Starting phenix.real_space_refine (version: dev) on Fri Mar 17 17:15:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/03_2023/6bqw_7134_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/03_2023/6bqw_7134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/03_2023/6bqw_7134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/03_2023/6bqw_7134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/03_2023/6bqw_7134_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/03_2023/6bqw_7134_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19953 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2186 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 267} Chain: "B" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2186 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 267} Chain: "C" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2186 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 267} Chain: "D" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2186 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 267} Chain: "E" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2186 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 267} Chain: "F" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2186 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 267} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2186 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 267} Chain: "H" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2186 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 267} Chain: "I" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2186 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 267} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.88, per 1000 atoms: 0.55 Number of scatterers: 19953 At special positions: 0 Unit cell: (100, 100, 270, 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 135 16.00 P 27 15.00 O 3942 8.00 N 3168 7.00 C 12681 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: 8.41 Conformation dependent library (CDL) restraints added in 2.7 seconds 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4518 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 36 sheets defined 31.3% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.870A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 201 through 211 Processing helix chain 'A' and resid 228 through 238 Processing helix chain 'A' and resid 254 through 274 removed outlier: 4.691A pdb=" N ASN A 258 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER A 259 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 266 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY A 267 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ARG A 268 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A 274 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 83 through 99 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.870A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 123 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 201 through 211 Processing helix chain 'B' and resid 228 through 238 Processing helix chain 'B' and resid 254 through 274 removed outlier: 4.691A pdb=" N ASN B 258 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER B 259 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B 266 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY B 267 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ARG B 268 " --> pdb=" O LYS B 265 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE B 274 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 83 through 99 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.870A pdb=" N VAL C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 123 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 157 Processing helix chain 'C' and resid 201 through 211 Processing helix chain 'C' and resid 228 through 238 Processing helix chain 'C' and resid 254 through 274 removed outlier: 4.691A pdb=" N ASN C 258 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER C 259 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR C 266 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY C 267 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ARG C 268 " --> pdb=" O LYS C 265 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE C 274 " --> pdb=" O GLU C 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 83 through 99 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.870A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D 123 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 157 Processing helix chain 'D' and resid 201 through 211 Processing helix chain 'D' and resid 228 through 238 Processing helix chain 'D' and resid 254 through 274 removed outlier: 4.691A pdb=" N ASN D 258 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER D 259 " --> pdb=" O TYR D 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR D 266 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY D 267 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ARG D 268 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE D 274 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 64 Processing helix chain 'E' and resid 83 through 99 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.869A pdb=" N VAL E 116 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL E 123 " --> pdb=" O LYS E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 157 Processing helix chain 'E' and resid 201 through 211 Processing helix chain 'E' and resid 228 through 238 Processing helix chain 'E' and resid 254 through 274 removed outlier: 4.691A pdb=" N ASN E 258 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER E 259 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR E 266 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLY E 267 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ARG E 268 " --> pdb=" O LYS E 265 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE E 274 " --> pdb=" O GLU E 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 