506 (tt0) cc_final: 0.6886 (tm-30) REVERT: O 133 LYS cc_start: 0.7453 (tttt) cc_final: 0.7050 (tppt) REVERT: O 180 GLU cc_start: 0.8481 (tt0) cc_final: 0.8081 (mt-10) REVERT: O 261 LYS cc_start: 0.9114 (mttp) cc_final: 0.8881 (mmtt) REVERT: O 300 MET cc_start: 0.9155 (ttp) cc_final: 0.8647 (ttp) REVERT: O 364 GLN cc_start: 0.7421 (tt0) cc_final: 0.6771 (tm-30) outliers start: 88 outliers final: 33 residues processed: 528 average time/residue: 1.6001 time to fit residues: 959.2382 Evaluate side-chains 460 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 425 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 141 ASN Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 386 ASP Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain J residue 188 GLN Chi-restraints excluded: chain J residue 261 LYS Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 256 THR Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 336 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 321 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 243 optimal weight: 8.9990 chunk 188 optimal weight: 0.0470 chunk 280 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 332 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 336 GLN A 349 GLN B 141 ASN B 336 GLN C 336 GLN D 336 GLN E 336 GLN F 141 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN ** J 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 ASN L 336 GLN N 141 ASN N 336 GLN O 336 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 27420 Z= 0.320 Angle : 0.572 8.335 37395 Z= 0.290 Chirality : 0.047 0.170 4920 Planarity : 0.005 0.039 4530 Dihedral : 8.109 95.339 5790 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.61 % Allowed : 22.93 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 3285 helix: -0.17 (0.29), residues: 345 sheet: -0.28 (0.11), residues: 2130 loop : -0.55 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 245 PHE 0.009 0.001 PHE O 194 TYR 0.019 0.003 TYR M 394 ARG 0.004 0.001 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 448 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9087 (tttt) cc_final: 0.8860 (ptpp) REVERT: A 180 GLU cc_start: 0.8344 (tt0) cc_final: 0.8069 (mt-10) REVERT: A 193 ASP cc_start: 0.6919 (OUTLIER) cc_final: 0.6711 (m-30) REVERT: B 133 LYS cc_start: 0.7398 (tttt) cc_final: 0.7110 (tttp) REVERT: B 180 GLU cc_start: 0.8333 (tt0) cc_final: 0.8050 (mt-10) REVERT: B 364 GLN cc_start: 0.7448 (tt0) cc_final: 0.6786 (tm-30) REVERT: C 364 GLN cc_start: 0.7380 (tt0) cc_final: 0.6782 (tm-30) REVERT: D 180 GLU cc_start: 0.8275 (tt0) cc_final: 0.7904 (mt-10) REVERT: D 364 GLN cc_start: 0.7483 (tt0) cc_final: 0.6876 (tm-30) REVERT: D 398 LYS cc_start: 0.9037 (tttm) cc_final: 0.8813 (tttp) REVERT: E 133 LYS cc_start: 0.7467 (tttt) cc_final: 0.7041 (tppt) REVERT: E 261 LYS cc_start: 0.9123 (mttp) cc_final: 0.8816 (mmmt) REVERT: F 261 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8954 (mmmt) REVERT: F 264 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8687 (tt) REVERT: F 400 THR cc_start: 0.8766 (m) cc_final: 0.8226 (p) REVERT: G 180 GLU cc_start: 0.8362 (tt0) cc_final: 0.8044 (mt-10) REVERT: G 261 LYS cc_start: 0.9209 (mmtm) cc_final: 0.8974 (mmtt) REVERT: G 364 GLN cc_start: 0.7719 (tt0) cc_final: 0.6879 (tm-30) REVERT: G 392 THR cc_start: 0.9167 (t) cc_final: 0.8870 (m) REVERT: G 398 LYS cc_start: 0.9157 (tttm) cc_final: 0.8924 (ttpp) REVERT: H 180 GLU cc_start: 0.8565 (tt0) cc_final: 0.8223 (mt-10) REVERT: H 264 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8462 (tt) REVERT: H 364 GLN cc_start: 0.7632 (tt0) cc_final: 0.6829 (tm-30) REVERT: I 115 LYS cc_start: 0.9036 (mttt) cc_final: 0.8769 (mtmm) REVERT: I 180 GLU cc_start: 0.8511 (tt0) cc_final: 0.8196 (mt-10) REVERT: I 261 LYS cc_start: 0.9187 (mmtm) cc_final: 0.8871 (mmtp) REVERT: I 364 GLN cc_start: 0.7438 (tt0) cc_final: 0.6887 (tm-30) REVERT: J 133 LYS cc_start: 0.7365 (tttt) cc_final: 0.6876 (tppt) REVERT: J 180 GLU cc_start: 0.8353 (tt0) cc_final: 0.7967 (mt-10) REVERT: J 261 LYS cc_start: 0.9269 (mmtt) cc_final: 0.8999 (mmmt) REVERT: J 364 GLN cc_start: 0.7505 (tt0) cc_final: 0.6821 (tm-30) REVERT: K 115 LYS cc_start: 0.9080 (mttt) cc_final: 0.8768 (mtmm) REVERT: K 133 LYS cc_start: 0.7918 (ttpp) cc_final: 0.7526 (ttmm) REVERT: K 180 GLU cc_start: 0.8501 (tt0) cc_final: 0.8086 (mt-10) REVERT: K 364 GLN cc_start: 0.7606 (tt0) cc_final: 0.7096 (tm-30) REVERT: K 398 LYS cc_start: 0.9134 (tttm) cc_final: 0.8786 (ttpp) REVERT: L 133 LYS cc_start: 0.7695 (tttm) cc_final: 0.7234 (tppt) REVERT: L 180 GLU cc_start: 0.8622 (tt0) cc_final: 0.8236 (mt-10) REVERT: L 364 GLN cc_start: 0.7556 (tt0) cc_final: 0.6962 (tm-30) REVERT: L 388 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8252 (t0) REVERT: M 264 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8589 (tt) REVERT: M 300 MET cc_start: 0.9102 (ttp) cc_final: 0.8625 (ttm) REVERT: N 180 GLU cc_start: 0.8257 (tt0) cc_final: 0.7871 (mt-10) REVERT: N 261 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8903 (mmtm) REVERT: N 364 GLN cc_start: 0.7525 (tt0) cc_final: 0.6879 (tm-30) REVERT: O 133 LYS cc_start: 0.7766 (tttt) cc_final: 0.7289 (tppt) REVERT: O 180 GLU cc_start: 0.8488 (tt0) cc_final: 0.8067 (mt-10) REVERT: O 261 LYS cc_start: 0.9094 (mttp) cc_final: 0.8849 (mmtt) REVERT: O 264 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8486 (tt) REVERT: O 300 MET cc_start: 0.9069 (ttp) cc_final: 0.8604 (ttp) REVERT: O 358 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8366 (m-30) REVERT: O 364 GLN cc_start: 0.7572 (tt0) cc_final: 0.6872 (tm-30) outliers start: 111 outliers final: 49 residues processed: 524 average time/residue: 1.7650 time to fit residues: 1041.2939 Evaluate side-chains 481 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 425 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 311 ASN Chi-restraints excluded: chain G residue 386 ASP Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 386 ASP Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 388 ASN Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 256 THR Chi-restraints excluded: chain L residue 336 GLN Chi-restraints excluded: chain L residue 388 ASN Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 294 GLN Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain O residue 358 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 205 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 198 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 211 optimal weight: 8.9990 chunk 226 optimal weight: 8.9990 chunk 164 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 141 ASN B 336 GLN C 336 GLN D 336 GLN F 141 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 GLN I 336 GLN J 141 ASN J 336 GLN K 141 ASN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 ASN N 336 GLN O 336 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27420 Z= 0.221 Angle : 0.508 7.772 37395 Z= 0.258 Chirality : 0.046 0.183 4920 Planarity : 0.005 0.040 4530 Dihedral : 7.794 98.018 5790 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.32 % Allowed : 23.02 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3285 helix: -0.02 (0.29), residues: 345 sheet: -0.23 (0.11), residues: 2130 loop : -0.55 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 245 PHE 0.008 0.001 PHE J 194 TYR 0.022 0.002 TYR F 394 ARG 0.004 0.000 ARG L 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 432 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9076 (tttt) cc_final: 0.8839 (ptpp) REVERT: A 180 GLU cc_start: 0.8329 (tt0) cc_final: 0.8056 (mt-10) REVERT: B 133 LYS cc_start: 0.7364 (tttt) cc_final: 0.6844 (tppt) REVERT: B 180 GLU cc_start: 0.8319 (tt0) cc_final: 0.8094 (mt-10) REVERT: B 264 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8559 (tt) REVERT: B 364 GLN cc_start: 0.7446 (tt0) cc_final: 0.6799 (tm-30) REVERT: C 253 ARG cc_start: 0.8571 (mtm180) cc_final: 0.8004 (mtt90) REVERT: C 364 GLN cc_start: 0.7397 (tt0) cc_final: 0.6781 (tm-30) REVERT: D 180 GLU cc_start: 0.8242 (tt0) cc_final: 0.7894 (mt-10) REVERT: D 364 GLN cc_start: 0.7410 (tt0) cc_final: 0.6787 (tm-30) REVERT: E 133 LYS cc_start: 0.7424 (tttt) cc_final: 0.7011 (tppt) REVERT: E 261 LYS cc_start: 0.9119 (mttp) cc_final: 0.8793 (mmmt) REVERT: F 264 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8583 (tt) REVERT: G 180 GLU cc_start: 0.8409 (tt0) cc_final: 0.8045 (mt-10) REVERT: G 261 LYS cc_start: 0.9206 (mmtm) cc_final: 0.8976 (mmtt) REVERT: G 364 GLN cc_start: 0.7736 (tt0) cc_final: 0.6918 (tm-30) REVERT: G 392 THR cc_start: 0.9171 (t) cc_final: 0.8854 (m) REVERT: G 398 LYS cc_start: 0.9141 (tttm) cc_final: 0.8921 (ttpp) REVERT: H 180 GLU cc_start: 0.8563 (tt0) cc_final: 0.8249 (mt-10) REVERT: H 264 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8462 (tt) REVERT: H 364 GLN cc_start: 0.7659 (tt0) cc_final: 0.6822 (tm-30) REVERT: I 115 LYS cc_start: 0.9021 (mttt) cc_final: 0.8748 (mtmm) REVERT: I 180 GLU cc_start: 0.8520 (tt0) cc_final: 0.8192 (mt-10) REVERT: I 261 LYS cc_start: 0.9193 (mmtm) cc_final: 0.8886 (mmtp) REVERT: I 364 GLN cc_start: 0.7409 (tt0) cc_final: 0.6853 (tm-30) REVERT: J 133 LYS cc_start: 0.7333 (tttt) cc_final: 0.6838 (tppt) REVERT: J 180 GLU cc_start: 0.8370 (tt0) cc_final: 0.8007 (mt-10) REVERT: J 261 LYS cc_start: 0.9265 (mmtt) cc_final: 0.8994 (mmmt) REVERT: J 364 GLN cc_start: 0.7463 (tt0) cc_final: 0.6788 (tm-30) REVERT: K 115 LYS cc_start: 0.9080 (mttt) cc_final: 0.8770 (mtmm) REVERT: K 133 LYS cc_start: 0.7869 (ttpp) cc_final: 0.7500 (ttmm) REVERT: K 180 GLU cc_start: 0.8501 (tt0) cc_final: 0.8084 (mt-10) REVERT: K 261 LYS cc_start: 0.9098 (mttm) cc_final: 0.8851 (mmmt) REVERT: K 364 GLN cc_start: 0.7642 (tt0) cc_final: 0.7114 (tm-30) REVERT: K 398 LYS cc_start: 0.9119 (tttm) cc_final: 0.8802 (ttpp) REVERT: L 133 LYS cc_start: 0.7648 (tttm) cc_final: 0.7174 (tppt) REVERT: L 180 GLU cc_start: 0.8604 (tt0) cc_final: 0.8247 (mt-10) REVERT: L 364 GLN cc_start: 0.7549 (tt0) cc_final: 0.6953 (tm-30) REVERT: M 180 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8310 (mt-10) REVERT: M 264 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8596 (tt) REVERT: M 300 MET cc_start: 0.9098 (ttp) cc_final: 0.8624 (ttm) REVERT: M 388 ASN cc_start: 0.8485 (t0) cc_final: 0.8234 (m-40) REVERT: N 180 GLU cc_start: 0.8190 (tt0) cc_final: 0.7850 (mt-10) REVERT: N 261 LYS cc_start: 0.9070 (mmtt) cc_final: 0.8862 (mmtm) REVERT: N 364 GLN cc_start: 0.7508 (tt0) cc_final: 0.6858 (tm-30) REVERT: O 133 LYS cc_start: 0.7696 (tttt) cc_final: 0.7249 (tppt) REVERT: O 180 GLU cc_start: 0.8520 (tt0) cc_final: 0.8107 (mt-10) REVERT: O 261 LYS cc_start: 0.9107 (mttp) cc_final: 0.8863 (mmtt) REVERT: O 264 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8487 (tt) REVERT: O 300 MET cc_start: 0.9125 (ttp) cc_final: 0.8655 (ttp) REVERT: O 364 GLN cc_start: 0.7545 (tt0) cc_final: 0.6854 (tm-30) outliers start: 102 outliers final: 45 residues processed: 514 average time/residue: 1.7840 time to fit residues: 1041.4315 Evaluate side-chains 464 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 414 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 311 ASN Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 301 SER Chi-restraints excluded: chain I residue 388 ASN Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 256 THR Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 383 SER Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 264 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 302 optimal weight: 8.9990 chunk 318 optimal weight: 9.9990 chunk 290 optimal weight: 2.9990 chunk 309 optimal weight: 6.9990 chunk 186 optimal weight: 0.0060 chunk 134 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 280 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 308 optimal weight: 10.0000 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 141 ASN B 336 GLN C 336 GLN D 336 GLN F 141 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 GLN J 141 ASN J 336 GLN K 141 ASN L 336 GLN N 141 ASN N 336 GLN O 336 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 27420 Z= 0.320 Angle : 0.577 7.724 37395 Z= 0.292 Chirality : 0.047 0.170 4920 Planarity : 0.005 0.043 4530 Dihedral : 8.292 101.284 5790 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.93 % Allowed : 23.48 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3285 helix: -0.13 (0.29), residues: 345 sheet: -0.27 (0.11), residues: 2130 loop : -0.57 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 245 PHE 0.009 0.001 PHE I 194 TYR 0.028 0.003 TYR F 394 ARG 0.004 0.001 ARG G 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 429 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9065 (tttt) cc_final: 0.8831 (ptpp) REVERT: A 180 GLU cc_start: 0.8249 (tt0) cc_final: 0.7953 (mt-10) REVERT: A 387 SER cc_start: 0.7772 (t) cc_final: 0.7502 (m) REVERT: B 133 LYS cc_start: 0.7415 (tttt) cc_final: 0.7124 (tttp) REVERT: B 180 GLU cc_start: 0.8357 (tt0) cc_final: 0.8068 (mt-10) REVERT: B 264 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8585 (tt) REVERT: C 253 ARG cc_start: 0.8636 (mtm180) cc_final: 0.8008 (mtt90) REVERT: C 364 GLN cc_start: 0.7491 (tt0) cc_final: 0.6888 (tm-30) REVERT: D 180 GLU cc_start: 0.8283 (tt0) cc_final: 0.7892 (mt-10) REVERT: D 307 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.6986 (mtt) REVERT: D 398 LYS cc_start: 0.9042 (tttm) cc_final: 0.8830 (tttp) REVERT: E 133 LYS cc_start: 0.7512 (tttt) cc_final: 0.7070 (tppt) REVERT: E 261 LYS cc_start: 0.9126 (mttp) cc_final: 0.8803 (mmmt) REVERT: E 392 THR cc_start: 0.9062 (t) cc_final: 0.8842 (m) REVERT: F 261 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8682 (mmmt) REVERT: F 264 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8709 (tt) REVERT: F 400 THR cc_start: 0.8768 (m) cc_final: 0.8220 (p) REVERT: G 180 GLU cc_start: 0.8351 (tt0) cc_final: 0.8016 (mt-10) REVERT: G 