Starting phenix.real_space_refine on Sun Aug 11 08:26:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/08_2024/7o1q_12696.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/08_2024/7o1q_12696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/08_2024/7o1q_12696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/08_2024/7o1q_12696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/08_2024/7o1q_12696.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/08_2024/7o1q_12696.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 49 5.16 5 C 10402 2.51 5 N 2842 2.21 5 O 3220 1.98 5 H 15921 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 32434 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4636 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain: "B" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4633 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain: "C" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4633 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain: "D" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4633 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain: "E" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4633 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain: "F" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4633 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain: "G" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4633 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Time building chain proxies: 14.06, per 1000 atoms: 0.43 Number of scatterers: 32434 At special positions: 0 Unit cell: (112.27, 112.27, 111.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 O 3220 8.00 N 2842 7.00 C 10402 6.00 H 15921 1.00 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: 26.56 Conformation dependent library (CDL) restraints added in 3.3 seconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3822 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 29 sheets defined 3.8% alpha, 58.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 217 through 222 removed outlier: 4.010A pdb=" N SER A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 217 through 222 removed outlier: 4.010A pdb=" N SER B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 217 through 222 removed outlier: 4.010A pdb=" N SER C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 217 through 222 removed outlier: 4.010A pdb=" N SER D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 217 through 222 removed outlier: 4.010A pdb=" N SER E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 217 through 222 removed outlier: 4.010A pdb=" N SER F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 209 Processing helix chain 'G' and resid 217 through 222 removed outlier: 4.010A pdb=" N SER G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 29 removed outlier: 6.577A pdb=" N THR A 233 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE A 98 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY A 77 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU A 70 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS A 75 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER A 82 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 166 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY A 77 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU A 70 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS A 75 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS A 75 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TRP A 260 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY A 77 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU A 258 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ALA A 79 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR A 256 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP A 254 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 83 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP A 255 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ASP A 272 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN A 257 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR A 270 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N HIS A 259 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR A 268 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 127 removed outlier: 7.798A pdb=" N PHE A 109 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL A 149 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 143 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE A 136 " --> pdb=" O PHE G 124 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE G 124 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 138 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE G 109 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL G 149 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY G 143 " --> pdb=" O TYR G 115 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE G 136 " --> pdb=" O PHE F 124 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE F 124 " --> pdb=" O ILE G 136 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY G 138 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE F 109 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL F 149 " --> pdb=" O PHE F 109 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY F 143 " --> pdb=" O TYR F 115 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE F 136 " --> pdb=" O PHE E 124 