Starting phenix.real_space_refine (version: dev) on Thu Feb 23 04:06:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bj2_12193/02_2023/7bj2_12193.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bj2_12193/02_2023/7bj2_12193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bj2_12193/02_2023/7bj2_12193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bj2_12193/02_2023/7bj2_12193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bj2_12193/02_2023/7bj2_12193.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bj2_12193/02_2023/7bj2_12193.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "a GLU 20": "OE1" <-> "OE2" Residue "a GLU 33": "OE1" <-> "OE2" Residue "a TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 202": "OD1" <-> "OD2" Residue "a GLU 267": "OE1" <-> "OE2" Residue "b GLU 20": "OE1" <-> "OE2" Residue "b GLU 33": "OE1" <-> "OE2" Residue "b TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 202": "OD1" <-> "OD2" Residue "b GLU 267": "OE1" <-> "OE2" Residue "c GLU 20": "OE1" <-> "OE2" Residue "c GLU 33": "OE1" <-> "OE2" Residue "c TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 202": "OD1" <-> "OD2" Residue "c GLU 267": "OE1" <-> "OE2" Residue "d GLU 20": "OE1" <-> "OE2" Residue "d GLU 33": "OE1" <-> "OE2" Residue "d TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 202": "OD1" <-> "OD2" Residue "d GLU 267": "OE1" <-> "OE2" Residue "e GLU 20": "OE1" <-> "OE2" Residue "e GLU 33": "OE1" <-> "OE2" Residue "e TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 202": "OD1" <-> "OD2" Residue "e GLU 267": "OE1" <-> "OE2" Residue "f GLU 20": "OE1" <-> "OE2" Residue "f GLU 33": "OE1" <-> "OE2" Residue "f TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 202": "OD1" <-> "OD2" Residue "f GLU 267": "OE1" <-> "OE2" Residue "g GLU 20": "OE1" <-> "OE2" Residue "g GLU 33": "OE1" <-> "OE2" Residue "g TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 202": "OD1" <-> "OD2" Residue "g GLU 267": "OE1" <-> "OE2" Residue "h GLU 20": "OE1" <-> "OE2" Residue "h GLU 33": "OE1" <-> "OE2" Residue "h TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 202": "OD1" <-> "OD2" Residue "h GLU 267": "OE1" <-> "OE2" Residue "i GLU 20": "OE1" <-> "OE2" Residue "i GLU 33": "OE1" <-> "OE2" Residue "i TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 202": "OD1" <-> "OD2" Residue "i GLU 267": "OE1" <-> "OE2" Residue "j GLU 20": "OE1" <-> "OE2" Residue "j GLU 33": "OE1" <-> "OE2" Residue "j TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 202": "OD1" <-> "OD2" Residue "j GLU 267": "OE1" <-> "OE2" Residue "k GLU 20": "OE1" <-> "OE2" Residue "k GLU 33": "OE1" <-> "OE2" Residue "k TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 202": "OD1" <-> "OD2" Residue "k GLU 267": "OE1" <-> "OE2" Residue "l GLU 20": "OE1" <-> "OE2" Residue "l GLU 33": "OE1" <-> "OE2" Residue "l TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 202": "OD1" <-> "OD2" Residue "l GLU 267": "OE1" <-> "OE2" Residue "m GLU 20": "OE1" <-> "OE2" Residue "m GLU 33": "OE1" <-> "OE2" Residue "m TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 202": "OD1" <-> "OD2" Residue "m GLU 267": "OE1" <-> "OE2" Residue "n GLU 20": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "n TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 202": "OD1" <-> "OD2" Residue "n GLU 267": "OE1" <-> "OE2" Residue "o GLU 20": "OE1" <-> "OE2" Residue "o GLU 33": "OE1" <-> "OE2" Residue "o TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 202": "OD1" <-> "OD2" Residue "o GLU 267": "OE1" <-> "OE2" Residue "p GLU 20": "OE1" <-> "OE2" Residue "p GLU 33": "OE1" <-> "OE2" Residue "p TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 202": "OD1" <-> "OD2" Residue "p GLU 267": "OE1" <-> "OE2" Residue "q GLU 20": "OE1" <-> "OE2" Residue "q GLU 33": "OE1" <-> "OE2" Residue "q TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 202": "OD1" <-> "OD2" Residue "q GLU 267": "OE1" <-> "OE2" Residue "r GLU 20": "OE1" <-> "OE2" Residue "r GLU 33": "OE1" <-> "OE2" Residue "r TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 202": "OD1" <-> "OD2" Residue "r GLU 267": "OE1" <-> "OE2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "s GLU 33": "OE1" <-> "OE2" Residue "s TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 202": "OD1" <-> "OD2" Residue "s GLU 267": "OE1" <-> "OE2" Residue "t GLU 20": "OE1" <-> "OE2" Residue "t GLU 33": "OE1" <-> "OE2" Residue "t TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 202": "OD1" <-> "OD2" Residue "t GLU 267": "OE1" <-> "OE2" Residue "u GLU 20": "OE1" <-> "OE2" Residue "u GLU 33": "OE1" <-> "OE2" Residue "u TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 202": "OD1" <-> "OD2" Residue "u GLU 267": "OE1" <-> "OE2" Residue "v GLU 20": "OE1" <-> "OE2" Residue "v GLU 33": "OE1" <-> "OE2" Residue "v TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 202": "OD1" <-> "OD2" Residue "v GLU 267": "OE1" <-> "OE2" Residue "w GLU 20": "OE1" <-> "OE2" Residue "w GLU 33": "OE1" <-> "OE2" Residue "w TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 202": "OD1" <-> "OD2" Residue "w GLU 267": "OE1" <-> "OE2" Residue "x GLU 20": "OE1" <-> "OE2" Residue "x GLU 33": "OE1" <-> "OE2" Residue "x TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 202": "OD1" <-> "OD2" Residue "x GLU 267": "OE1" <-> "OE2" Residue "y GLU 20": "OE1" <-> "OE2" Residue "y GLU 33": "OE1" <-> "OE2" Residue "y TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ASP 202": "OD1" <-> "OD2" Residue "y GLU 267": "OE1" <-> "OE2" Residue "z GLU 20": "OE1" <-> "OE2" Residue "z GLU 33": "OE1" <-> "OE2" Residue "z TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 202": "OD1" <-> "OD2" Residue "z GLU 267": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 58552 Number of models: 1 Model: "" Number of chains: 26 Chain: "a" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "b" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "c" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "d" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "e" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "f" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "g" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "h" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "i" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "j" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "k" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "l" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "m" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "n" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "o" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "p" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "q" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "r" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "s" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "t" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "u" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "v" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "w" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "x" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "y" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "z" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2252 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Time building chain proxies: 23.92, per 1000 atoms: 0.41 Number of scatterers: 58552 At special positions: 0 Unit cell: (263.744, 262.08, 77.