261 LYS cc_start: 0.9204 (mmtm) cc_final: 0.8971 (mmtt) REVERT: G 364 GLN cc_start: 0.7720 (tt0) cc_final: 0.6878 (tm-30) REVERT: G 392 THR cc_start: 0.9178 (t) cc_final: 0.8866 (m) REVERT: G 398 LYS cc_start: 0.9166 (tttm) cc_final: 0.8935 (ttpp) REVERT: H 180 GLU cc_start: 0.8526 (tt0) cc_final: 0.8205 (mt-10) REVERT: H 264 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8469 (tt) REVERT: H 364 GLN cc_start: 0.7607 (tt0) cc_final: 0.6775 (tm-30) REVERT: H 388 ASN cc_start: 0.8281 (t0) cc_final: 0.7989 (m-40) REVERT: I 115 LYS cc_start: 0.9115 (mttt) cc_final: 0.8836 (mtmm) REVERT: I 180 GLU cc_start: 0.8510 (tt0) cc_final: 0.8187 (mt-10) REVERT: I 261 LYS cc_start: 0.9190 (mmtm) cc_final: 0.8875 (mmtp) REVERT: I 364 GLN cc_start: 0.7465 (tt0) cc_final: 0.6853 (tm-30) REVERT: J 133 LYS cc_start: 0.7374 (tttt) cc_final: 0.6842 (tppt) REVERT: J 180 GLU cc_start: 0.8364 (tt0) cc_final: 0.7971 (mt-10) REVERT: J 261 LYS cc_start: 0.9267 (mmtt) cc_final: 0.8991 (mmmt) REVERT: J 364 GLN cc_start: 0.7501 (tt0) cc_final: 0.6820 (tm-30) REVERT: K 115 LYS cc_start: 0.9073 (mttt) cc_final: 0.8766 (mtmm) REVERT: K 133 LYS cc_start: 0.8065 (ttpp) cc_final: 0.7691 (ttmm) REVERT: K 180 GLU cc_start: 0.8483 (tt0) cc_final: 0.8040 (mt-10) REVERT: K 261 LYS cc_start: 0.9113 (mttm) cc_final: 0.8870 (mmmt) REVERT: K 364 GLN cc_start: 0.7636 (tt0) cc_final: 0.7080 (tm-30) REVERT: K 398 LYS cc_start: 0.9135 (tttm) cc_final: 0.8791 (ttpp) REVERT: L 133 LYS cc_start: 0.7674 (tttm) cc_final: 0.7209 (tppt) REVERT: L 180 GLU cc_start: 0.8615 (tt0) cc_final: 0.8262 (mt-10) REVERT: L 388 ASN cc_start: 0.8719 (t0) cc_final: 0.8379 (m-40) REVERT: M 180 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8368 (mt-10) REVERT: M 193 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6813 (m-30) REVERT: M 253 ARG cc_start: 0.8713 (mtp-110) cc_final: 0.8041 (mtt90) REVERT: M 264 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8595 (tt) REVERT: M 300 MET cc_start: 0.9105 (ttp) cc_final: 0.8609 (ttm) REVERT: M 388 ASN cc_start: 0.8532 (t0) cc_final: 0.8283 (m-40) REVERT: N 180 GLU cc_start: 0.8179 (tt0) cc_final: 0.7818 (mt-10) REVERT: N 261 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8912 (mmtm) REVERT: N 364 GLN cc_start: 0.7471 (tt0) cc_final: 0.6872 (tm-30) REVERT: O 133 LYS cc_start: 0.7694 (tttt) cc_final: 0.7219 (tppt) REVERT: O 180 GLU cc_start: 0.8477 (tt0) cc_final: 0.8066 (mt-10) REVERT: O 261 LYS cc_start: 0.9092 (mttp) cc_final: 0.8848 (mmtt) REVERT: O 264 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8502 (tt) REVERT: O 300 MET cc_start: 0.9069 (ttp) cc_final: 0.8613 (ttp) REVERT: O 358 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8386 (m-30) REVERT: O 364 GLN cc_start: 0.7613 (tt0) cc_final: 0.6897 (tm-30) outliers start: 90 outliers final: 55 residues processed: 504 average time/residue: 1.7417 time to fit residues: 984.8896 Evaluate side-chains 482 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 419 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 311 ASN Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain H residue 386 ASP Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 388 ASN Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 256 THR Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 336 GLN Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 193 ASP Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 325 SER Chi-restraints excluded: chain M residue 383 