Starting phenix.real_space_refine on Mon Mar 18 05:41:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/03_2024/6bqw_7134_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/03_2024/6bqw_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_2024/6bqw_7134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/03_2024/6bqw_7134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/03_2024/6bqw_7134_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/03_2024/6bqw_7134_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 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. 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-5265/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: 10.89, 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: 8.37 Conformation dependent library (CDL) restraints added in 3.5 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: 3.68 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: 6.38 Time building geometry restraints manager: 9.02 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: 12024 35.79 - 71.58: 153 71.58 - 107.37: 18 107.37 - 143.16: 0 143.16 - 178.95: 9 Dihedral angle restraints: 12204 sinusoidal: 5040 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 12201 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 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.050 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 54.880 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 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 : 1.278 9.026 27486 Z= 0.807 Chirality : 0.073 0.307 2970 Planarity : 0.006 0.025 3447 Dihedral : 13.915 178.952 7686 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 % Allowed : 2.92 % Favored : 97.08 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 34 PHE 0.010 0.003 PHE A 64 TYR 0.032 0.006 TYR G 56 ARG 0.003 0.001 ARG C 130 *********************** 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 : 2.462 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 REVERT: A 202 MET cc_start: 0.7448 (mmm) cc_final: 0.7098 (tpp) REVERT: B 48 VAL cc_start: 0.8139 (t) cc_final: 0.7654 (p) REVERT: B 88 LEU cc_start: 0.8119 (tp) cc_final: 0.7901 (tp) REVERT: B 95 ILE cc_start: 0.8275 (pt) cc_final: 0.7868 (pt) REVERT: C 187 MET cc_start: 0.5628 (ptt) cc_final: 0.5051 (ptp) REVERT: C 201 ILE cc_start: 0.8640 (mt) cc_final: 0.8402 (tp) REVERT: C 211 THR cc_start: 0.8373 (p) cc_final: 0.7331 (p) REVERT: C 235 LEU cc_start: 0.8170 (mt) cc_final: 0.7657 (mm) REVERT: C 259 SER cc_start: 0.8407 (p) cc_final: 0.8192 (t) REVERT: D 5 THR cc_start: 0.7657 (p) cc_final: 0.7448 (p) REVERT: D 32 ILE cc_start: 0.9133 (mt) cc_final: 0.7760 (mt) REVERT: D 180 ILE cc_start: 0.8687 (mt) cc_final: 0.8419 (pt) REVERT: D 202 MET cc_start: 0.7947 (mmm) cc_final: 0.7689 (tpp) REVERT: E 99 THR cc_start: 0.8488 (p) cc_final: 0.8173 (p) REVERT: E 159 SER cc_start: 0.8344 (m) cc_final: 0.8069 (p) REVERT: E 184 ILE cc_start: 0.8996 (mt) cc_final: 0.8779 (mt) REVERT: F 95 ILE cc_start: 0.8715 (pt) cc_final: 0.8268 (pt) REVERT: F 108 LEU cc_start: 0.8473 (mt) cc_final: 0.8118 (mt) REVERT: F 115 MET cc_start: 0.7695 (mtp) cc_final: 0.7295 (mtm) REVERT: F 159 SER cc_start: 0.8623 (m) cc_final: 0.8316 (p) REVERT: F 187 MET cc_start: 0.6185 (ptt) cc_final: 0.5639 (ptt) REVERT: F 259 SER cc_start: 0.8797 (p) cc_final: 0.8548 (p) REVERT: G 5 THR cc_start: 0.7288 (p) cc_final: 0.7022 (p) REVERT: G 95 ILE cc_start: 0.8708 (pt) cc_final: 0.8331 (pt) REVERT: H 88 LEU cc_start: 0.7980 (tp) cc_final: 0.7693 (tp) REVERT: H 222 VAL cc_start: 0.7908 (t) cc_final: 0.7694 (t) REVERT: H 235 LEU cc_start: 0.8311 (mt) cc_final: 0.7361 (mt) REVERT: I 211 THR cc_start: 0.8198 (p) cc_final: 0.7536 (p) outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.4038 time to fit residues: 380.6914 Evaluate side-chains 368 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 2.362 ------------------------------------------------------------------------------- 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: 5.