Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 07:09:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ofh_12874/04_2023/7ofh_12874_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ofh_12874/04_2023/7ofh_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_12874/04_2023/7ofh_12874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ofh_12874/04_2023/7ofh_12874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ofh_12874/04_2023/7ofh_12874_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ofh_12874/04_2023/7ofh_12874_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 14.17, per 1000 atoms: 0.52 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: 9.96 Conformation dependent library (CDL) restraints added in 3.8 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: 2.14 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: 9.02 Time building geometry restraints manager: 10.68 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: 14910 21.18 - 42.36: 997 42.36 - 63.54: 353 63.54 - 84.73: 30 84.73 - 105.91: 15 Dihedral angle restraints: 16305 sinusoidal: 6390 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 16302 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.070 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 64.740 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.200 ------------------------------------------------------------------------------- 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 : 16.726 105.907 9795 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 % 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 *********************** 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 : 3.413 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 outliers start: 120 outliers final: 19 residues processed: 987 average time/residue: 1.2569 time to fit residues: 1455.2207 Evaluate side-chains 609 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 590 time to evaluate : 3.312 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 4 average time/residue: 0.4124 time to fit residues: 7.1402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 270 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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** 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 328 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN E 187 GLN E 328 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 ASN G 328 GLN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 361 ASN H 112 GLN H 187 GLN H 328 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 GLN H 361 ASN H 388 ASN I 328 GLN ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 ASN J 328 GLN ** J 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 328 GLN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 GLN L 388 ASN M 328 GLN M 349 GLN M 361 ASN N 187 GLN N 336 GLN N 361 ASN N 388 ASN O 112 GLN O 328 GLN O 336 GLN O 361 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 27420 Z= 0.239 Angle : 0.637 7.612 37395 Z= 0.325 Chirality : 0.049 0.216 4920 Planarity : 0.005 0.045 4530 Dihedral : 10.133 89.022 3750 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 3.87 % 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: -2.67 (0.14), residues: 3285 helix: -1.74 (0.25), residues: 345 sheet: -1.70 (0.10), residues: 2235 loop : -0.97 (0.22), residues: 705 *********************** 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 654 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 535 time to evaluate : 3.312 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 outliers start: 119 outliers final: 44 residues processed: 615 average time/residue: 1.5460 time to fit residues: 1082.5928 Evaluate side-chains 551 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 507 time to evaluate : 3.400 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 31 residues processed: 13 average time/residue: 0.8783 time to fit residues: 18.5916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 313 optimal weight: 4.9990 chunk 339 optimal weight: 6.9990 chunk 279 optimal weight: 10.0000 chunk 311 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 251 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 C 328 GLN C 336 GLN D 336 GLN E 336 GLN F 141 ASN F 336 GLN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN J 336 GLN K 141 ASN K 187 GLN K 336 GLN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 344 ASN N 187 GLN N 336 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 27420 Z= 0.347 Angle : 0.659 8.012 37395 Z= 0.332 Chirality : 0.049 0.185 4920 Planarity : 0.005 0.044 4530 Dihedral : 8.911 86.393 3750 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer Outliers : 4.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.60 (0.14), residues: 3285 helix: -1.18 (0.33), residues: 255 sheet: -1.03 (0.11), residues: 2175 loop : -0.46 (0.19), residues: 855 *********************** 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 613 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 473 time to evaluate : 3.485 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 outliers start: 140 outliers final: 61 residues processed: 575 average time/residue: 1.6768 time to fit residues: 1090.9725 Evaluate side-chains 511 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 450 time to evaluate : 3.425 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 46 residues processed: 16 average time/residue: 0.9099 time to fit residues: 22.5541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 6.9990 chunk 235 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 314 optimal weight: 1.9990 chunk 333 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 187 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN D 328 GLN D 336 GLN D 344 ASN E 328 GLN E 336 GLN F 141 ASN F 336 GLN G 328 GLN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 GLN H 336 GLN I 328 GLN ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN J 328 GLN J 336 GLN K 141 ASN L 328 