SER Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 294 GLN Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 193 ASP Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain O residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 203 optimal weight: 10.0000 chunk 327 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 227 optimal weight: 0.1980 chunk 343 optimal weight: 10.0000 chunk 316 optimal weight: 7.9990 chunk 273 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 141 ASN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN D 336 GLN F 141 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN J 336 GLN K 141 ASN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 ASN N 336 GLN O 336 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 27420 Z= 0.395 Angle : 0.625 7.624 37395 Z= 0.316 Chirality : 0.049 0.178 4920 Planarity : 0.005 0.046 4530 Dihedral : 8.671 106.994 5790 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.83 % Allowed : 23.48 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3285 helix: -0.26 (0.28), residues: 345 sheet: -0.36 (0.11), residues: 2130 loop : -0.63 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS D 245 PHE 0.013 0.001 PHE H 303 TYR 0.026 0.003 TYR F 394 ARG 0.006 0.001 ARG J 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 437 time to evaluate : 3.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8266 (tt0) cc_final: 0.7965 (mt-10) REVERT: B 133 LYS cc_start: 0.7459 (tttt) cc_final: 0.7171 (tttp) REVERT: B 180 GLU cc_start: 0.8345 (tt0) cc_final: 0.8050 (mt-10) REVERT: B 264 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8568 (tt) REVERT: B 364 GLN cc_start: 0.7382 (tt0) cc_final: 0.6801 (tm-30) REVERT: C 364 GLN cc_start: 0.7513 (tt0) cc_final: 0.6891 (tm-30) REVERT: D 180 GLU cc_start: 0.8289 (tt0) cc_final: 0.7879 (mt-10) REVERT: D 307 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.6928 (mtt) REVERT: E 133 LYS cc_start: 0.7493 (tttt) cc_final: 0.7049 (tppt) REVERT: E 261 LYS cc_start: 0.9148 (mttp) cc_final: 0.8824 (mmmt) REVERT: E 392 THR cc_start: 0.9062 (t) cc_final: 0.8837 (m) REVERT: F 141 ASN cc_start: 0.8715 (m-40) cc_final: 0.8500 (m110) REVERT: F 264 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8739 (tt) REVERT: G 180 GLU cc_start: 0.8351 (tt0) cc_final: 0.8043 (mt-10) REVERT: G 261 LYS cc_start: 0.9203 (mmtm) cc_final: 0.8970 (mmtt) REVERT: G 346 ARG cc_start: 0.8264 (mtt180) cc_final: 0.8011 (ttm110) REVERT: G 392 THR cc_start: 0.9190 (t) cc_final: 0.8863 (m) REVERT: G 398 LYS cc_start: 0.9158 (tttm) cc_final: 0.8931 (ttpp) REVERT: H 180 GLU cc_start: 0.8569 (tt0) cc_final: 0.8217 (mt-10) REVERT: H 264 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8533 (tt) REVERT: H 346 ARG cc_start: 0.8201 (mtm180) cc_final: 0.7967 (ttp-170) REVERT: H 364 GLN cc_start: 0.7649 (tt0) cc_final: 0.6794 (tm-30) REVERT: I 115 LYS cc_start: 0.9090 (mttt) cc_final: 0.8816 (mtmm) REVERT: I 180 GLU cc_start: 0.8446 (tt0) cc_final: 0.8134 (mt-10) REVERT: I 261 LYS cc_start: 0.9185 (mmtm) cc_final: 0.8866 (mmtp) REVERT: I 364 GLN cc_start: 0.7528 (tt0) cc_final: 0.6887 (tm-30) REVERT: J 133 LYS cc_start: 0.7387 (tttt) cc_final: 0.6837 (tppt) REVERT: J 180 GLU cc_start: 0.8359 (tt0) cc_final: 0.7967 (mt-10) REVERT: J 261 LYS cc_start: 0.9245 (mmtt) cc_final: 0.9013 (mmmt) REVERT: J 364 GLN cc_start: 0.7465 (tt0) cc_final: 0.6786 (tm-30) REVERT: K 115 LYS cc_start: 0.9066 (mttt) cc_final: 0.8768 (mtmm) REVERT: K 133 LYS