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 220 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 34 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 E 163 ASN 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20367 Z= 0.209 Angle : 0.751 8.352 27486 Z= 0.406 Chirality : 0.047 0.192 2970 Planarity : 0.005 0.035 3447 Dihedral : 13.570 179.570 2997 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 2.52 % Allowed : 12.01 % Favored : 85.47 % Rotamer: Outliers : 0.09 % Allowed : 2.69 % Favored : 97.22 % 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: -2.59 (0.16), residues: 2457 helix: -0.52 (0.18), residues: 729 sheet: -2.40 (0.18), residues: 531 loop : -2.11 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 125 PHE 0.029 0.002 PHE E 158 TYR 0.023 0.002 TYR G 266 ARG 0.006 0.001 ARG D 78 *********************** 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 493 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 491 time to evaluate : 2.276 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: A 202 MET cc_start: 0.7520 (mmm) cc_final: 0.7123 (tpp) REVERT: A 211 THR cc_start: 0.8208 (p) cc_final: 0.7560 (p) REVERT: B 126 PHE cc_start: 0.7260 (m-10) cc_final: 0.6095 (m-10) REVERT: B 141 PHE cc_start: 0.5271 (p90) cc_final: 0.5064 (p90) REVERT: C 15 LYS cc_start: 0.6696 (ptpp) cc_final: 0.6482 (ptpp) REVERT: C 63 ASN cc_start: 0.7614 (m110) cc_final: 0.7269 (t0) REVERT: C 187 MET cc_start: 0.5694 (ptt) cc_final: 0.5371 (ptp) REVERT: C 259 SER cc_start: 0.8548 (p) cc_final: 0.8123 (t) REVERT: E 108 LEU cc_start: 0.8482 (mt) cc_final: 0.7965 (mt) REVERT: E 163 ASN cc_start: 0.5121 (m110) cc_final: 0.4162 (m110) REVERT: E 202 MET cc_start: 0.7705 (mmm) cc_final: 0.7208 (mmm) REVERT: E 211 THR cc_start: 0.8441 (p) cc_final: 0.8011 (p) REVERT: F 73 TYR cc_start: 0.7265 (m-80) cc_final: 0.6926 (m-80) REVERT: F 95 ILE cc_start: 0.8610 (pt) cc_final: 0.8176 (mm) REVERT: F 98 GLU cc_start: 0.6968 (pt0) cc_final: 0.6516 (pt0) REVERT: F 108 LEU cc_start: 0.8124 (mt) cc_final: 0.7678 (mt) REVERT: F 259 SER cc_start: 0.8721 (p) cc_final: 0.8477 (t) REVERT: G 1 MET cc_start: 0.6857 (mtm) cc_final: 0.5801 (mpp) REVERT: G 73 TYR cc_start: 0.7405 (m-80) cc_final: 0.7177 (m-80) REVERT: H 88 LEU cc_start: 0.7867 (tp) cc_final: 0.7633 (tp) REVERT: H 126 PHE cc_start: 0.6911 (m-80) cc_final: 0.6638 (m-10) REVERT: H 266 TYR cc_start: 0.6466 (m-10) cc_final: 0.6024 (m-10) outliers start: 2 outliers final: 0 residues processed: 492 average time/residue: 0.3509 time to fit residues: 251.6750 Evaluate side-chains 326 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 2.275 ------------------------------------------------------------------------------- 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: 5.9990 chunk 68 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 221 optimal weight: 30.0000 chunk 238 optimal weight: 10.0000 chunk 196 optimal weight: 0.0270 chunk 219 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS B 63 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS C 63 ASN ** C 105 ASN ** 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** D 144 HIS ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 HIS ** F 163 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.929 20367 Z= 0.818 Angle : 0.822 28.041 27486 Z= 0.445 Chirality : 0.047 0.170 2970 Planarity : 0.005 0.044 3447 Dihedral : 13.405 174.680 2997 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 30.50 Ramachandran Plot: Outliers : 2.36 % Allowed : 14.37 % Favored : 83.27 % Rotamer: Outliers : 0.19 % Allowed : 3.75 % Favored : 96.06 % 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: -2.73 (0.16), residues: 2457 helix: -0.90 (0.17), residues: 756 sheet: -2.44 (0.18), residues: 603 loop : -1.97 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 190 PHE 0.024 0.002 PHE E 104 TYR 0.039 0.003 TYR H 217 ARG 0.036 0.002 ARG G 78 *********************** 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 388 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 384 time to evaluate : 2.241 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: A 211 THR cc_start: 0.8470 (p) cc_final: 0.8203 (p) REVERT: A 259 SER cc_start: 0.8646 (p) cc_final: 0.8418 (p) REVERT: C 15 LYS cc_start: 0.7219 (ptpp) cc_final: 0.6932 (ptpp) REVERT: C 63 ASN cc_start: 0.7684 (m-40) cc_final: 0.7330 (m-40) REVERT: C 73 TYR cc_start: 0.7183 (m-80) cc_final: 0.6969 (m-80) REVERT: C 187 MET cc_start: 0.5538 (ptt) cc_final: 0.4959 (ptp) REVERT: C 259 SER cc_start: 0.8543 (p) cc_final: 0.8115 (t) REVERT: D 68 ARG cc_start: 0.6915 (mmm160) cc_final: 0.6532 (mmm160) REVERT: D 118 ASP cc_start: 0.7417 (m-30) cc_final: 0.7041 (m-30) REVERT: D 148 MET cc_start: 0.6928 (tpt) cc_final: 0.6511 (tpt) REVERT: E 5 THR cc_start: 0.8557 (p) cc_final: 0.8326 (p) REVERT: F 1 MET cc_start: 0.7778 (mtm) cc_final: 0.7494 (mtm) REVERT: F 72 MET cc_start: 0.7718 (mpp) cc_final: 0.7517 (mpp) REVERT: F 73 TYR cc_start: 0.7529 (m-80) cc_final: 0.7275 (m-80) REVERT: F 259 SER cc_start: 0.8713 (p) cc_final: 0.8466 (t) REVERT: G 1 MET cc_start: 0.7158 (mtm) cc_final: 0.5998 (mpp) REVERT: G 115 MET cc_start: 0.7162 (tpp) cc_final: 0.6667 (tpp) REVERT: I 151 GLU cc_start: 0.5919 (tp30) cc_final: 0.4731 (tp30) outliers start: 4 outliers final: 2 residues processed: 387 average time/residue: 0.3551 time to fit residues: 200.6094 Evaluate side-chains 275 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 273 time to evaluate : 2.353 ------------------------------------------------------------------------------- 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: 10.0000 chunk 166 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 221 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 51 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 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN ** 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 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 144 HIS ** 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: 0.7120 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.994 20367 Z= 0.775 Angle : 0.688 28.461 27486 Z= 0.380 Chirality : 0.045 0.151 2970 Planarity : 0.005 0.094 3447 Dihedral : 13.295 174.426 2997 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 1.99 % Allowed : 12.90 % Favored : 85.10 % Rotamer: Outliers : 0.05 % Allowed : 2.64 % Favored : 97.31 % 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: -2.58 (0.16), residues: 2457 helix: -0.97 (0.17), residues: 792 sheet: -2.23 (0.18), residues: 603 loop : -1.81 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 125 PHE 0.017 0.001 PHE D 104 TYR 0.019 0.002 TYR H 56 ARG 0.029 0.001 ARG G 78 *********************** 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 403 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 402 time to evaluate : 1.886 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: A 202 MET cc_start: 0.7642 (tpp) cc_final: 0.7368 (tpp) REVERT: B 141 PHE cc_start: 0.5495 (p90) cc_final: 0.5212 (p90) REVERT: B 148 MET cc_start: 0.7308 (mpp) cc_final: 0.6640 (mtp) REVERT: C 63 ASN cc_start: 0.7556 (m-40) cc_final: 0.7312 (m-40) REVERT: C 73 TYR cc_start: 0.7152 (m-80) cc_final: 0.6779 (m-80) REVERT: C 187 MET cc_start: 0.5506 (ptt) cc_final: 0.4895 (ptp) REVERT: C 259 SER cc_start: 0.8426 (p) cc_final: 0.8099 (t) REVERT: D 102 LYS cc_start: 0.6012 (tttt) cc_final: 0.5551 (ttpt) REVERT: E 202 MET cc_start: 0.7699 (mmm) cc_final: 0.7340 (mmm) REVERT: E 204 LEU cc_start: 0.8292 (mt) cc_final: 0.8083 (mt) REVERT: F 1 MET cc_start: 0.7509 (mtm) cc_final: 0.7279 (mtm) REVERT: I 148 MET cc_start: 0.5500 (tpt) cc_final: 0.5269 (mmt) outliers start: 1 outliers final: 0 residues processed: 402 average time/residue: 0.3461 time to fit residues: 207.6893 Evaluate side-chains 279 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 2.164 ------------------------------------------------------------------------------- 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: 0.6980 chunk 133 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 210 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- 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** B 34 HIS ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 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 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 HIS ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** I 81 HIS ** 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: 0.7369 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.968 20367 Z= 0.859 Angle : 0.845 28.378 27486 Z= 0.452 Chirality : 0.048 0.195 2970 Planarity : 0.006 0.138 3447 Dihedral : 13.565 173.866 2997 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 34.49 Ramachandran Plot: Outliers : 1.79 % Allowed : 14.86 % Favored : 83.35 % Rotamer: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.62 % 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: -2.80 (0.16), residues: 2457 helix: -1.01 (0.18), residues: 738 sheet: -2.09 (0.19), residues: 585 loop : -2.24 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS H 125 PHE 0.029 0.003 PHE B 126 TYR 0.028 0.003 TYR G 90 ARG 0.042 0.001 