64 Processing helix chain 'F' and resid 83 through 99 Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.871A pdb=" N VAL F 116 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL F 123 " --> pdb=" O LYS F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 157 Processing helix chain 'F' and resid 201 through 211 Processing helix chain 'F' and resid 228 through 238 Processing helix chain 'F' and resid 254 through 274 removed outlier: 4.691A pdb=" N ASN F 258 " --> pdb=" O TYR F 255 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER F 259 " --> pdb=" O TYR F 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR F 266 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLY F 267 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ARG F 268 " --> pdb=" O LYS F 265 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE F 274 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 64 Processing helix chain 'G' and resid 83 through 99 Processing helix chain 'G' and resid 112 through 126 removed outlier: 4.870A pdb=" N VAL G 116 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL G 123 " --> pdb=" O LYS G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 157 Processing helix chain 'G' and resid 201 through 211 Processing helix chain 'G' and resid 228 through 238 Processing helix chain 'G' and resid 254 through 274 removed outlier: 4.691A pdb=" N ASN G 258 " --> pdb=" O TYR G 255 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER G 259 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR G 266 " --> pdb=" O LEU G 263 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY G 267 " --> pdb=" O LEU G 264 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ARG G 268 " --> pdb=" O LYS G 265 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE G 274 " --> pdb=" O GLU G 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 64 Processing helix chain 'H' and resid 83 through 99 Processing helix chain 'H' and resid 112 through 126 removed outlier: 4.870A pdb=" N VAL H 116 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL H 123 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 157 Processing helix chain 'H' and resid 201 through 211 Processing helix chain 'H' and resid 228 through 238 Processing helix chain 'H' and resid 254 through 274 removed outlier: 4.692A pdb=" N ASN H 258 " --> pdb=" O TYR H 255 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER H 259 " --> pdb=" O TYR H 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR H 266 " --> pdb=" O LEU H 263 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY H 267 " --> pdb=" O LEU H 264 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ARG H 268 " --> pdb=" O LYS H 265 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE H 274 " --> pdb=" O GLU H 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 64 Processing helix chain 'I' and resid 83 through 99 Processing helix chain 'I' and resid 112 through 126 removed outlier: 4.870A pdb=" N VAL I 116 " --> pdb=" O GLU I 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL I 123 " --> pdb=" O LYS I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 157 Processing helix chain 'I' and resid 201 through 211 Processing helix chain 'I' and resid 228 through 238 Processing helix chain 'I' and resid 254 through 274 removed outlier: 4.691A pdb=" N ASN I 258 " --> pdb=" O TYR I 255 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER I 259 " --> pdb=" O TYR I 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR I 266 " --> pdb=" O LEU I 263 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY I 267 " --> pdb=" O LEU I 264 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ARG I 268 " --> pdb=" O LYS I 265 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE I 274 " --> pdb=" O GLU I 271 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 15 through 17 removed outlier: 4.633A pdb=" N VAL A 6 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN A 105 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 7 " --> pdb=" O ASN A 105 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE A 107 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 147 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N CYS A 110 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA A 149 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 33 through 35 Processing sheet with id= C, first strand: chain 'A' and resid 128 through 131 Processing sheet with id= D, first strand: chain 'A' and resid 243 through 245 removed outlier: 6.309A pdb=" N ILE A 221 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A 165 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR A 224 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL A 167 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 15 through 17 removed outlier: 4.633A pdb=" N VAL B 6 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN B 105 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 7 " --> pdb=" O ASN B 105 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE B 107 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 147 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N CYS B 110 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA B 149 " --> pdb=" O CYS B 110 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 33 through 35 Processing sheet with id= G, first strand: chain 'B' and resid 128 through 131 Processing sheet with id= H, first strand: chain 'B' and resid 243 through 245 removed outlier: 6.309A pdb=" N ILE B 221 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 165 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR B 224 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL B 167 " --> pdb=" O THR B 224 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 15 through 17 removed outlier: 4.633A pdb=" N VAL C 6 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN C 105 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE C 7 " --> pdb=" O ASN C 105 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE C 107 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL C 147 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N CYS C 110 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA C 149 " --> pdb=" O CYS C 110 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 33 through 35 Processing sheet with id= K, first strand: chain 'C' and resid 128 through 131 Processing sheet with id= L, first strand: chain 'C' and resid 243 through 245 removed outlier: 6.310A pdb=" N ILE C 221 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 165 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR C 224 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL C 167 " --> pdb=" O THR C 224 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 15 through 17 removed outlier: 4.633A pdb=" N VAL D 6 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN D 105 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE D 7 " --> pdb=" O ASN D 105 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE D 107 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL D 147 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N CYS D 110 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA D 149 " --> pdb=" O CYS D 110 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 33 through 35 Processing sheet with id= O, first strand: chain 'D' and resid 128 through 131 Processing sheet with id= P, first strand: chain 'D' and resid 243 through 245 removed outlier: 6.310A pdb=" N ILE D 221 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL D 165 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR D 224 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL D 167 " --> pdb=" O THR D 224 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 15 through 17 removed outlier: 4.632A pdb=" N VAL E 6 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN E 105 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE E 7 " --> pdb=" O ASN E 105 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE E 107 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL E 147 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N CYS E 110 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA E 149 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 33 through 35 Processing sheet with id= S, first strand: chain 'E' and resid 128 through 131 Processing sheet with id= T, first strand: chain 'E' and resid 243 through 245 removed outlier: 6.310A pdb=" N ILE E 221 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL E 165 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR E 224 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL E 167 " --> pdb=" O THR E 224 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 15 through 17 removed outlier: 4.633A pdb=" N VAL F 6 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN F 105 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE F 7 " --> pdb=" O ASN F 105 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE F 107 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL F 147 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N CYS F 110 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA F 149 " --> pdb=" O CYS F 110 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 33 through 35 Processing sheet with id= W, first strand: chain 'F' and resid 128 through 131 Processing sheet with id= X, first strand: chain 'F' and resid 243 through 245 removed outlier: 6.309A pdb=" N ILE F 221 " --> pdb=" O SER F 244 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL F 165 " --> pdb=" O VAL F 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR F 224 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL F 167 " --> pdb=" O THR F 224 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 15 through 17 removed outlier: 4.633A pdb=" N VAL G 6 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN G 105 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE G 7 " --> pdb=" O ASN G 105 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE G 107 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL G 147 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N CYS G 110 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA G 149 " --> pdb=" O CYS G 110 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 33 through 35 Processing sheet with id= AA, first strand: chain 'G' and resid 128 through 131 Processing sheet with id= AB, first strand: chain 'G' and resid 243 through 245 removed outlier: 6.309A pdb=" N ILE G 221 " --> pdb=" O SER G 244 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL G 165 " --> pdb=" O VAL G 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR G 224 " --> pdb=" O VAL G 165 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL G 167 " --> pdb=" O THR G 224 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 15 through 17 removed outlier: 4.633A pdb=" N VAL H 6 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN H 105 " --> pdb=" O THR H 5 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE H 7 " --> pdb=" O ASN H 105 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE H 107 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL H 147 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N CYS H 110 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA H 149 " --> pdb=" O CYS H 110 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 33 through 35 Processing sheet with id= AE, first strand: chain 'H' and resid 128 through 131 Processing sheet with id= AF, first strand: chain 'H' and resid 243 through 245 removed outlier: 6.309A pdb=" N ILE H 221 " --> pdb=" O SER H 244 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL H 165 " --> pdb=" O VAL H 222 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR H 224 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL H 167 " --> pdb=" O THR H 224 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 15 through 17 removed outlier: 4.633A pdb=" N VAL I 6 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN I 105 " --> pdb=" O THR I 5 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE I 7 " --> pdb=" O ASN I 105 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE I 107 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL I 147 " --> pdb=" O LEU I 108 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N CYS I 110 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA I 149 " --> pdb=" O CYS I 110 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 33 through 35 Processing sheet with id= AI, first strand: chain 'I' and resid 128 through 131 Processing sheet with id= AJ, first strand: chain 'I' and resid 243 through 245 removed outlier: 6.309A pdb=" N ILE I 221 " --> pdb=" O SER I 244 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL I 165 " --> pdb=" O VAL I 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR I 224 " --> pdb=" O VAL I 165 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL I 167 " --> pdb=" O THR I 224 " (cutoff:3.500A) 711 hydrogen bonds defined for protein. 1242 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: 7.76 Time building geometry restraints manager: 9.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5496 1.33 - 1.45: 4579 1.45 - 1.57: 10049 1.57 - 1.69: 18 1.69 - 1.82: 225 Bond restraints: 20367 Sorted by residual: bond pdb=" N3B ANP G 301 " pdb=" PG ANP G 301 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" N3B ANP A 301 " pdb=" PG ANP A 301 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" N3B ANP C 301 " pdb=" PG ANP C 301 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.05e+01 bond pdb=" N3B ANP H 301 " pdb=" PG ANP H 301 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.03e+01 bond pdb=" N3B ANP B 301 " pdb=" PG ANP B 301 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.03e+01 ... (remaining 20362 not shown) Histogram of bond angle deviations from ideal: 97.27 - 104.27: 247 104.27 - 111.26: 8235 111.26 - 118.26: 7078 118.26 - 125.26: 11755 125.26 - 132.26: 171 Bond angle restraints: 27486 Sorted by residual: angle pdb=" C LYS A 252 " pdb=" N PRO A 253 " pdb=" CA PRO A 253 " ideal model delta sigma weight residual 119.93 128.43 -8.50 1.07e+00 8.73e-01 6.31e+01 angle pdb=" C LYS E 252 " pdb=" N PRO E 253 " pdb=" CA PRO E 253 " ideal model delta sigma weight residual 119.93 128.43 -8.50 1.07e+00 8.73e-01 6.30e+01 angle pdb=" C LYS G 252 " pdb=" N PRO G 253 " pdb=" CA PRO G 253 " ideal model delta sigma weight residual 119.93 128.42 -8.49 1.07e+00 8.73e-01 6.30e+01 angle pdb=" C LYS I 252 " pdb=" N PRO I 253 " pdb=" CA PRO I 253 " ideal model delta sigma weight residual 119.93 128.41 -8.48 1.07e+00 8.73e-01 6.28e+01 angle pdb=" C LYS H 252 " pdb=" N PRO H 253 " pdb=" CA PRO H 253 " ideal model delta sigma weight residual 119.93 128.40 -8.47 1.07e+00 8.73e-01 6.27e+01 ... (remaining 27481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 11808 35.79 - 71.58: 126 71.58 - 107.37: 9 107.37 - 143.16: 0 143.16 - 178.95: 9 Dihedral angle restraints: 11952 sinusoidal: 4788 harmonic: 7164 Sorted by residual: dihedral pdb=" CA CYS H 164 " pdb=" C CYS H 164 " pdb=" N VAL H 165 " pdb=" CA VAL H 165 " ideal model delta harmonic sigma weight residual -180.00 -155.75 -24.25 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA CYS E 164 " pdb=" C CYS E 164 " pdb=" N VAL E 165 " pdb=" CA VAL E 165 " ideal model delta harmonic sigma weight residual 180.00 -155.76 -24.24 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA CYS D 164 " pdb=" C CYS D 164 " pdb=" N VAL D 165 " pdb=" CA VAL D 165 " ideal model delta harmonic sigma weight residual 180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 11949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1739 0.061 - 0.123: 1002 0.123 - 0.184: 198 0.184 - 0.245: 22 0.245 - 0.307: 9 Chirality restraints: 2970 Sorted by residual: chirality pdb=" C2' ANP E 301 " pdb=" C1' ANP E 301 " pdb=" C3' ANP E 301 " pdb=" O2' ANP E 301 " both_signs ideal model delta sigma weight residual False -2.72 -2.42 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' ANP D 301 " pdb=" C1' ANP D 301 " pdb=" C3' ANP D 301 " pdb=" O2' ANP D 301 " both_signs ideal model delta sigma weight residual False -2.72 -2.42 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' ANP H 301 " pdb=" C1' ANP H 301 " pdb=" C3' ANP H 301 " pdb=" O2' ANP H 301 " both_signs ideal model delta sigma weight residual False -2.72 -2.42 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 2967 not shown) Planarity restraints: 3447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 164 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C CYS A 164 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS A 164 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 165 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 164 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C CYS C 164 " 0.043 2.00e-02 2.50e+03 pdb=" O CYS C 164 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL C 165 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 164 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C CYS D 164 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS D 164 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL D 165 " 0.014 2.00e-02 2.50e+03 ... (remaining 3444 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7575 2.83 - 3.34: 21147 3.34 - 3.86: 36580 3.86 - 4.38: 45001 4.38 - 4.90: 67985 Nonbonded interactions: 178288 Sorted by model distance: nonbonded pdb=" OG SER H 171 " pdb=" N LYS H 172 " model vdw 2.307 2.520 nonbonded pdb=" OG SER F 171 " pdb=" N LYS F 172 " model vdw 2.307 2.520 nonbonded pdb=" OG SER G 171 " pdb=" N LYS G 172 " model vdw 2.307 2.520 nonbonded pdb=" OG SER A 171 " pdb=" N LYS A 172 " model vdw 2.307 2.520 nonbonded pdb=" OG SER D 171 " pdb=" N LYS D 172 " model vdw 2.307 2.520 ... (remaining 178283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 27 5.49 5 S 135 5.16 5 C 12681 2.51 5 N 3168 2.21 5 O 3942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.100 Check model and map are aligned: 0.290 Process input model: 55.050 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.190 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 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 : 0.016 0.168 20367 Z= 1.053 Angle : 1.277 9.026 27486 Z= 0.806 Chirality : 0.073 0.307 2970 Planarity : 0.006 0.025 3447 Dihedral : 13.449 178.952 7434 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 5.86 % Allowed : 10.26 % Favored : 83.