cc_start: 0.8080 (ttpp) cc_final: 0.7715 (ttmm) REVERT: K 180 GLU cc_start: 0.8462 (tt0) cc_final: 0.8021 (mt-10) REVERT: K 364 GLN cc_start: 0.7656 (tt0) cc_final: 0.7087 (tm-30) REVERT: K 398 LYS cc_start: 0.9143 (tttm) cc_final: 0.8809 (ttpp) REVERT: L 133 LYS cc_start: 0.7666 (tttm) cc_final: 0.7178 (tppt) REVERT: L 180 GLU cc_start: 0.8611 (tt0) cc_final: 0.8258 (mt-10) REVERT: M 253 ARG cc_start: 0.8731 (mtp-110) cc_final: 0.7998 (mtt90) REVERT: M 264 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8599 (tt) REVERT: M 300 MET cc_start: 0.9110 (ttp) cc_final: 0.8611 (ttm) REVERT: M 346 ARG cc_start: 0.7970 (mtm110) cc_final: 0.7704 (ttm110) REVERT: N 180 GLU cc_start: 0.8198 (tt0) cc_final: 0.7847 (mt-10) REVERT: N 261 LYS cc_start: 0.9155 (mmtt) cc_final: 0.8932 (mmtm) REVERT: N 364 GLN cc_start: 0.7478 (tt0) cc_final: 0.6877 (tm-30) REVERT: O 133 LYS cc_start: 0.7737 (tttt) cc_final: 0.7230 (tppt) REVERT: O 180 GLU cc_start: 0.8482 (tt0) cc_final: 0.8057 (mt-10) REVERT: O 261 LYS cc_start: 0.9070 (mttp) cc_final: 0.8822 (mmtt) REVERT: O 264 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8505 (tt) REVERT: O 292 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8377 (pp20) REVERT: O 300 MET cc_start: 0.9092 (ttp) cc_final: 0.8642 (ttp) REVERT: O 358 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8373 (m-30) REVERT: O 364 GLN cc_start: 0.7706 (tt0) cc_final: 0.6951 (tm-30) outliers start: 87 outliers final: 55 residues processed: 507 average time/residue: 1.8301 time to fit residues: 1042.7381 Evaluate side-chains 485 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 423 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 311 ASN Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain G residue 336 GLN Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain H residue 386 ASP Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 256 THR Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 325 SER Chi-restraints excluded: chain M residue 383 SER Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 294 GLN Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 193 ASP Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain O residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 274 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 281 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 141 ASN B 336 GLN C 336 GLN D 336 GLN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN J 336 GLN K 141 ASN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 ASN N 336 GLN O 336 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.143167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.114014 restraints weight = 28468.861| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.44 r_work: 0.3085 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 27420 Z= 0.266 Angle : 0.546 7.820 37395 Z= 0.276 Chirality : 0.047 0.173 4920 Planarity : 0.005 0.043 4530 Dihedral : 8.276 108.145 5790 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.60 % Allowed : 23.71 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.15), residues: 3285 helix: -0.11 (0.29), residues: 345 sheet: -0.28 (0.11), residues: 2130 loop : -0.56 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 245 PHE 0.008 0.001 PHE H 303 TYR 0.023 0.002 TYR F 394 ARG 0.005 0.001 ARG J 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14107.03 seconds wall clock time: 247 minutes 33.95 seconds (14853.95 seconds total)