ARG G 78 *********************** 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 343 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 342 time to evaluate : 2.194 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: B 98 GLU cc_start: 0.6267 (pt0) cc_final: 0.6015 (pt0) REVERT: C 187 MET cc_start: 0.5426 (ptt) cc_final: 0.4870 (ptp) REVERT: D 102 LYS cc_start: 0.6080 (tttt) cc_final: 0.5756 (ttpt) REVERT: D 118 ASP cc_start: 0.7434 (m-30) cc_final: 0.7170 (m-30) REVERT: G 115 MET cc_start: 0.7028 (tpp) cc_final: 0.6621 (tpp) REVERT: I 115 MET cc_start: 0.7554 (mmt) cc_final: 0.6546 (mmt) REVERT: I 148 MET cc_start: 0.5349 (tpt) cc_final: 0.4843 (mmt) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.3584 time to fit residues: 179.2348 Evaluate side-chains 245 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.292 ------------------------------------------------------------------------------- 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: 6.9990 chunk 211 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 235 optimal weight: 0.0370 chunk 195 optimal weight: 0.0170 chunk 108 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 overall best weight: 0.7898 ------------------------------------------------------------------------------- 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 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 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** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.999 20367 Z= 0.777 Angle : 0.705 28.436 27486 Z= 0.381 Chirality : 0.046 0.152 2970 Planarity : 0.005 0.120 3447 Dihedral : 13.323 177.258 2997 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 1.59 % Allowed : 12.98 % Favored : 85.43 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: -1.00 (0.17), residues: 783 sheet: -1.86 (0.20), residues: 585 loop : -2.19 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 34 PHE 0.020 0.001 PHE H 270 TYR 0.032 0.002 TYR D 219 ARG 0.032 0.001 ARG G 78 *********************** 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 363 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 ASN cc_start: 0.7343 (m-40) cc_final: 0.7064 (m-40) REVERT: C 187 MET cc_start: 0.5423 (ptt) cc_final: 0.4910 (ptp) REVERT: C 202 MET cc_start: 0.7789 (mmm) cc_final: 0.7405 (mmm) REVERT: E 46 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6510 (tp30) REVERT: F 73 TYR cc_start: 0.7390 (m-80) cc_final: 0.7149 (m-80) REVERT: F 98 GLU cc_start: 0.6820 (pt0) cc_final: 0.6367 (pt0) REVERT: H 89 VAL cc_start: 0.8438 (t) cc_final: 0.8195 (p) REVERT: I 1 MET cc_start: -0.1205 (tpt) cc_final: -0.2275 (tmm) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.3420 time to fit residues: 183.6526 Evaluate side-chains 262 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 2.370 ------------------------------------------------------------------------------- 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: 9.9990 chunk 26 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 131 optimal weight: 0.6980 chunk 234 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 142 optimal weight: 0.1980 chunk 108 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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** ** C 23 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** ** F 63 ASN ** 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 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.6526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.987 20367 Z= 0.789 Angle : 0.701 28.916 27486 Z= 0.381 Chirality : 0.045 0.254 2970 Planarity : 0.005 0.118 3447 Dihedral : 13.212 177.242 2997 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 25.75 Ramachandran Plot: Outliers : 1.42 % Allowed : 14.25 % Favored : 84.33 % Rotamer: Outliers : 0.05 % Allowed : 1.62 % Favored : 98.33 % 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: -2.65 (0.16), residues: 2457 helix: -0.86 (0.18), residues: 774 sheet: -1.78 (0.20), residues: 585 loop : -2.34 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 125 PHE 0.023 0.002 PHE B 126 TYR 0.028 0.002 TYR E 256 ARG 0.038 0.001 ARG G 78 *********************** 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 336 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 335 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6654 (tmm) cc_final: 0.6356 (ttt) REVERT: A 133 ILE cc_start: 0.7034 (tp) cc_final: 0.6820 (pt) REVERT: B 202 MET cc_start: 0.7525 (mmp) cc_final: 0.7240 (mmp) REVERT: C 63 ASN cc_start: 0.7382 (m-40) cc_final: 0.7099 (m-40) REVERT: C 187 MET cc_start: 0.5282 (ptt) cc_final: 0.4767 (ptp) REVERT: D 1 MET cc_start: 0.7586 (ttt) cc_final: 0.7239 (ttt) REVERT: E 202 MET cc_start: 0.7786 (mmt) cc_final: 0.7217 (tpp) REVERT: F 73 TYR cc_start: 0.7493 (m-80) cc_final: 0.7217 (m-80) REVERT: F 98 GLU cc_start: 0.6939 (pt0) cc_final: 0.6438 (pt0) REVERT: F 148 MET cc_start: 0.7234 (mpp) cc_final: 0.6911 (mtt) REVERT: I 1 MET cc_start: -0.1005 (tpt) cc_final: -0.2125 (tmm) REVERT: I 115 MET cc_start: 0.7046 (mmm) cc_final: 0.6715 (mmm) outliers start: 1 outliers final: 0 residues processed: 336 average time/residue: 0.3525 time to fit residues: 178.5397 Evaluate side-chains 247 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 2.399 ------------------------------------------------------------------------------- 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: 0.7980 chunk 139 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 148 optimal weight: 0.7980 chunk 159 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 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** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** H 11 ASN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.6730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.983 20367 Z= 0.782 Angle : 0.680 28.361 27486 Z= 0.371 Chirality : 0.045 0.199 2970 Planarity : 0.005 0.130 3447 Dihedral : 13.103 176.019 2997 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 1.42 % Allowed : 13.76 % Favored : 84.82 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -2.69 (0.16), residues: 2457 helix: -0.97 (0.17), residues: 810 sheet: -1.72 (0.19), residues: 603 loop : -2.39 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 125 PHE 0.023 0.001 PHE C 64 TYR 0.026 0.002 TYR E 256 ARG 0.039 0.001 ARG G 78 *********************** 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 348 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 2.295 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: A 1 MET cc_start: 0.6548 (tmm) cc_final: 0.6116 (ttt) REVERT: A 202 MET cc_start: 0.7244 (tpp) cc_final: 0.6828 (tpp) REVERT: B 202 MET cc_start: 0.7701 (mmp) cc_final: 0.7389 (mmp) REVERT: C 187 MET cc_start: 0.5142 (ptt) cc_final: 0.4597 (ptp) REVERT: F 148 MET cc_start: 0.7231 (mpp) cc_final: 0.6986 (mtt) REVERT: F 202 MET cc_start: 0.7624 (tpp) cc_final: 0.6943 (tpp) REVERT: I 1 MET cc_start: -0.0948 (tpt) cc_final: -0.2703 (tmm) REVERT: I 115 MET cc_start: 0.7033 (mmm) cc_final: 0.6715 (mmm) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.3325 time to fit residues: 172.9946 Evaluate side-chains 256 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 2.301 ------------------------------------------------------------------------------- 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: 20.0000 chunk 204 optimal weight: 2.9990 chunk 218 optimal weight: 0.0570 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- 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 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 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 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN ** F 125 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** ** 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 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.6901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.984 20367 Z= 0.786 Angle : 0.693 28.001 27486 Z= 0.377 Chirality : 0.045 0.238 2970 Planarity : 0.005 0.142 3447 Dihedral : 13.080 175.954 2997 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 1.38 % Allowed : 13.84 % Favored : 84.78 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: -0.76 (0.18), residues: 738 sheet: -1.82 (0.19), residues: 621 loop : -2.21 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 125 PHE 0.018 0.002 PHE B 126 TYR 0.020 0.002 TYR H 42 ARG 0.039 0.001 ARG G 78 *********************** 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 329 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 2.290 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: A 1 MET cc_start: 0.7309 (tmm) cc_final: 0.7023 (ttt) REVERT: A 215 ILE cc_start: 0.8986 (mm) cc_final: 0.8457 (tt) REVERT: B 202 MET cc_start: 0.7721 (mmp) cc_final: 0.7392 (mmp) REVERT: C 187 