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -3.51 (0.14), residues: 2457 helix: -1.08 (0.16), residues: 747 sheet: -2.61 (0.17), residues: 432 loop : -3.07 (0.15), residues: 1278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 660 time to evaluate : 2.661 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: 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: 0 outliers final: 0 residues processed: 660 average time/residue: 0.4155 time to fit residues: 391.8309 Evaluate side-chains 360 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 2.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 220 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN A 144 HIS A 163 ASN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 HIS ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 105 ASN ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN E 144 HIS F 34 HIS ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN G 23 GLN G 34 HIS G 105 ASN ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 HIS ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 20367 Z= 0.220 Angle : 0.755 9.675 27486 Z= 0.407 Chirality : 0.046 0.191 2970 Planarity : 0.005 0.033 3447 Dihedral : 12.335 179.829 2745 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 2.52 % Allowed : 12.09 % Favored : 85.39 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -2.57 (0.16), residues: 2457 helix: -0.49 (0.18), residues: 729 sheet: -2.55 (0.18), residues: 549 loop : -2.00 (0.18), residues: 1179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 484 time to evaluate : 2.616 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: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 485 average time/residue: 0.3781 time to fit residues: 265.8892 Evaluate side-chains 318 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 2.496 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 183 optimal weight: 0.1980 chunk 150 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 221 optimal weight: 30.0000 chunk 238 optimal weight: 0.9990 chunk 196 optimal weight: 0.0370 chunk 219 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 HIS ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN ** H 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 20367 Z= 0.188 Angle : 0.682 8.410 27486 Z= 0.366 Chirality : 0.045 0.176 2970 Planarity : 0.004 0.042 3447 Dihedral : 11.983 175.126 2745 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 2.32 % Allowed : 13.19 % Favored : 84.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -2.44 (0.16), residues: 2457 helix: -0.46 (0.18), residues: 738 sheet: -2.41 (0.18), residues: 603 loop : -1.85 (0.19), residues: 1116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 2.615 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.3564 time to fit residues: 228.1621 Evaluate side-chains 296 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 24 optimal weight: 0.0010 chunk 105 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 221 optimal weight: 20.0000 chunk 234 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 HIS B 63 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 HIS ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 HIS ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS G 163 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS ** H 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 20367 Z= 0.184 Angle : 0.661 7.286 27486 Z= 0.356 Chirality : 0.045 0.218 2970 Planarity : 0.004 0.040 3447 Dihedral : 11.881 176.123 2745 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 2.36 % Allowed : 13.06 % Favored : 84.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -2.34 (0.16), residues: 2457 helix: -0.54 (0.18), residues: 756 sheet: -2.20 (0.18), residues: 603 loop : -1.78 (0.20), residues: 1098 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 2.515 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.3632 time to fit residues: 220.7470 Evaluate side-chains 287 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 2.566 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 9.9990 chunk 133 optimal weight: 0.0870 chunk 3 optimal weight: 8.9990 chunk 174 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 200 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 0.0570 chunk 210 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 overall best weight: 3.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 HIS ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN ** G 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 20367 Z= 0.284 Angle : 0.714 7.200 27486 Z= 0.382 Chirality : 0.046 0.225 2970 Planarity : 0.005 0.052 3447 Dihedral : 11.939 172.293 2745 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 25.42 Ramachandran Plot: Outliers : 1.79 % Allowed : 13.84 % Favored : 84.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.56 (0.16), residues: 2457 helix: -0.86 (0.18), residues: 792 sheet: -2.10 (0.19), residues: 603 loop : -1.98 (0.19), residues: 1062 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 2.718 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.3645 time to fit residues: 198.8859 Evaluate side-chains 265 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.161 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.8980 chunk 211 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 137 optimal weight: 0.0980 chunk 57 optimal weight: 8.9990 chunk 235 optimal weight: 20.0000 chunk 195 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 20367 Z= 0.238 Angle : 0.679 10.829 27486 Z= 0.361 Chirality : 0.045 0.223 2970 Planarity : 0.004 0.047 3447 Dihedral : 11.822 174.889 2745 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 1.42 % Allowed : 13.76 % Favored : 84.