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 338 16.00 O 11726 8.00 N 10634 7.00 C 35854 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: 18.41 Conformation dependent library (CDL) restraints added in 7.1 seconds 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14352 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 104 sheets defined 25.2% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'a' and resid 21 through 24 Processing helix chain 'a' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR a 59 " --> pdb=" O THR a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 208 Processing helix chain 'a' and resid 228 through 241 removed outlier: 3.897A pdb=" N ASN a 241 " --> pdb=" O ALA a 237 " (cutoff:3.500A) Processing helix chain 'a' and resid 327 through 338 Processing helix chain 'a' and resid 341 through 355 removed outlier: 3.749A pdb=" N SER a 347 " --> pdb=" O MET a 343 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 24 Processing helix chain 'b' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR b 59 " --> pdb=" O THR b 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 193 through 208 Processing helix chain 'b' and resid 228 through 241 removed outlier: 3.897A pdb=" N ASN b 241 " --> pdb=" O ALA b 237 " (cutoff:3.500A) Processing helix chain 'b' and resid 327 through 338 Processing helix chain 'b' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER b 347 " --> pdb=" O MET b 343 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 24 Processing helix chain 'c' and resid 55 through 70 removed outlier: 4.126A pdb=" N THR c 59 " --> pdb=" O THR c 55 " (cutoff:3.500A) Processing helix chain 'c' and resid 193 through 208 Processing helix chain 'c' and resid 228 through 241 removed outlier: 3.897A pdb=" N ASN c 241 " --> pdb=" O ALA c 237 " (cutoff:3.500A) Processing helix chain 'c' and resid 327 through 338 Processing helix chain 'c' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER c 347 " --> pdb=" O MET c 343 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 24 Processing helix chain 'd' and resid 55 through 70 removed outlier: 4.126A pdb=" N THR d 59 " --> pdb=" O THR d 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 193 through 208 Processing helix chain 'd' and resid 228 through 241 removed outlier: 3.898A pdb=" N ASN d 241 " --> pdb=" O ALA d 237 " (cutoff:3.500A) Processing helix chain 'd' and resid 327 through 338 Processing helix chain 'd' and resid 341 through 355 removed outlier: 3.749A pdb=" N SER d 347 " --> pdb=" O MET d 343 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 24 Processing helix chain 'e' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR e 59 " --> pdb=" O THR e 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 193 through 208 Processing helix chain 'e' and resid 228 through 241 removed outlier: 3.897A pdb=" N ASN e 241 " --> pdb=" O ALA e 237 " (cutoff:3.500A) Processing helix chain 'e' and resid 327 through 338 Processing helix chain 'e' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER e 347 " --> pdb=" O MET e 343 " (cutoff:3.500A) Processing helix chain 'f' and resid 21 through 24 Processing helix chain 'f' and resid 55 through 70 removed outlier: 4.128A pdb=" N THR f 59 " --> pdb=" O THR f 55 " (cutoff:3.500A) Processing helix chain 'f' and resid 193 through 208 Processing helix chain 'f' and resid 228 through 241 removed outlier: 3.896A pdb=" N ASN f 241 " --> pdb=" O ALA f 237 " (cutoff:3.500A) Processing helix chain 'f' and resid 327 through 338 Processing helix chain 'f' and resid 341 through 355 removed outlier: 3.749A pdb=" N SER f 347 " --> pdb=" O MET f 343 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 24 Processing helix chain 'g' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR g 59 " --> pdb=" O THR g 55 " (cutoff:3.500A) Processing helix chain 'g' and resid 193 through 208 Processing helix chain 'g' and resid 228 through 241 removed outlier: 3.897A pdb=" N ASN g 241 " --> pdb=" O ALA g 237 " (cutoff:3.500A) Processing helix chain 'g' and resid 327 through 338 Processing helix chain 'g' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER g 347 " --> pdb=" O MET g 343 " (cutoff:3.500A) Processing helix chain 'h' and resid 21 through 24 Processing helix chain 'h' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR h 59 " --> pdb=" O THR h 55 " (cutoff:3.500A) Processing helix chain 'h' and resid 193 through 208 Processing helix chain 'h' and resid 228 through 241 removed outlier: 3.898A pdb=" N ASN h 241 " --> pdb=" O ALA h 237 " (cutoff:3.500A) Processing helix chain 'h' and resid 327 through 338 Processing helix chain 'h' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER h 347 " --> pdb=" O MET h 343 " (cutoff:3.500A) Processing helix chain 'i' and resid 21 through 24 Processing helix chain 'i' and resid 55 through 70 removed outlier: 4.128A pdb=" N THR i 59 " --> pdb=" O THR i 55 " (cutoff:3.500A) Processing helix chain 'i' and resid 193 through 208 Processing helix chain 'i' and resid 228 through 241 removed outlier: 3.898A pdb=" N ASN i 241 " --> pdb=" O ALA i 237 " (cutoff:3.500A) Processing helix chain 'i' and resid 327 through 338 Processing helix chain 'i' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER i 347 " --> pdb=" O MET i 343 " (cutoff:3.500A) Processing helix chain 'j' and resid 21 through 24 Processing helix chain 'j' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR j 59 " --> pdb=" O THR j 55 " (cutoff:3.500A) Processing helix chain 'j' and resid 193 through 208 Processing helix chain 'j' and resid 228 through 241 removed outlier: 3.897A pdb=" N ASN j 241 " --> pdb=" O ALA j 237 " (cutoff:3.500A) Processing helix chain 'j' and resid 327 through 338 Processing helix chain 'j' and resid 341 through 355 removed outlier: 3.749A pdb=" N SER j 347 " --> pdb=" O MET j 343 " (cutoff:3.500A) Processing helix chain 'k' and resid 21 through 24 Processing helix chain 'k' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR k 59 " --> pdb=" O THR k 55 " (cutoff:3.500A) Processing helix chain 'k' and resid 193 through 208 Processing helix chain 'k' and resid 228 through 241 removed outlier: 3.898A pdb=" N ASN k 241 " --> pdb=" O ALA k 237 " (cutoff:3.500A) Processing helix chain 'k' and resid 327 through 338 Processing helix chain 'k' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER k 347 " --> pdb=" O MET k 343 " (cutoff:3.500A) Processing helix chain 'l' and resid 21 through 24 Processing helix chain 'l' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR l 59 " --> pdb=" O THR l 55 " (cutoff:3.500A) Processing helix chain 'l' and resid 193 through 208 Processing helix chain 'l' and resid 228 through 241 removed outlier: 3.897A pdb=" N ASN l 241 " --> pdb=" O ALA l 237 " (cutoff:3.500A) Processing helix chain 'l' and resid 327 through 338 Processing helix chain 'l' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER l 347 " --> pdb=" O MET l 343 " (cutoff:3.500A) Processing helix chain 'm' and resid 21 through 24 Processing helix chain 'm' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR m 59 " --> pdb=" O THR m 55 " (cutoff:3.500A) Processing helix chain 'm' and resid 193 through 208 Processing helix chain 'm' and resid 228 through 241 removed outlier: 3.897A pdb=" N ASN m 241 " --> pdb=" O ALA m 237 " (cutoff:3.500A) Processing helix chain 'm' and resid 327 through 338 Processing helix chain 'm' and resid 341 through 355 removed outlier: 3.751A pdb=" N SER m 347 " --> pdb=" O MET m 343 " (cutoff:3.500A) Processing helix chain 'n' and resid 21 through 24 Processing helix chain 'n' and resid 55 through 70 removed outlier: 4.126A pdb=" N THR n 59 " --> pdb=" O THR n 55 " (cutoff:3.500A) Processing helix chain 'n' and resid 193 through 208 Processing helix chain 'n' and resid 228 through 241 removed outlier: 3.898A pdb=" N ASN n 241 " --> pdb=" O ALA n 237 " (cutoff:3.500A) Processing helix chain 'n' and resid 327 through 338 Processing helix chain 'n' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER n 347 " --> pdb=" O MET n 343 " (cutoff:3.500A) Processing helix chain 'o' and resid 21 through 24 Processing helix chain 'o' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR o 59 " --> pdb=" O THR o 55 " (cutoff:3.500A) Processing helix chain 'o' and resid 193 through 208 Processing helix chain 'o' and resid 228 through 241 removed outlier: 3.898A pdb=" N ASN o 241 " --> pdb=" O ALA o 237 " (cutoff:3.500A) Processing helix chain 'o' and resid 327 through 338 Processing helix chain 'o' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER o 347 " --> pdb=" O MET o 343 " (cutoff:3.500A) Processing helix chain 'p' and resid 21 through 24 Processing helix chain 'p' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR p 59 " --> pdb=" O THR p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 193 through 208 Processing helix chain 'p' and resid 228 through 241 removed outlier: 3.897A pdb=" N ASN p 241 " --> pdb=" O ALA p 237 " (cutoff:3.500A) Processing helix chain 'p' and resid 327 through 338 Processing helix chain 'p' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER p 347 " --> pdb=" O MET p 343 " (cutoff:3.500A) Processing helix chain 'q' and resid 