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE E 124 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY F 138 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE E 109 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL E 149 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY E 143 " --> pdb=" O TYR E 115 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER E 131 " --> pdb=" O GLU E 127 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE E 136 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE D 124 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY E 138 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE D 109 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL D 149 " --> pdb=" O PHE D 109 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 143 " --> pdb=" O TYR D 115 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE D 136 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE C 124 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY D 138 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE C 109 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N VAL C 149 " --> pdb=" O PHE C 109 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY C 143 " --> pdb=" O TYR C 115 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE C 136 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE B 124 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 138 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE B 109 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL B 149 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY B 143 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE B 136 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A 124 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 138 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 29 removed outlier: 6.577A pdb=" N THR B 233 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE B 98 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY B 77 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU B 70 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS B 75 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER B 82 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY B 166 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY B 77 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU B 70 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS B 75 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS B 75 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N TRP B 260 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY B 77 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 258 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ALA B 79 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR B 256 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP B 254 " --> pdb=" O PRO B 81 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 83 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASP B 255 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ASP B 272 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLN B 257 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR B 270 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N HIS B 259 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR B 268 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 175 Processing sheet with id=AB1, first strand: chain 'C' and resid 20 through 29 removed outlier: 6.578A pdb=" N THR C 233 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE C 98 " --> pdb=" O THR C 233 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.959A pdb=" N GLY C 77 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU C 70 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS C 75 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER C 82 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY C 166 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.959A pdb=" N GLY C 77 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU C 70 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS C 75 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS C 75 " --> pdb=" O TRP C 260 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TRP C 260 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY C 77 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU C 258 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ALA C 79 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR C 256 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP C 254 " --> pdb=" O PRO C 81 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 83 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASP C 255 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP C 272 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLN C 257 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR C 270 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N HIS C 259 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR C 268 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 174 through 175 Processing sheet with id=AB5, first strand: chain 'D' and resid 20 through 29 removed outlier: 6.578A pdb=" N THR D 233 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE D 98 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY D 77 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLU D 70 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LYS D 75 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER D 82 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY D 166 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY D 77 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLU D 70 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LYS D 75 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS D 75 " --> pdb=" O TRP D 260 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N TRP D 260 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY D 77 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU D 258 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ALA D 79 " --> pdb=" O TYR D 256 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR D 256 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASP D 254 " --> pdb=" O PRO D 81 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 83 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP D 255 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ASP D 272 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLN D 257 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR D 270 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N HIS D 259 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR D 268 " --> pdb=" O HIS D 259 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 174 through 175 Processing sheet with id=AB9, first strand: chain 'E' and resid 20 through 29 removed outlier: 6.578A pdb=" N THR E 233 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE E 98 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU E 70 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS E 75 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N SER E 82 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY E 166 " --> pdb=" O GLU E 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU E 70 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS E 75 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS E 75 " --> pdb=" O TRP E 260 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TRP E 260 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY E 77 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU E 258 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ALA E 79 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR E 256 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP E 254 " --> pdb=" O PRO E 81 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA E 83 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASP E 255 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ASP E 272 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN E 257 " --> pdb=" O THR E 270 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR E 270 " --> pdb=" O GLN E 257 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N HIS E 259 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR E 268 " --> pdb=" O HIS E 259 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 174 through 175 Processing sheet with id=AC4, first strand: chain 'F' and resid 20 through 29 removed outlier: 6.577A pdb=" N THR F 233 " --> pdb=" O ILE F 98 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE F 98 " --> pdb=" O THR F 233 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 66 through 70 removed outlier: 6.959A pdb=" N GLY F 77 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU F 70 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LYS F 75 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER F 82 " --> pdb=" O PHE F 171 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY F 166 " --> pdb=" O GLU F 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 66 through 70 removed outlier: 6.959A pdb=" N GLY F 77 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU F 70 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LYS F 75 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS F 75 " --> pdb=" O TRP F 260 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TRP F 260 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY F 77 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU F 258 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ALA F 79 " --> pdb=" O TYR F 256 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR F 256 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP F 254 " --> pdb=" O PRO F 81 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA F 83 " --> pdb=" O VAL F 252 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP F 255 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP F 272 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN F 257 " --> pdb=" O THR F 270 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR F 270 " --> pdb=" O GLN F 257 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N HIS F 259 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR F 268 " --> pdb=" O HIS F 259 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 174 through 175 Processing sheet with id=AC8, first strand: chain 'G' and resid 20 through 29 removed outlier: 6.578A pdb=" N THR G 233 " --> pdb=" O ILE G 98 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE G 98 " --> pdb=" O THR G 233 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY G 77 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU G 70 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS G 75 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N SER G 82 " --> pdb=" O PHE G 171 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY G 166 " --> pdb=" O GLU G 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY G 77 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU G 70 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS G 75 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS G 75 " --> pdb=" O TRP G 260 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TRP G 260 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY G 77 " --> pdb=" O LEU G 258 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU G 258 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ALA G 79 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR G 256 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP G 254 " --> pdb=" O PRO G 81 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA G 83 " --> pdb=" O VAL G 252 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASP G 255 " --> pdb=" O ASP G 272 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP G 272 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLN G 257 " --> pdb=" O THR G 270 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR G 270 " --> pdb=" O GLN G 257 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N HIS G 259 " --> pdb=" O THR G 268 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR G 268 " --> pdb=" O HIS G 259 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 174 through 175 763 hydrogen bonds defined for protein. 2121 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: 12.97 Time building geometry restraints manager: 27.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15921 1.03 - 1.22: 0 1.22 - 1.41: 7260 1.41 - 1.61: 9540 1.61 - 1.80: 98 Bond restraints: 32819 Sorted by residual: bond pdb=" CB PRO F 103 " pdb=" CG PRO F 103 " ideal model delta sigma weight residual 1.506 1.445 0.061 3.90e-02 6.57e+02 2.43e+00 bond pdb=" CB PRO A 103 " pdb=" CG PRO A 103 " ideal model delta sigma weight residual 1.506 1.446 0.060 3.90e-02 6.57e+02 2.40e+00 bond pdb=" CB PRO G 103 " pdb=" CG PRO G 103 " ideal model delta sigma weight residual 1.506 1.446 0.060 3.90e-02 6.57e+02 2.38e+00 bond pdb=" CB PRO E 103 " pdb=" CG PRO E 103 " ideal model delta sigma weight residual 1.506 1.446 0.060 3.90e-02 6.57e+02 2.37e+00 bond pdb=" CB PRO B 103 " pdb=" CG PRO B 103 " ideal model delta sigma weight residual 1.506 1.446 0.060 3.90e-02 6.57e+02 2.36e+00 ... (remaining 32814 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.86: 276 105.86 - 112.90: 37654 112.90 - 119.94: 8699 119.94 - 126.98: 12204 126.98 - 134.02: 239 Bond angle restraints: 59072 Sorted by residual: angle pdb=" N SER F 262 " pdb=" CA SER F 262 " pdb=" CB SER F 262 " ideal model delta sigma weight residual 114.17 110.74 3.43 1.14e+00 7.69e-01 9.04e+00 angle pdb=" N SER G 262 " pdb=" CA SER G 262 " pdb=" CB SER G 262 " ideal model delta sigma weight residual 114.17 110.74 3.43 1.14e+00 7.69e-01 9.04e+00 angle pdb=" N SER B 262 " pdb=" CA SER B 262 " pdb=" CB SER B 262 " ideal model delta sigma weight residual 114.17 110.75 3.42 1.14e+00 7.69e-01 9.00e+00 angle pdb=" N SER A 262 " pdb=" CA SER A 262 " pdb=" CB SER A 262 " ideal model delta sigma weight residual 114.17 110.78 3.39 1.14e+00 7.69e-01 8.87e+00 angle pdb=" N SER D 262 " pdb=" CA SER D 262 " pdb=" CB SER D 262 " ideal model delta sigma weight residual 114.17 110.78 3.39 1.14e+00 7.69e-01 8.86e+00 ... (remaining 59067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 14722 17.84 - 35.68: 576 35.68 - 53.53: 136 53.53 - 71.37: 29 71.37 - 89.21: 14 Dihedral angle restraints: 15477 sinusoidal: 8274 harmonic: 7203 Sorted by residual: dihedral pdb=" CA PRO G 226 " pdb=" C PRO G 226 " pdb=" N ASP G 227 " pdb=" CA ASP G 227 " ideal model delta harmonic sigma weight residual 180.00 165.99 14.01 0 5.00e+00 4.00e-02 7.85e+00 dihedral pdb=" CA PRO C 226 " pdb=" C PRO C 226 " pdb=" N ASP C 227 " pdb=" CA ASP C 227 " ideal model delta harmonic sigma weight residual 180.00 166.03 13.97 0 5.00e+00 4.00e-02 7.81e+00 dihedral pdb=" CA PRO B 226 " pdb=" C PRO B 226 " pdb=" N ASP B 227 " pdb=" CA ASP B 227 " ideal model delta harmonic sigma weight residual 180.00 166.03 13.97 0 5.00e+00 4.00e-02 7.81e+00 ... (remaining 15474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1188 0.029 - 0.058: 826 0.058 - 0.087: 179 0.087 - 0.116: 166 0.116 - 0.145: 56 Chirality restraints: 2415 Sorted by residual: chirality pdb=" CA ILE A 232 " pdb=" N ILE A 232 " pdb=" C ILE A 232 " pdb=" CB ILE A 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE F 232 " pdb=" N ILE F 232 " pdb=" C ILE F 232 " pdb=" CB ILE F 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 2412 not shown) Planarity restraints: 4949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 159 " 0.019 5.00e-02 4.00e+02 2.83e-02 1.29e+00 pdb=" N PRO B 160 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 159 " -0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO F 160 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO F 160 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 160 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 159 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO C 160 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " 0.016 5.00e-02 4.00e+02 ... (remaining 4946 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 833 2.11 - 2.73: 58933 2.73 - 3.35: 88631 3.35 - 3.98: 123965 3.98 - 4.60: 194743 Nonbonded interactions: 467105 Sorted by model distance: nonbonded pdb=" HG1 THR A 60 " pdb=" OH TYR G 101 " model vdw 1.486 2.450 nonbonded pdb=" OH TYR E 101 " pdb=" HG1 THR F 60 " model vdw 1.488 2.450 nonbonded pdb=" OH TYR B 101 " pdb=" HG1 THR C 60 " model vdw 1.489 2.450 nonbonded