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -2.45 (0.16), residues: 2457 helix: -0.69 (0.18), residues: 756 sheet: -1.87 (0.19), residues: 585 loop : -2.07 (0.19), residues: 1116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 2.485 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.3535 time to fit residues: 191.7564 Evaluate side-chains 259 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.325 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 234 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 20367 Z= 0.200 Angle : 0.662 7.882 27486 Z= 0.354 Chirality : 0.045 0.220 2970 Planarity : 0.004 0.047 3447 Dihedral : 11.611 174.163 2745 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 1.47 % Allowed : 13.63 % Favored : 84.90 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -2.62 (0.16), residues: 2457 helix: -0.86 (0.18), residues: 792 sheet: -1.88 (0.20), residues: 603 loop : -2.24 (0.19), residues: 1062 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 2.441 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: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.3524 time to fit residues: 189.3114 Evaluate side-chains 266 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 2.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 0.3980 chunk 70 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.6642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 20367 Z= 0.206 Angle : 0.666 9.288 27486 Z= 0.355 Chirality : 0.045 0.231 2970 Planarity : 0.004 0.051 3447 Dihedral : 11.586 172.425 2745 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 1.42 % Allowed : 13.59 % Favored : 84.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -2.71 (0.16), residues: 2457 helix: -1.04 (0.17), residues: 819 sheet: -1.82 (0.20), residues: 603 loop : -2.29 (0.20), residues: 1035 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 2.489 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.3572 time to fit residues: 188.7983 Evaluate side-chains 253 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 2.465 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 206 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 ASN ** H 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.6840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 20367 Z= 0.279 Angle : 0.696 8.645 27486 Z= 0.371 Chirality : 0.046 0.255 2970 Planarity : 0.005 0.055 3447 Dihedral : 11.606 170.687 2745 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 27.35 Ramachandran Plot: Outliers : 1.51 % Allowed : 14.16 % Favored : 84.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -2.66 (0.16), residues: 2457 helix: -0.82 (0.18), residues: 747 sheet: -1.83 (0.20), residues: 621 loop : -2.33 (0.18), residues: 1089 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 2.522 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.3557 time to fit residues: 176.1103 Evaluate side-chains 248 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.495 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 242 optimal weight: 0.4980 chunk 222 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 ASN ** H 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.7048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 20367 Z= 0.198 Angle : 0.666 9.457 27486 Z= 0.353 Chirality : 0.045 0.210 2970 Planarity : 0.004 0.055 3447 Dihedral : 11.440 171.398 2745 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 23.97 Ramachandran Plot: Outliers : 1.47 % Allowed : 13.47 % Favored : 85.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -2.63 (0.17), residues: 2457 helix: -0.83 (0.18), residues: 738 sheet: -1.93 (0.20), residues: 639 loop : -2.19 (0.19), residues: 1080 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 2.775 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.3586 time to fit residues: 190.5538 Evaluate side-chains 260 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 2.576 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 198 optimal weight: 0.2980 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.064107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.051429 restraints weight = 97397.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.053235 restraints weight = 53688.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.054500 restraints weight = 34445.506| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.7188 Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 302, in __init__ self.caller(self.show_stats) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 337, in show_stats self.structure_monitor.show(prefix="",log=self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/mmtbx/refinement/real_space/__init__.py", line 150, in show self.update_statistics(prefix = prefix, log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/mmtbx/refinement/real_space/__init__.py", line 157, in update_statistics gs.show(prefix=prefix, log=log, uppercase=False) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/mmtbx/model/statistics.py", line 306, in show res = self.result() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/mmtbx/model/statistics.py", line 251, in result clash = self.clash(), File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/mmtbx/model/statistics.py", line 179, in clash nuclear = self.model.is_neutron()) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/mmtbx/validation/clashscore.py", line 139, in __init__ log=out) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/mmtbx/validation/clashscore.py", line 667, in check_and_add_hydrogen output_fname="reduce_fail.pdb") File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/mmtbx/validation/clashscore.py", line 568, in check_and_report_reduce_failure f.write(input_lines) IOError: [Errno 28] No space left on device