21 through 24 Processing helix chain 'q' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR q 59 " --> pdb=" O THR q 55 " (cutoff:3.500A) Processing helix chain 'q' and resid 193 through 208 Processing helix chain 'q' and resid 228 through 241 removed outlier: 3.898A pdb=" N ASN q 241 " --> pdb=" O ALA q 237 " (cutoff:3.500A) Processing helix chain 'q' and resid 327 through 338 Processing helix chain 'q' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER q 347 " --> pdb=" O MET q 343 " (cutoff:3.500A) Processing helix chain 'r' and resid 21 through 24 Processing helix chain 'r' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR r 59 " --> pdb=" O THR r 55 " (cutoff:3.500A) Processing helix chain 'r' and resid 193 through 208 Processing helix chain 'r' and resid 228 through 241 removed outlier: 3.897A pdb=" N ASN r 241 " --> pdb=" O ALA r 237 " (cutoff:3.500A) Processing helix chain 'r' and resid 327 through 338 Processing helix chain 'r' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER r 347 " --> pdb=" O MET r 343 " (cutoff:3.500A) Processing helix chain 's' and resid 21 through 24 Processing helix chain 's' and resid 55 through 70 removed outlier: 4.128A pdb=" N THR s 59 " --> pdb=" O THR s 55 " (cutoff:3.500A) Processing helix chain 's' and resid 193 through 208 Processing helix chain 's' and resid 228 through 241 removed outlier: 3.898A pdb=" N ASN s 241 " --> pdb=" O ALA s 237 " (cutoff:3.500A) Processing helix chain 's' and resid 327 through 338 Processing helix chain 's' and resid 341 through 355 removed outlier: 3.749A pdb=" N SER s 347 " --> pdb=" O MET s 343 " (cutoff:3.500A) Processing helix chain 't' and resid 21 through 24 Processing helix chain 't' and resid 55 through 70 removed outlier: 4.126A pdb=" N THR t 59 " --> pdb=" O THR t 55 " (cutoff:3.500A) Processing helix chain 't' and resid 193 through 208 Processing helix chain 't' and resid 228 through 241 removed outlier: 3.897A pdb=" N ASN t 241 " --> pdb=" O ALA t 237 " (cutoff:3.500A) Processing helix chain 't' and resid 327 through 338 Processing helix chain 't' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER t 347 " --> pdb=" O MET t 343 " (cutoff:3.500A) Processing helix chain 'u' and resid 21 through 24 Processing helix chain 'u' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR u 59 " --> pdb=" O THR u 55 " (cutoff:3.500A) Processing helix chain 'u' and resid 193 through 208 Processing helix chain 'u' and resid 228 through 241 removed outlier: 3.898A pdb=" N ASN u 241 " --> pdb=" O ALA u 237 " (cutoff:3.500A) Processing helix chain 'u' and resid 327 through 338 Processing helix chain 'u' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER u 347 " --> pdb=" O MET u 343 " (cutoff:3.500A) Processing helix chain 'v' and resid 21 through 24 Processing helix chain 'v' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR v 59 " --> pdb=" O THR v 55 " (cutoff:3.500A) Processing helix chain 'v' and resid 193 through 208 Processing helix chain 'v' and resid 228 through 241 removed outlier: 3.897A pdb=" N ASN v 241 " --> pdb=" O ALA v 237 " (cutoff:3.500A) Processing helix chain 'v' and resid 327 through 338 Processing helix chain 'v' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER v 347 " --> pdb=" O MET v 343 " (cutoff:3.500A) Processing helix chain 'w' and resid 21 through 24 Processing helix chain 'w' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR w 59 " --> pdb=" O THR w 55 " (cutoff:3.500A) Processing helix chain 'w' and resid 193 through 208 Processing helix chain 'w' and resid 228 through 241 removed outlier: 3.897A pdb=" N ASN w 241 " --> pdb=" O ALA w 237 " (cutoff:3.500A) Processing helix chain 'w' and resid 327 through 338 Processing helix chain 'w' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER w 347 " --> pdb=" O MET w 343 " (cutoff:3.500A) Processing helix chain 'x' and resid 21 through 24 Processing helix chain 'x' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR x 59 " --> pdb=" O THR x 55 " (cutoff:3.500A) Processing helix chain 'x' and resid 193 through 208 Processing helix chain 'x' and resid 228 through 241 removed outlier: 3.897A pdb=" N ASN x 241 " --> pdb=" O ALA x 237 " (cutoff:3.500A) Processing helix chain 'x' and resid 327 through 338 Processing helix chain 'x' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER x 347 " --> pdb=" O MET x 343 " (cutoff:3.500A) Processing helix chain 'y' and resid 21 through 24 Processing helix chain 'y' and resid 55 through 70 removed outlier: 4.128A pdb=" N THR y 59 " --> pdb=" O THR y 55 " (cutoff:3.500A) Processing helix chain 'y' and resid 193 through 208 Processing helix chain 'y' and resid 228 through 241 removed outlier: 3.898A pdb=" N ASN y 241 " --> pdb=" O ALA y 237 " (cutoff:3.500A) Processing helix chain 'y' and resid 327 through 338 Processing helix chain 'y' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER y 347 " --> pdb=" O MET y 343 " (cutoff:3.500A) Processing helix chain 'z' and resid 21 through 24 Processing helix chain 'z' and resid 55 through 70 removed outlier: 4.127A pdb=" N THR z 59 " --> pdb=" O THR z 55 " (cutoff:3.500A) Processing helix chain 'z' and resid 193 through 208 Processing helix chain 'z' and resid 228 through 241 removed outlier: 3.897A pdb=" N ASN z 241 " --> pdb=" O ALA z 237 " (cutoff:3.500A) Processing helix chain 'z' and resid 327 through 338 Processing helix chain 'z' and resid 341 through 355 removed outlier: 3.750A pdb=" N SER z 347 " --> pdb=" O MET z 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'a' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR a 39 " --> pdb=" O PRO a 125 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA a 135 " --> pdb=" O LEU a 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN a 167 " --> pdb=" O ILE a 103 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE a 103 " --> pdb=" O ASN a 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP a 104 " --> pdb=" O SER a 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER a 92 " --> pdb=" O ASP a 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU a 36 " --> pdb=" O ALA a 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 361 through 364 Processing sheet with id=AA4, first strand: chain 'a' and resid 269 through 270 removed outlier: 3.659A pdb=" N THR a 269 " --> pdb=" O ARG a 359 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 320 through 322 Processing sheet with id=AA6, first strand: chain 'b' and resid 26 through 28 Processing sheet with id=AA7, first strand: chain 'b' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR b 39 " --> pdb=" O PRO b 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA b 135 " --> pdb=" O LEU b 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN b 167 " --> pdb=" O ILE b 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE b 103 " --> pdb=" O ASN b 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP b 104 " --> pdb=" O SER b 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER b 92 " --> pdb=" O ASP b 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU b 36 " --> pdb=" O ALA b 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 361 through 364 Processing sheet with id=AA9, first strand: chain 'b' and resid 269 through 270 removed outlier: 3.658A pdb=" N THR b 269 " --> pdb=" O ARG b 359 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 26 through 28 Processing sheet with id=AB2, first strand: chain 'c' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR c 39 " --> pdb=" O PRO c 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA c 135 " --> pdb=" O LEU c 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN c 167 " --> pdb=" O ILE c 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE c 103 " --> pdb=" O ASN c 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP c 104 " --> pdb=" O SER c 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER c 92 " --> pdb=" O ASP c 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU c 36 " --> pdb=" O ALA c 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 361 through 364 Processing sheet with id=AB4, first strand: chain 'c' and resid 269 through 270 removed outlier: 3.658A pdb=" N THR c 269 " --> pdb=" O ARG c 359 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 26 through 28 Processing sheet with id=AB6, first strand: chain 