pdb=" OH TYR A 101 " pdb=" HG1 THR B 60 " model vdw 1.489 2.450 nonbonded pdb=" OH TYR C 101 " pdb=" HG1 THR D 60 " model vdw 1.489 2.450 ... (remaining 467100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name HA or name HB1 or name HB2 or name HB3)) or resid 2 through 293)) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.480 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: 0.520 Extract box with map and model: 1.350 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 104.630 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.007 0.061 16898 Z= 0.434 Angle : 0.550 4.080 22869 Z= 0.322 Chirality : 0.047 0.145 2415 Planarity : 0.003 0.028 2968 Dihedral : 9.972 89.210 6202 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.39 % Allowed : 2.33 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.18), residues: 2037 helix: -4.43 (0.08), residues: 42 sheet: 0.32 (0.16), residues: 1057 loop : -0.35 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 274 HIS 0.003 0.001 HIS B 48 PHE 0.010 0.001 PHE E 125 TYR 0.014 0.002 TYR G 65 ARG 0.002 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 370 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.0822 (tpt) cc_final: -0.0917 (ppp) REVERT: A 170 ILE cc_start: 0.9196 (mm) cc_final: 0.8932 (tp) REVERT: B 140 MET cc_start: 0.1324 (tpt) cc_final: -0.0810 (ppp) REVERT: B 170 ILE cc_start: 0.9186 (mm) cc_final: 0.8892 (tp) REVERT: C 140 MET cc_start: 0.1085 (tpt) cc_final: -0.0644 (ppp) REVERT: C 162 ASP cc_start: 0.7892 (p0) cc_final: 0.7688 (p0) REVERT: C 170 ILE cc_start: 0.9209 (mm) cc_final: 0.8910 (tp) REVERT: D 140 MET cc_start: 0.1541 (tpt) cc_final: -0.0895 (ppp) REVERT: D 170 ILE cc_start: 0.9166 (mm) cc_final: 0.8896 (tp) REVERT: E 140 MET cc_start: 0.1484 (tpt) cc_final: -0.0027 (ppp) REVERT: E 162 ASP cc_start: 0.7893 (p0) cc_final: 0.7688 (p0) REVERT: E 170 ILE cc_start: 0.9104 (mm) cc_final: 0.8859 (tp) REVERT: F 140 MET cc_start: 0.1209 (tpt) cc_final: -0.0470 (ppp) REVERT: F 170 ILE cc_start: 0.9201 (mm) cc_final: 0.8938 (tp) REVERT: G 140 MET cc_start: 0.0599 (tpt) cc_final: -0.0794 (ppp) REVERT: G 162 ASP cc_start: 0.7977 (p0) cc_final: 0.7773 (p0) REVERT: G 170 ILE cc_start: 0.9166 (mm) cc_final: 0.8900 (tp) outliers start: 7 outliers final: 0 residues processed: 377 average time/residue: 0.8289 time to fit residues: 424.9211 Evaluate side-chains 214 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 5.9990 chunk 153 optimal weight: 0.6980 chunk 85 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 50.0000 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 184 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 ASN F 177 GLN G 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16898 Z= 0.157 Angle : 0.517 5.057 22869 Z= 0.277 Chirality : 0.047 0.163 2415 Planarity : 0.003 0.045 2968 Dihedral : 4.578 17.123 2219 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.55 % Allowed : 9.41 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.12 (0.19), residues: 2037 helix: -4.41 (0.10), residues: 42 sheet: 0.38 (0.16), residues: 1043 loop : 0.12 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 260 HIS 0.005 0.001 HIS E 48 PHE 0.006 0.001 PHE G 124 TYR 0.011 0.001 TYR C 65 ARG 0.006 0.001 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 254 time to evaluate : 2.813 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: A 170 ILE cc_start: 0.9080 (mm) cc_final: 0.8876 (tp) REVERT: B 170 ILE cc_start: 0.9101 (mm) cc_final: 0.8891 (tp) REVERT: C 170 ILE cc_start: 0.9101 (mm) cc_final: 0.8890 (tp) REVERT: F 140 MET cc_start: 0.1129 (tpt) cc_final: -0.0912 (ppp) REVERT: F 170 ILE cc_start: 0.9086 (mm) cc_final: 0.8861 (tp) outliers start: 10 outliers final: 10 residues processed: 261 average time/residue: 0.8499 time to fit residues: 312.1886 Evaluate side-chains 235 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 225 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 139 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 153 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN C 177 GLN C 214 ASN E 177 GLN F 177 GLN F 259 HIS G 259 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16898 Z= 0.255 Angle : 0.489 4.220 22869 Z= 0.262 Chirality : 0.046 0.148 2415 Planarity : 0.003 0.047 2968 Dihedral : 4.535 20.847 2219 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.83 % Allowed : 10.41 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.20 (0.19), residues: 2037 helix: -4.35 (0.10), residues: 42 sheet: 0.43 (0.16), residues: 1057 loop : 0.17 (0.22), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 187 HIS 0.006 0.001 HIS F 259 PHE 0.007 0.001 PHE E 196 TYR 0.013 0.001 TYR C 65 ARG 0.008 0.000 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 230 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 240 average time/residue: 0.8556 time to fit residues: 285.7060 Evaluate side-chains 228 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 214 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 139 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 185 optimal weight: 50.0000 chunk 196 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 ASN D 177 GLN F 177 GLN G 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16898 Z= 0.136 Angle : 0.464 5.141 22869 Z= 0.247 Chirality : 0.046 0.146 2415 Planarity : 0.003 0.030 2968 Dihedral : 4.295 13.692 2219 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.72 % Allowed : 10.91 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.19), residues: 