GLN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN M 328 GLN N 336 GLN O 328 GLN O 336 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 27420 Z= 0.332 Angle : 0.618 7.891 37395 Z= 0.313 Chirality : 0.048 0.178 4920 Planarity : 0.005 0.046 4530 Dihedral : 8.487 90.366 3750 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 5.37 % 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: -1.12 (0.15), residues: 3285 helix: -0.85 (0.33), residues: 255 sheet: -0.68 (0.11), residues: 2175 loop : -0.29 (0.20), residues: 855 *********************** 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 622 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 457 time to evaluate : 3.231 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 outliers start: 165 outliers final: 69 residues processed: 579 average time/residue: 1.6718 time to fit residues: 1096.3900 Evaluate side-chains 520 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 451 time to evaluate : 3.331 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 54 residues processed: 15 average time/residue: 1.3451 time to fit residues: 28.9263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 0.2980 chunk 189 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 284 optimal weight: 10.0000 chunk 230 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 299 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 D 344 ASN 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 336 GLN ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN J 336 GLN K 141 ASN K 336 GLN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN N 141 ASN N 336 GLN O 336 GLN O 344 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 27420 Z= 0.233 Angle : 0.543 7.811 37395 Z= 0.276 Chirality : 0.046 0.168 4920 Planarity : 0.005 0.043 4530 Dihedral : 8.118 86.618 3750 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 4.59 % 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: -0.77 (0.15), residues: 3285 helix: -0.17 (0.34), residues: 255 sheet: -0.47 (0.11), residues: 2160 loop : -0.21 (0.21), residues: 870 *********************** 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 596 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 455 time to evaluate : 3.405 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 outliers start: 141 outliers final: 75 residues processed: 561 average time/residue: 1.6721 time to fit residues: 1064.4053 Evaluate side-chains 504 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 429 time to evaluate : 3.182 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 59 residues processed: 16 average time/residue: 0.8764 time to fit residues: 21.6451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 0.0870 chunk 300 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 333 optimal weight: 0.7980 chunk 277 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 175 optimal weight: 8.9990 overall best weight: 2.9362 ------------------------------------------------------------------------------- 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 328 GLN F 336 GLN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 GLN ** I 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** M 141 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: 0.8145 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 27420 Z= 0.312 Angle : 0.599 7.868 37395 Z= 0.303 Chirality : 0.047 0.169 4920 Planarity : 0.005 0.044 4530 Dihedral : 8.399 89.187 3750 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 4.65 % 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: -0.64 (0.15), residues: 3285 helix: 0.08 (0.33), residues: 255 sheet: -0.39 (0.11), residues: 2160 loop : -0.17 (0.21), residues: 870 *********************** 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 580 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 437 time to evaluate : 3.412 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 outliers start: 143 outliers final: 87 residues processed: 548 average time/residue: 1.7359 time to fit residues: 1073.4761 Evaluate side-chains 511 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 424 time to evaluate : 3.242 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 72 residues processed: 15 average time/residue: 1.1226 time to fit residues: 24.8391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 321 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 243 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 280 optimal weight: 0.5980 chunk 186 optimal weight: 0.9990 chunk 332 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 202 optimal weight: 0.4980 chunk 153 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 D 336 GLN F 141 ASN F 336 GLN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 GLN ** I 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** M 141 ASN 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: 0.8106 moved from start: 0.4404 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= 0.165 Angle : 0.504 7.207 37395 Z= 0.256 Chirality : 0.045 0.168 4920 Planarity : 0.004 0.039 4530 Dihedral : 7.765 87.388 3750 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.37 (0.15), residues: 3285 helix: 0.54 (0.34), residues: 255 sheet: -0.22 (0.11), residues: 2160 loop : -0.10 (0.21), residues: 870 *********************** 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 549 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 429 time to evaluate : 3.495 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 outliers start: 120 outliers final: 74 residues processed: 533 average time/residue: 1.7303 time to fit residues: 1044.4215 Evaluate side-chains 485 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 411 time to evaluate : 3.022 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 68 residues processed: 6 average time/residue: 0.7651 time to fit residues: 9.9186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 198 optimal weight: 0.8980 chunk 100 optimal weight: 0.0000 chunk 65 optimal weight: 7.9990 chunk 64 