'd' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR d 39 " --> pdb=" O PRO d 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA d 135 " --> pdb=" O LEU d 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN d 167 " --> pdb=" O ILE d 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE d 103 " --> pdb=" O ASN d 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP d 104 " --> pdb=" O SER d 92 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER d 92 " --> pdb=" O ASP d 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU d 36 " --> pdb=" O ALA d 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 361 through 364 Processing sheet with id=AB8, first strand: chain 'd' and resid 269 through 270 removed outlier: 3.658A pdb=" N THR d 269 " --> pdb=" O ARG d 359 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'e' and resid 26 through 28 Processing sheet with id=AC1, first strand: chain 'e' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR e 39 " --> pdb=" O PRO e 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA e 135 " --> pdb=" O LEU e 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN e 167 " --> pdb=" O ILE e 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE e 103 " --> pdb=" O ASN e 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP e 104 " --> pdb=" O SER e 92 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER e 92 " --> pdb=" O ASP e 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU e 36 " --> pdb=" O ALA e 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'e' and resid 361 through 364 Processing sheet with id=AC3, first strand: chain 'e' and resid 269 through 270 removed outlier: 3.658A pdb=" N THR e 269 " --> pdb=" O ARG e 359 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'f' and resid 26 through 28 Processing sheet with id=AC5, first strand: chain 'f' and resid 120 through 121 removed outlier: 4.833A pdb=" N TYR f 39 " --> pdb=" O PRO f 125 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA f 135 " --> pdb=" O LEU f 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN f 167 " --> pdb=" O ILE f 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE f 103 " --> pdb=" O ASN f 167 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP f 104 " --> pdb=" O SER f 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER f 92 " --> pdb=" O ASP f 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU f 36 " --> pdb=" O ALA f 91 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 361 through 364 Processing sheet with id=AC7, first strand: chain 'f' and resid 269 through 270 removed outlier: 3.658A pdb=" N THR f 269 " --> pdb=" O ARG f 359 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'g' and resid 26 through 28 Processing sheet with id=AC9, first strand: chain 'g' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR g 39 " --> pdb=" O PRO g 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA g 135 " --> pdb=" O LEU g 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN g 167 " --> pdb=" O ILE g 103 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE g 103 " --> pdb=" O ASN g 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP g 104 " --> pdb=" O SER g 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER g 92 " --> pdb=" O ASP g 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU g 36 " --> pdb=" O ALA g 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'g' and resid 361 through 364 Processing sheet with id=AD2, first strand: chain 'g' and resid 269 through 270 removed outlier: 3.658A pdb=" N THR g 269 " --> pdb=" O ARG g 359 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'h' and resid 26 through 28 Processing sheet with id=AD4, first strand: chain 'h' and resid 120 through 121 removed outlier: 4.833A pdb=" N TYR h 39 " --> pdb=" O PRO h 125 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA h 135 " --> pdb=" O LEU h 126 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN h 167 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE h 103 " --> pdb=" O ASN h 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP h 104 " --> pdb=" O SER h 92 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER h 92 " --> pdb=" O ASP h 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU h 36 " --> pdb=" O ALA h 91 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'h' and resid 361 through 364 Processing sheet with id=AD6, first strand: chain 'h' and resid 269 through 270 removed outlier: 3.659A pdb=" N THR h 269 " --> pdb=" O ARG h 359 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'i' and resid 26 through 28 Processing sheet with id=AD8, first strand: chain 'i' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR i 39 " --> pdb=" O PRO i 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA i 135 " --> pdb=" O LEU i 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN i 167 " --> pdb=" O ILE i 103 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE i 103 " --> pdb=" O ASN i 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP i 104 " --> pdb=" O SER i 92 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER i 92 " --> pdb=" O ASP i 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU i 36 " --> pdb=" O ALA i 91 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'i' and resid 361 through 364 Processing sheet with id=AE1, first strand: chain 'i' and resid 269 through 270 removed outlier: 3.658A pdb=" N THR i 269 " --> pdb=" O ARG i 359 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'j' and resid 26 through 28 Processing sheet with id=AE3, first strand: chain 'j' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR j 39 " --> pdb=" O PRO j 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA j 135 " --> pdb=" O LEU j 126 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN j 167 " --> pdb=" O ILE j 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE j 103 " --> pdb=" O ASN j 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP j 104 " --> pdb=" O SER j 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER j 92 " --> pdb=" O ASP j 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU j 36 " --> pdb=" O ALA j 91 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'j' and resid 361 through 364 Processing sheet with id=AE5, first strand: chain 'j' and resid 269 through 270 removed outlier: 3.658A pdb=" N THR j 269 " --> pdb=" O ARG j 359 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'k' and resid 26 through 28 Processing sheet with id=AE7, first strand: chain 'k' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR k 39 " --> pdb=" O PRO k 125 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA k 135 " --> pdb=" O LEU k 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN k 167 " --> pdb=" O ILE k 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE k 103 " --> pdb=" O ASN k 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP k 104 " --> pdb=" O SER k 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER k 92 " --> pdb=" O ASP k 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU k 36 " --> pdb=" O ALA k 91 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'k' and resid 361 through 364 Processing sheet with id=AE9, first strand: chain 'k' and resid 269 through 270 removed outlier: 3.659A pdb=" N THR k 269 " --> pdb=" O ARG k 359 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'l' and resid 26 through 28 Processing sheet with id=AF2, first strand: chain 'l' and resid 120 through 121 removed outlier: 4.833A pdb=" N TYR l 39 " --> pdb=" O PRO l 125 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA l 135 " --> pdb=" O LEU l 126 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN l 167 " --> pdb=" O ILE l 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE l 103 " --> pdb=" O ASN l 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP l 104 " --> pdb=" O SER l 92 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER l 92 " --> pdb=" O ASP l 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU l 36 " --> pdb=" O ALA l 91 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'l' and resid 361 through 364 Processing sheet with id=AF4, first strand: chain 'l' and resid 269 through 270 removed outlier: 3.659A pdb=" N THR l 269 " --> pdb=" O ARG l 359 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'm' and resid 26 through 28 Processing