2037 helix: -4.33 (0.11), residues: 42 sheet: 0.39 (0.16), residues: 1071 loop : 0.22 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 286 HIS 0.005 0.001 HIS E 48 PHE 0.007 0.001 PHE A 196 TYR 0.009 0.001 TYR E 65 ARG 0.004 0.000 ARG E 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 252 time to evaluate : 2.667 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: B 234 MET cc_start: 0.7702 (ttm) cc_final: 0.7261 (tpp) REVERT: F 140 MET cc_start: 0.0439 (tpt) cc_final: -0.1619 (ppp) outliers start: 13 outliers final: 12 residues processed: 261 average time/residue: 0.7906 time to fit residues: 288.8123 Evaluate side-chains 238 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 226 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 139 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 50.0000 chunk 176 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 259 HIS B 105 ASN B 177 GLN C 105 ASN C 177 GLN C 214 ASN D 105 ASN E 105 ASN E 177 GLN E 259 HIS F 177 GLN F 259 HIS G 105 ASN G 177 GLN G 259 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16898 Z= 0.341 Angle : 0.498 4.837 22869 Z= 0.269 Chirality : 0.046 0.139 2415 Planarity : 0.004 0.070 2968 Dihedral : 4.498 24.296 2219 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.83 % Allowed : 11.90 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.13 (0.19), residues: 2037 helix: -3.92 (0.13), residues: 42 sheet: 0.44 (0.16), residues: 1057 loop : 0.01 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 286 HIS 0.005 0.001 HIS C 48 PHE 0.012 0.001 PHE F 196 TYR 0.012 0.001 TYR A 65 ARG 0.004 0.000 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 214 time to evaluate : 2.791 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 outliers start: 15 outliers final: 14 residues processed: 224 average time/residue: 0.8454 time to fit residues: 261.8589 Evaluate side-chains 219 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 205 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 139 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 0.6980 chunk 176 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN C 177 GLN E 177 GLN E 259 HIS F 177 GLN F 259 HIS G 177 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16898 Z= 0.233 Angle : 0.471 4.628 22869 Z= 0.252 Chirality : 0.045 0.144 2415 Planarity : 0.004 0.057 2968 Dihedral : 4.392 20.404 2219 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.83 % Allowed : 11.46 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.20 (0.19), residues: 2037 helix: -3.70 (0.15), residues: 42 sheet: 0.46 (0.16), residues: 1078 loop : 0.07 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 286 HIS 0.004 0.001 HIS E 48 PHE 0.008 0.001 PHE D 196 TYR 0.010 0.001 TYR A 65 ARG 0.004 0.000 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 219 time to evaluate : 2.484 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 outliers start: 15 outliers final: 15 residues processed: 228 average time/residue: 0.8219 time to fit residues: 257.4866 Evaluate side-chains 224 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 209 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 139 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 111 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 109 optimal weight: 0.1980 chunk 195 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN G 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 16898 Z= 0.158 Angle : 0.457 4.794 22869 Z= 0.243 Chirality : 0.046 0.143 2415 Planarity : 0.003 0.048 2968 Dihedral : 4.264 16.746 2219 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.72 % Allowed : 11.46 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.23 (0.19), residues: 2037 helix: -3.12 (0.27), residues: 42 sheet: 0.43 (0.16), residues: 1085 loop : 0.13 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 260 HIS 0.004 0.001 HIS E 48 PHE 0.022 0.001 PHE B 196 TYR 0.009 0.001 TYR E 65 ARG 0.003 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 228 time to evaluate : 2.725 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 outliers start: 13 outliers final: 13 residues processed: 237 average time/residue: 0.8057 time to fit residues: 264.6288 Evaluate side-chains 232 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 219 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 139 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 307, in __init__ self.caller(self.nqh_flips) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 710, in nqh_flips phenix.refinement.nqh_flips.ncs_aware(model = self.model, log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/nqh_flips.py", line 12, in __init__ self.model.flip_nqh() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/model/model.py", line 698, in flip_nqh mon_lib_srv = self.get_mon_lib_srv()) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/rotamer/nqh.py", line 218, in flip pdb_hierarchy = tmp_pdb_hierarchy) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/rotamer/nqh.py", line 82, in get_nqh_flips output = run_reduce(pdb_string=pdb_string, remove_hydrogens=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/rotamer/nqh.py", line 143, in run_reduce check_and_report_reduce_failure(clean, pdb_string, "reduce_failure.pdb") File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/validation/clashscore.py", line 647, in check_and_report_reduce_failure f.write(input_lines) IOError: [Errno 28] No space left on device