optimal weight: 0.4980 chunk 211 optimal weight: 7.9990 chunk 226 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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 ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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** M 141 ASN 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: 0.8131 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 27420 Z= 0.255 Angle : 0.559 7.623 37395 Z= 0.283 Chirality : 0.046 0.160 4920 Planarity : 0.005 0.039 4530 Dihedral : 8.012 86.662 3750 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 3.87 % 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: -0.34 (0.15), residues: 3285 helix: 0.50 (0.34), residues: 255 sheet: -0.19 (0.11), residues: 2160 loop : -0.10 (0.21), residues: 870 *********************** 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 544 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 425 time to evaluate : 3.318 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 outliers start: 119 outliers final: 80 residues processed: 523 average time/residue: 1.8239 time to fit residues: 1075.8700 Evaluate side-chains 501 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 421 time to evaluate : 3.263 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 68 residues processed: 12 average time/residue: 0.9844 time to fit residues: 18.9601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 302 optimal weight: 10.0000 chunk 318 optimal weight: 6.9990 chunk 290 optimal weight: 7.9990 chunk 309 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 280 optimal weight: 0.5980 chunk 293 optimal weight: 3.9990 chunk 308 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 G 336 GLN H 187 GLN H 328 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 GLN J 141 ASN ** J 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 ASN L 336 GLN M 141 ASN N 141 ASN N 336 GLN O 311 ASN O 336 GLN O 344 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4476 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= 0.381 Angle : 0.649 9.308 37395 Z= 0.326 Chirality : 0.048 0.182 4920 Planarity : 0.005 0.047 4530 Dihedral : 8.618 92.580 3750 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 3.74 % 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: -0.46 (0.15), residues: 3285 helix: 0.28 (0.34), residues: 255 sheet: -0.26 (0.11), residues: 2160 loop : -0.13 (0.21), residues: 870 *********************** 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 551 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 436 time to evaluate : 3.564 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 outliers start: 115 outliers final: 79 residues processed: 529 average time/residue: 1.7684 time to fit residues: 1053.7128 Evaluate side-chains 495 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 416 time to evaluate : 3.498 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 71 residues processed: 8 average time/residue: 1.2183 time to fit residues: 16.1105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 203 optimal weight: 6.9990 chunk 327 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 343 optimal weight: 6.9990 chunk 316 optimal weight: 7.9990 chunk 273 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 211 optimal weight: 0.4980 chunk 167 optimal weight: 6.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 D 336 GLN D 344 ASN F 141 ASN F 336 GLN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN J 336 GLN K 141 ASN M 141 ASN N 141 ASN N 336 GLN O 336 GLN ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4538 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= 0.311 Angle : 0.605 7.930 37395 Z= 0.304 Chirality : 0.047 0.187 4920 Planarity : 0.005 0.043 4530 Dihedral : 8.392 90.756 3750 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 3.06 % 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: -0.39 (0.15), residues: 3285 helix: 0.39 (0.34), residues: 255 sheet: -0.22 (0.11), residues: 2160 loop : -0.11 (0.21), residues: 870 ********************** 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 512 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 418 time to evaluate : 3.204 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 outliers start: 94 outliers final: 76 residues processed: 504 average time/residue: 1.7968 time to fit residues: 1024.3638 Evaluate side-chains 485 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 409 time to evaluate : 3.175 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 71 residues processed: 5 average time/residue: 1.2116 time to fit residues: 11.2599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 0.6980 chunk 291 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 252 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 274 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 281 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 50 optimal weight: 0.0770 overall best weight: 1.3142 ------------------------------------------------------------------------------- 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 D 336 GLN F 141 ASN F 336 GLN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 GLN J 141 ASN J 336 GLN K 141 ASN M 141 ASN N 141 ASN N 336 GLN O 336 GLN ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.145563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.116731 restraints weight = 28061.674| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.45 r_work: 0.3113 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 27420 Z= 0.183 Angle : 0.529 8.073 37395 Z= 0.267 Chirality : 0.045 0.165 4920 Planarity : 0.004 0.039 4530 Dihedral : 7.845 87.375 3750 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3285 helix: 0.70 (0.35), residues: 255 sheet: -0.11 (0.12), residues: 2160 loop : -0.05 (0.21), residues: 870 =============================================================================== Job complete usr+sys time: 14096.18 seconds wall clock time: 248 minutes 51.27 seconds (14931.27 seconds total)