sheet with id=AF6, first strand: chain 'm' and resid 120 through 121 removed outlier: 4.833A pdb=" N TYR m 39 " --> pdb=" O PRO m 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA m 135 " --> pdb=" O LEU m 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN m 167 " --> pdb=" O ILE m 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE m 103 " --> pdb=" O ASN m 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP m 104 " --> pdb=" O SER m 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER m 92 " --> pdb=" O ASP m 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU m 36 " --> pdb=" O ALA m 91 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'm' and resid 361 through 364 Processing sheet with id=AF8, first strand: chain 'm' and resid 269 through 270 removed outlier: 3.659A pdb=" N THR m 269 " --> pdb=" O ARG m 359 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'n' and resid 26 through 28 Processing sheet with id=AG1, first strand: chain 'n' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR n 39 " --> pdb=" O PRO n 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA n 135 " --> pdb=" O LEU n 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN n 167 " --> pdb=" O ILE n 103 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE n 103 " --> pdb=" O ASN n 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP n 104 " --> pdb=" O SER n 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER n 92 " --> pdb=" O ASP n 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU n 36 " --> pdb=" O ALA n 91 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'n' and resid 361 through 364 Processing sheet with id=AG3, first strand: chain 'n' and resid 269 through 270 removed outlier: 3.659A pdb=" N THR n 269 " --> pdb=" O ARG n 359 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'o' and resid 26 through 28 Processing sheet with id=AG5, first strand: chain 'o' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR o 39 " --> pdb=" O PRO o 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA o 135 " --> pdb=" O LEU o 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN o 167 " --> pdb=" O ILE o 103 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE o 103 " --> pdb=" O ASN o 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP o 104 " --> pdb=" O SER o 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER o 92 " --> pdb=" O ASP o 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU o 36 " --> pdb=" O ALA o 91 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'o' and resid 361 through 364 Processing sheet with id=AG7, first strand: chain 'o' and resid 269 through 270 removed outlier: 3.659A pdb=" N THR o 269 " --> pdb=" O ARG o 359 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'p' and resid 26 through 28 Processing sheet with id=AG9, first strand: chain 'p' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR p 39 " --> pdb=" O PRO p 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA p 135 " --> pdb=" O LEU p 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN p 167 " --> pdb=" O ILE p 103 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE p 103 " --> pdb=" O ASN p 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP p 104 " --> pdb=" O SER p 92 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER p 92 " --> pdb=" O ASP p 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU p 36 " --> pdb=" O ALA p 91 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'p' and resid 361 through 364 Processing sheet with id=AH2, first strand: chain 'p' and resid 269 through 270 removed outlier: 3.659A pdb=" N THR p 269 " --> pdb=" O ARG p 359 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'q' and resid 26 through 28 Processing sheet with id=AH4, first strand: chain 'q' and resid 120 through 121 removed outlier: 4.833A pdb=" N TYR q 39 " --> pdb=" O PRO q 125 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA q 135 " --> pdb=" O LEU q 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN q 167 " --> pdb=" O ILE q 103 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE q 103 " --> pdb=" O ASN q 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP q 104 " --> pdb=" O SER q 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER q 92 " --> pdb=" O ASP q 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU q 36 " --> pdb=" O ALA q 91 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'q' and resid 361 through 364 Processing sheet with id=AH6, first strand: chain 'q' and resid 269 through 270 removed outlier: 3.658A pdb=" N THR q 269 " --> pdb=" O ARG q 359 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'r' and resid 26 through 28 Processing sheet with id=AH8, first strand: chain 'r' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR r 39 " --> pdb=" O PRO r 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA r 135 " --> pdb=" O LEU r 126 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN r 167 " --> pdb=" O ILE r 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE r 103 " --> pdb=" O ASN r 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP r 104 " --> pdb=" O SER r 92 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER r 92 " --> pdb=" O ASP r 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU r 36 " --> pdb=" O ALA r 91 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'r' and resid 361 through 364 Processing sheet with id=AI1, first strand: chain 'r' and resid 269 through 270 removed outlier: 3.659A pdb=" N THR r 269 " --> pdb=" O ARG r 359 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 's' and resid 26 through 28 Processing sheet with id=AI3, first strand: chain 's' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR s 39 " --> pdb=" O PRO s 125 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA s 135 " --> pdb=" O LEU s 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN s 167 " --> pdb=" O ILE s 103 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE s 103 " --> pdb=" O ASN s 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP s 104 " --> pdb=" O SER s 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER s 92 " --> pdb=" O ASP s 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU s 36 " --> pdb=" O ALA s 91 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 's' and resid 361 through 364 Processing sheet with id=AI5, first strand: chain 's' and resid 269 through 270 removed outlier: 3.659A pdb=" N THR s 269 " --> pdb=" O ARG s 359 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 't' and resid 26 through 28 Processing sheet with id=AI7, first strand: chain 't' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR t 39 " --> pdb=" O PRO t 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA t 135 " --> pdb=" O LEU t 126 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN t 167 " --> pdb=" O ILE t 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE t 103 " --> pdb=" O ASN t 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP t 104 " --> pdb=" O SER t 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER t 92 " --> pdb=" O ASP t 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU t 36 " --> pdb=" O ALA t 91 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 't' and resid 361 through 364 Processing sheet with id=AI9, first strand: chain 't' and resid 269 through 270 removed outlier: 3.659A pdb=" N THR t 269 " --> pdb=" O ARG t 359 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'u' and resid 26 through 28 Processing sheet with id=AJ2, first strand: chain 'u' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR u 39 " --> pdb=" O PRO u 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA u 135 " --> pdb=" O LEU u 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN u 167 " --> pdb=" O ILE u 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE u 103 " --> pdb=" O ASN u 167 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP u 104 " --> pdb=" O SER u 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER u 92 " --> pdb=" O ASP u 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU u 36 " --> pdb=" O ALA u 91 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'u' and resid 361 through 364 Processing sheet with id=AJ4, first strand: chain 'u' and resid 269 through 270 removed outlier: 3.659A pdb=" N THR u 269 " --> pdb=" O ARG