MET cc_start: 0.4985 (ptt) cc_final: 0.4439 (ptp) REVERT: C 202 MET cc_start: 0.7581 (mmm) cc_final: 0.7214 (mmm) REVERT: G 115 MET cc_start: 0.6963 (tpp) cc_final: 0.6688 (tpp) REVERT: H 45 MET cc_start: 0.7598 (mmm) cc_final: 0.7117 (mmm) REVERT: I 1 MET cc_start: -0.1145 (tpt) cc_final: -0.2725 (tmm) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.3298 time to fit residues: 162.7056 Evaluate side-chains 252 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.957 ------------------------------------------------------------------------------- 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: 10.0000 chunk 140 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 160 optimal weight: 0.0470 chunk 242 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 chunk 192 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 118 optimal weight: 0.0370 chunk 153 optimal weight: 7.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- 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** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 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 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 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 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.7065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.972 20367 Z= 0.786 Angle : 0.692 28.630 27486 Z= 0.378 Chirality : 0.045 0.182 2970 Planarity : 0.005 0.146 3447 Dihedral : 13.061 175.910 2997 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 1.38 % Allowed : 13.63 % Favored : 84.98 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -0.87 (0.18), residues: 756 sheet: -1.69 (0.20), residues: 603 loop : -2.32 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 125 PHE 0.016 0.002 PHE C 104 TYR 0.021 0.002 TYR B 56 ARG 0.041 0.001 ARG G 78 ********************** 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 335 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7348 (tmm) cc_final: 0.6919 (ttt) REVERT: B 1 MET cc_start: 0.7399 (tmm) cc_final: 0.7013 (tmm) REVERT: C 187 MET cc_start: 0.5028 (ptt) cc_final: 0.4451 (ptp) REVERT: C 202 MET cc_start: 0.7626 (mmm) cc_final: 0.7198 (mmm) REVERT: F 148 MET cc_start: 0.7102 (mpp) cc_final: 0.6837 (mtt) REVERT: F 202 MET cc_start: 0.7621 (tpp) cc_final: 0.7017 (tpp) REVERT: G 73 TYR cc_start: 0.7644 (m-80) cc_final: 0.7324 (m-80) REVERT: G 115 MET cc_start: 0.6983 (tpp) cc_final: 0.6711 (tpp) REVERT: H 45 MET cc_start: 0.7502 (mmm) cc_final: 0.7079 (tpt) REVERT: I 1 MET cc_start: -0.1222 (tpt) cc_final: -0.2742 (tmm) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.3392 time to fit residues: 170.3835 Evaluate side-chains 268 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.237 ------------------------------------------------------------------------------- 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: 8.9990 chunk 59 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 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 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN F 23 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 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** ** 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 163 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 = 0.3416 r_free = 0.3416 target = 0.064714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.052212 restraints weight = 96403.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054050 restraints weight = 52746.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.055315 restraints weight = 33556.110| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.7190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.979 20367 Z= 0.795 Angle : 0.715 28.617 27486 Z= 0.389 Chirality : 0.045 0.172 2970 Planarity : 0.005 0.137 3447 Dihedral : 13.089 176.704 2997 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 27.30 Ramachandran Plot: Outliers : 1.26 % Allowed : 14.12 % Favored : 84.62 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -2.85 (0.16), residues: 2457 helix: -1.06 (0.17), residues: 810 sheet: -1.91 (0.19), residues: 693 loop : -2.44 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 125 PHE 0.017 0.002 PHE A 126 TYR 0.030 0.002 TYR G 90 ARG 0.040 0.001 ARG G 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4364.37 seconds wall clock time: 80 minutes 57.82 seconds (4857.82 seconds total)