u 359 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'v' and resid 26 through 28 Processing sheet with id=AJ6, first strand: chain 'v' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR v 39 " --> pdb=" O PRO v 125 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA v 135 " --> pdb=" O LEU v 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN v 167 " --> pdb=" O ILE v 103 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE v 103 " --> pdb=" O ASN v 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP v 104 " --> pdb=" O SER v 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER v 92 " --> pdb=" O ASP v 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU v 36 " --> pdb=" O ALA v 91 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'v' and resid 361 through 364 Processing sheet with id=AJ8, first strand: chain 'v' and resid 269 through 270 removed outlier: 3.658A pdb=" N THR v 269 " --> pdb=" O ARG v 359 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'w' and resid 26 through 28 Processing sheet with id=AK1, first strand: chain 'w' and resid 120 through 121 removed outlier: 4.833A pdb=" N TYR w 39 " --> pdb=" O PRO w 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA w 135 " --> pdb=" O LEU w 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN w 167 " --> pdb=" O ILE w 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE w 103 " --> pdb=" O ASN w 167 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP w 104 " --> pdb=" O SER w 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER w 92 " --> pdb=" O ASP w 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU w 36 " --> pdb=" O ALA w 91 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'w' and resid 361 through 364 Processing sheet with id=AK3, first strand: chain 'w' and resid 269 through 270 removed outlier: 3.658A pdb=" N THR w 269 " --> pdb=" O ARG w 359 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'x' and resid 26 through 28 Processing sheet with id=AK5, first strand: chain 'x' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR x 39 " --> pdb=" O PRO x 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA x 135 " --> pdb=" O LEU x 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN x 167 " --> pdb=" O ILE x 103 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE x 103 " --> pdb=" O ASN x 167 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP x 104 " --> pdb=" O SER x 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER x 92 " --> pdb=" O ASP x 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU x 36 " --> pdb=" O ALA x 91 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'x' and resid 361 through 364 Processing sheet with id=AK7, first strand: chain 'x' and resid 269 through 270 removed outlier: 3.658A pdb=" N THR x 269 " --> pdb=" O ARG x 359 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'y' and resid 26 through 28 Processing sheet with id=AK9, first strand: chain 'y' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR y 39 " --> pdb=" O PRO y 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA y 135 " --> pdb=" O LEU y 126 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN y 167 " --> pdb=" O ILE y 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE y 103 " --> pdb=" O ASN y 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP y 104 " --> pdb=" O SER y 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER y 92 " --> pdb=" O ASP y 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU y 36 " --> pdb=" O ALA y 91 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'y' and resid 361 through 364 Processing sheet with id=AL2, first strand: chain 'y' and resid 269 through 270 removed outlier: 3.658A pdb=" N THR y 269 " --> pdb=" O ARG y 359 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'z' and resid 26 through 28 Processing sheet with id=AL4, first strand: chain 'z' and resid 120 through 121 removed outlier: 4.832A pdb=" N TYR z 39 " --> pdb=" O PRO z 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA z 135 " --> pdb=" O LEU z 126 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN z 167 " --> pdb=" O ILE z 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE z 103 " --> pdb=" O ASN z 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP z 104 " --> pdb=" O SER z 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER z 92 " --> pdb=" O ASP z 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU z 36 " --> pdb=" O ALA z 91 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'z' and resid 269 through 270 removed outlier: 3.658A pdb=" N THR z 269 " --> pdb=" O ARG z 359 " (cutoff:3.500A) 2574 hydrogen bonds defined for protein. 7254 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: 23.74 Time building geometry restraints manager: 20.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 20722 1.34 - 1.46: 10344 1.46 - 1.58: 27252 1.58 - 1.70: 0 1.70 - 1.81: 624 Bond restraints: 58942 Sorted by residual: bond pdb=" C ALA i 355 " pdb=" N GLY i 356 " ideal model delta sigma weight residual 1.331 1.316 0.015 1.46e-02 4.69e+03 1.05e+00 bond pdb=" C ALA t 355 " pdb=" N GLY t 356 " ideal model delta sigma weight residual 1.331 1.316 0.015 1.46e-02 4.69e+03 1.05e+00 bond pdb=" C ALA e 355 " pdb=" N GLY e 356 " ideal model delta sigma weight residual 1.331 1.316 0.015 1.46e-02 4.69e+03 1.05e+00 bond pdb=" C ALA v 355 " pdb=" N GLY v 356 " ideal model delta sigma weight residual 1.331 1.316 0.015 1.46e-02 4.69e+03 1.05e+00 bond pdb=" C ALA h 355 " pdb=" N GLY h 356 " ideal model delta sigma weight residual 1.331 1.316 0.015 1.46e-02 4.69e+03 1.03e+00 ... (remaining 58937 not shown) Histogram of bond angle deviations from ideal: 99.07 - 104.92: 884 104.92 - 110.78: 20626 110.78 - 116.63: 22145 116.63 - 122.48: 26772 122.48 - 128.34: 9523 Bond angle restraints: 79950 Sorted by residual: angle pdb=" CA LEU k 160 " pdb=" CB LEU k 160 " pdb=" CG LEU k 160 " ideal model delta sigma weight residual 116.30 124.89 -8.59 3.50e+00 8.16e-02 6.02e+00 angle pdb=" CA LEU e 160 " pdb=" CB LEU e 160 " pdb=" CG LEU e 160 " ideal model delta sigma weight residual 116.30 124.88 -8.58 3.50e+00 8.16e-02 6.01e+00 angle pdb=" CA LEU o 160 " pdb=" CB LEU o 160 " pdb=" CG LEU o 160 " ideal model delta sigma weight residual 116.30 124.87 -8.57 3.50e+00 8.16e-02 6.00e+00 angle pdb=" CA LEU z 160 " pdb=" CB LEU z 160 " pdb=" CG LEU z 160 " ideal model delta sigma weight residual 116.30 124.86 -8.56 3.50e+00 8.16e-02 5.98e+00 angle pdb=" CA LEU q 160 " pdb=" CB LEU q 160 " pdb=" CG LEU q 160 " ideal model delta sigma weight residual 116.30 124.86 -8.56 3.50e+00 8.16e-02 5.98e+00 ... (remaining 79945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 32334 17.96 - 35.93: 3052 35.93 - 53.89: 520 53.89 - 71.85: 130 71.85 - 89.82: 78 Dihedral angle restraints: 36114 sinusoidal: 13780 harmonic: 22334 Sorted by residual: dihedral pdb=" CA GLY p 44 " pdb=" C GLY p 44 " pdb=" N LEU p 45 " pdb=" CA LEU p 45 " ideal model delta harmonic sigma weight residual 180.00 160.77 19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLY n 44 " pdb=" C GLY n 44 " pdb=" N LEU n 45 " pdb=" CA LEU n 45 " ideal model delta harmonic sigma weight residual 180.00 160.77 19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLY u 44 " pdb=" C GLY u 44 " pdb=" N LEU u 45 " pdb=" CA LEU u 45 " ideal model delta harmonic sigma weight residual 180.00 160.77 19.23 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 36111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 5796 0.027 - 0.053: 2242 0.053 - 0.080: 861 0.080 - 0.107: 634 0.107 - 0.134: 399 Chirality restraints: 9932 Sorted by residual: chirality pdb=" CA LEU h 45 " pdb=" N LEU h 45 " pdb=" C LEU h 45 " pdb=" CB LEU h 45 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA LEU y 45 " pdb=" N LEU y 45 " pdb=" C LEU y 45 " pdb=" CB LEU y 45 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA LEU g 45 " pdb=" N LEU g 45 " pdb=" C LEU g 45 " pdb=" CB LEU g 45 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 9929 not shown) Planarity restraints: 10582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR c 341 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO c 342 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO c 342 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO c 342 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR m 341 " 0.028 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO m 342 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO m 342 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO m 342 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR u 341 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO u 342 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO u 342 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO u 342 " -0.024 5.00e-02 4.00e+02 ... (remaining 10579 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 11023 2.78 - 3.31: 57230 3.31 - 3.84: 97413 3.84 - 4.37: 115472 4.37 - 4.90: 205409 Nonbonded interactions: 486547 Sorted by model distance: nonbonded pdb=" O ASP z 250 " pdb=" ND2 ASN z 265 " model vdw 2.246 2.520 nonbonded pdb=" O ASP n 250 " pdb=" ND2 ASN n 265 " model vdw 2.246 2.520 nonbonded pdb=" O ASP x 250 " pdb=" ND2 ASN x 265 " model vdw 2.246 2.520 nonbonded pdb=" O ASP c 250 " pdb=" ND2 ASN c 265 " model vdw 2.247 2.520 nonbonded pdb=" O ASP w 250 " pdb=" ND2 ASN w 265 " model vdw 2.247 2.520 ... (remaining 486542 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' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 338 5.16 5 C 35854 2.51 5 N 10634 2.21 5 O 11726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 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: 0.040 Extract box with map and model: 19.210 Check model and map are aligned: 0.650 Process input model: 118.810 Find NCS groups from input model: 3.260 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Set scattering table: 0.400 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.003 0.023 58942 Z= 0.200 Angle : 0.621 8.587 79950 Z= 0.324 Chirality : 0.044 0.134 9932 Planarity : 0.004 0.043 10582 Dihedral : 14.871 89.818 21762 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.10), residues: 7800 helix: 2.70 (0.12), residues: 1872 sheet: 0.19 (0.12), residues: 1716 loop : -1.14 (0.09), residues: 4212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 843 time to evaluate : 5.468 Fit side-chains outliers start: 0 outliers final: 11 residues processed: 843 average time/residue: 1.7473 time to fit residues: 1793.9231 Evaluate side-chains 574 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 563 time to evaluate : 5.307 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 10 average time/residue: 1.2319 time to fit residues: 23.0546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 658 optimal weight: 8.9990 chunk 591 optimal weight: 10.0000 chunk 328 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 398 optimal weight: 9.9990 chunk 315 optimal weight: 20.0000 chunk 611 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 371 optimal weight: 6.9990 chunk 455 optimal weight: 9.9990 chunk 708 optimal weight: 20.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 80 GLN a 112 ASN b 78 ASN b 80 GLN b 112 ASN c 112 ASN d 80 GLN e 80 GLN f 78 ASN f 80 GLN g 78 ASN g 80 GLN g 112 ASN h 78 ASN i 78 ASN j 80 GLN k 78 ASN k 80 GLN k 112 ASN l 80 GLN m 112 ASN n 80 GLN n 112 ASN o 78 ASN o 80 GLN o 112 ASN p 112 ASN s 78 ASN t 78 ASN t 80 GLN t 112 ASN u 78 ASN v 78 ASN v 80 GLN v 112 ASN w 78 ASN w 112 ASN x 78 ASN x 80 GLN x 112 ASN y 78 ASN y 112 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.063 58942 Z= 0.586 Angle : 0.722 8.339 79950 Z= 0.366 Chirality : 0.048 0.154 9932 Planarity : 0.005 0.046 10582 Dihedral : 5.627 32.013 8450 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.09), residues: 7800 helix: 2.51 (0.12), residues: 1872 sheet: 0.64 (0.13), residues: 1664 loop : -1.52 (0.09), residues: 4264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 593 time to evaluate : 5.909 Fit side-chains outliers start: 141 outliers final: 38 residues processed: 638 average time/residue: 1.9435 time to fit residues: 1493.5683 Evaluate side-chains 601 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 563 time to evaluate : 5.342 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 26 residues processed: 14 average time/residue: 0.8881 time to fit residues: 24.9055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 393 optimal weight: 7.9990 chunk 219 optimal weight: 2.9990 chunk 589 optimal weight: 7.9990 chunk 482 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 709 optimal weight: 8.9990 chunk 766 optimal weight: 10.0000 chunk 631 optimal weight: 7.9990 chunk 703 optimal weight: 1.9990 chunk 241 optimal weight: 8.9990 chunk 569 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 54 GLN d 54 GLN e 54 GLN g 54 GLN h 54 GLN h 80 GLN i 80 GLN k 54 GLN ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 80 GLN o 54 GLN p 80 GLN q 54 GLN q 80 GLN r 54 GLN r 80 GLN s 54 GLN s 80 GLN u 54 GLN u 80 GLN x 54 GLN z 80 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 58942 Z= 0.344 Angle : 0.590 7.505 79950 Z= 0.301 Chirality : 0.044 0.133 9932 Planarity : 0.004 0.048 10582 Dihedral : 5.224 29.677 8450 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.10), residues: 7800 helix: 2.45 (0.12), residues: 1872 sheet: 0.26 (0.12), residues: 1872 loop : -1.48 (0.09), residues: 4056 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 598 time to evaluate : 5.473 Fit side-chains outliers start: 105 outliers final: 42 residues processed: 639 average time/residue: 1.9483 time to fit residues: 1500.4770 Evaluate side-chains 583 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 541 time to evaluate : 5.371 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 32 residues processed: 10 average time/residue: 0.8802 time to fit residues: 19.7012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 701 optimal weight: 10.0000 chunk 533 optimal weight: 10.0000 chunk 368 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 338 optimal weight: 2.9990 chunk 476 optimal weight: 9.9990 chunk 712 optimal weight: 5.9990 chunk 753 optimal weight: 5.9990 chunk 372 optimal weight: 8.9990 chunk 674 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 54 GLN b 54 GLN i 54 GLN j 54 GLN ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 78 ASN n 54 GLN p 54 GLN ** s 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 54 GLN v 54 GLN z 54 GLN z 78 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 58942 Z= 0.378 Angle : 0.606 6.855 79950 Z= 0.309 Chirality : 0.044 0.135 9932 Planarity : 0.004 0.048 10582 Dihedral : 5.276 29.483 8450 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.09), residues: 7800 helix: 2.39 (0.12), residues: 1898 sheet: 0.54 (0.13), residues: 1664 loop : -1.55 (0.09), residues: 4238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 590 time to evaluate : 5.483 Fit side-chains outliers start: 105 outliers final: 53 residues processed: 631 average time/residue: 2.0059 time to fit residues: 1535.0310 Evaluate side-chains 598 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 545 time to evaluate : 5.383 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 34 residues processed: 19 average time/residue: 0.8114 time to fit residues: 30.7591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 627 optimal weight: 4.9990 chunk 427 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 561 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 chunk 643 optimal weight: 7.9990 chunk 521 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 384 optimal weight: 10.0000 chunk 676 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 78 ASN l 54 GLN l 78 ASN ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 78 ASN w 54 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 58942 Z= 0.355 Angle : 0.592 6.589 79950 Z= 0.303 Chirality : 0.044 0.134 9932 Planarity : 0.004 0.048 10582 Dihedral : 5.222 29.161 8450 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.09), residues: 7800 helix: 2.40 (0.12), residues: 1898 sheet: 0.18 (0.12), residues: 1794 loop : -1.46 (0.09), residues: 4108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 583 time to evaluate : 5.428 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 49 residues processed: 642 average time/residue: 1.9250 time to fit residues: 1498.9399 Evaluate side-chains 595 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 546 time to evaluate : 5.370 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 35 residues processed: 14 average time/residue: 0.8207 time to fit residues: 24.1790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 253 optimal weight: 10.0000 chunk 678 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 442 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 754 optimal weight: 5.9990 chunk 626 optimal weight: 10.0000 chunk 349 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 396 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 54 GLN ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 58942 Z= 0.311 Angle : 0.584 9.790 79950 Z= 0.297 Chirality : 0.043 0.132 9932 Planarity : 0.004 0.048 10582 Dihedral : 5.138 29.039 8450 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.10), residues: 7800 helix: 2.40 (0.12), residues: 1898 sheet: -0.26 (0.12), residues: 2002 loop : -1.24 (0.10), residues: 3900 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 594 time to evaluate : 5.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 50 residues processed: 658 average time/residue: 1.9483 time to fit residues: 1550.9593 Evaluate side-chains 596 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 546 time to evaluate : 5.295 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 38 residues processed: 12 average time/residue: 0.7522 time to fit residues: 20.8353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 727 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 429 optimal weight: 10.0000 chunk 551 optimal weight: 7.9990 chunk 427 optimal weight: 9.9990 chunk 635 optimal weight: 10.0000 chunk 421 optimal weight: 7.9990 chunk 751 optimal weight: 3.9990 chunk 470 optimal weight: 5.9990 chunk 458 optimal weight: 0.9990 chunk 347 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 161 ASN ** v 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 58942 Z= 0.214 Angle : 0.549 7.864 79950 Z= 0.281 Chirality : 0.042 0.140 9932 Planarity : 0.004 0.049 10582 Dihedral : 4.888 27.720 8450 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.10), residues: 7800 helix: 2.43 (0.12), residues: 1898 sheet: -0.26 (0.12), residues: 2002 loop : -1.12 (0.10), residues: 3900 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 586 time to evaluate : 6.104 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 outliers start: 117 outliers final: 61 residues processed: 670 average time/residue: 1.8634 time to fit residues: 1521.0537 Evaluate side-chains 605 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 544 time to evaluate : 5.325 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 49 residues processed: 12 average time/residue: 0.5911 time to fit residues: 18.8880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 465 optimal weight: 20.0000 chunk 300 optimal weight: 10.0000 chunk 449 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 477 optimal weight: 8.9990 chunk 512 optimal weight: 5.9990 chunk 371 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 590 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 161 ASN f 161 ASN i 161 ASN ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 161 ASN s 161 ASN v 161 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.053 58942 Z= 0.546 Angle : 0.704 9.078 79950 Z= 0.360 Chirality : 0.046 0.148 9932 Planarity : 0.004 0.050 10582 Dihedral : 5.509 30.526 8450 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.09), residues: 7800 helix: 2.28 (0.12), residues: 1898 sheet: 0.02 (0.12), residues: 1794 loop : -1.40 (0.09), residues: 4108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 592 time to evaluate : 5.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 51 residues processed: 674 average time/residue: 1.8835 time to fit residues: 1543.6786 Evaluate side-chains 593 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 542 time to evaluate : 5.287 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 37 residues processed: 14 average time/residue: 0.8505 time to fit residues: 24.2981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 683 optimal weight: 4.9990 chunk 720 optimal weight: 7.9990 chunk 657 optimal weight: 0.9980 chunk 700 optimal weight: 0.9990 chunk 421 optimal weight: 6.9990 chunk 305 optimal weight: 0.9980 chunk 550 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 633 optimal weight: 6.9990 chunk 662 optimal weight: 8.9990 chunk 698 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 161 ASN b 161 ASN d 161 ASN f 161 ASN ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 161 ASN m 161 ASN n 161 ASN o 161 ASN q 161 ASN s 161 ASN y 161 ASN z 161 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 58942 Z= 0.196 Angle : 0.564 8.746 79950 Z= 0.290 Chirality : 0.042 0.128 9932 Planarity : 0.004 0.049 10582 Dihedral : 4.932 28.764 8450 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.10), residues: 7800 helix: 2.37 (0.12), residues: 1898 sheet: -0.37 (0.12), residues: 2054 loop : -1.11 (0.10), residues: 3848 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 570 time to evaluate : 5.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 44 residues processed: 641 average time/residue: 1.8685 time to fit residues: 1455.5467 Evaluate side-chains 572 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 528 time to evaluate : 5.355 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 40 residues processed: 4 average time/residue: 0.4530 time to fit residues: 10.4293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 460 optimal weight: 6.9990 chunk 740 optimal weight: 10.0000 chunk 452 optimal weight: 3.9990 chunk 351 optimal weight: 0.9990 chunk 514 optimal weight: 5.9990 chunk 777 optimal weight: 0.9980 chunk 715 optimal weight: 10.0000 chunk 618 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 477 optimal weight: 3.9990 chunk 379 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 GLN d 161 ASN f 161 ASN g 161 ASN ** h 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 161 ASN ** m 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 161 ASN ** o 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 161 ASN s 161 ASN ** t 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 161 ASN ** v 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 54 GLN ** y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 161 ASN z 161 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 58942 Z= 0.200 Angle : 0.578 12.415 79950 Z= 0.293 Chirality : 0.042 0.128 9932 Planarity : 0.004 0.049 10582 Dihedral : 4.818 29.195 8450 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.10), residues: 7800 helix: 2.39 (0.12), residues: 1898 sheet: -0.29 (0.12), residues: 1898 loop : -0.95 (0.10), residues: 4004 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15600 Ramachandran restraints generated. 7800 Oldfield, 0 Emsley, 7800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 567 time to evaluate : 5.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 44 residues processed: 618 average time/residue: 1.9205 time to fit residues: 1449.9142 Evaluate side-chains 575 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 531 time to evaluate : 5.390 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 39 residues processed: 6 average time/residue: 0.9080 time to fit residues: 14.9842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 491 optimal weight: 7.9990 chunk 659 optimal weight: 0.6980 chunk 189 optimal weight: 9.9990 chunk 570 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 619 optimal weight: 8.9990 chunk 259 optimal weight: 8.9990 chunk 636 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 overall best weight: 6.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.052801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.042886 restraints weight = 200770.122| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.33 r_work: 0.2652 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.045 58942 Z= 0.432 Angle : 0.671 12.595 79950 Z= 0.344 Chirality : 0.044 0.137 9932 Planarity : 0.004 0.049 10582 Dihedral : 5.326 30.196 8450 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.10), residues: 7800 helix: 2.28 (0.12), residues: 1898 sheet: -0.33 (0.12), residues: 2028 loop : -1.08 (0.10), residues: 3874 =============================================================================== Job complete usr+sys time: 19817.28 seconds wall clock time: 344 minutes 50.53 seconds (20690.53 seconds total)