Starting phenix.real_space_refine on Mon Mar 11 17:00:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bj2_12193/03_2024/7bj2_12193.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bj2_12193/03_2024/7bj2_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_12193/03_2024/7bj2_12193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bj2_12193/03_2024/7bj2_12193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bj2_12193/03_2024/7bj2_12193.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bj2_12193/03_2024/7bj2_12193.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 22.17, per 1000 atoms: 0.38 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: 16.79 Conformation dependent library (CDL) restraints added in 8.0 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: 5.30 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: 23.91 Time building geometry restraints manager: 18.55 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 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: 3.630 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: 0.050 Extract box with map and model: 17.950 Check model and map are aligned: 0.650 Set scattering table: 0.410 Process input model: 118.390 Find NCS groups from input model: 3.340 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 % Allowed : 0.67 % Favored : 99.33 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE w 57 TYR 0.008 0.001 TYR l 134 ARG 0.007 0.001 ARG p 224 *********************** 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 : 4.996 Fit side-chains outliers start: 0 outliers final: 11 residues processed: 843 average time/residue: 1.6959 time to fit residues: 1745.3775 Evaluate side-chains 574 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 563 time to evaluate : 4.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 196 MET Chi-restraints excluded: chain c residue 196 MET Chi-restraints excluded: chain e residue 196 MET Chi-restraints excluded: chain k residue 196 MET Chi-restraints excluded: chain m residue 196 MET Chi-restraints excluded: chain o residue 196 MET Chi-restraints excluded: chain p residue 196 MET Chi-restraints excluded: chain v residue 185 ILE Chi-restraints excluded: chain w residue 196 MET Chi-restraints excluded: chain x residue 196 MET Chi-restraints excluded: chain z residue 196 MET 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: 0.8010 moved from start: 0.2035 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= 0.584 Angle : 0.718 8.351 79950 Z= 0.365 Chirality : 0.048 0.153 9932 Planarity : 0.005 0.046 10582 Dihedral : 5.845 37.955 8482 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.07 % Allowed : 11.20 % Favored : 86.73 % 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: 0.02 (0.10), residues: 7800 helix: 2.53 (0.12), residues: 1872 sheet: 0.64 (0.13), residues: 1664 loop : -1.51 (0.09), residues: 4264 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE c 96 TYR 0.012 0.002 TYR k 39 ARG 0.003 0.001 ARG z 266 *********************** 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 728 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 593 time to evaluate : 5.077 Fit side-chains REVERT: m 192 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7495 (pm20) REVERT: z 192 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7521 (pm20) outliers start: 135 outliers final: 39 residues processed: 642 average time/residue: 1.8768 time to fit residues: 1449.9391 Evaluate side-chains 608 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 567 time to evaluate : 5.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 344 ASP Chi-restraints excluded: chain c residue 344 ASP Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain d residue 112 ASN Chi-restraints excluded: chain d residue 344 ASP Chi-restraints excluded: chain e residue 112 ASN Chi-restraints excluded: chain f residue 79 MET Chi-restraints excluded: chain g residue 79 MET Chi-restraints excluded: chain h residue 365 ILE Chi-restraints excluded: chain i residue 112 ASN Chi-restraints excluded: chain i residue 344 ASP Chi-restraints excluded: chain j residue 79 MET Chi-restraints excluded: chain j residue 112 ASN Chi-restraints excluded: chain j residue 344 ASP Chi-restraints excluded: chain k residue 344 ASP Chi-restraints excluded: chain l residue 112 ASN Chi-restraints excluded: chain l residue 196 MET Chi-restraints excluded: chain l residue 344 ASP Chi-restraints excluded: chain m residue 82 LYS Chi-restraints excluded: chain m residue 192 GLU Chi-restraints excluded: chain m residue 344 ASP Chi-restraints excluded: chain o residue 344 ASP Chi-restraints excluded: chain p residue 344 ASP Chi-restraints excluded: chain p residue 365 ILE Chi-restraints excluded: chain q residue 112 ASN Chi-restraints excluded: chain q residue 344 ASP Chi-restraints excluded: chain r residue 196 MET Chi-restraints excluded: chain s residue 344 ASP Chi-restraints excluded: chain t residue 79 MET Chi-restraints excluded: chain t residue 365 ILE Chi-restraints excluded: chain u residue 365 ILE Chi-restraints excluded: chain v residue 344 ASP Chi-restraints excluded: chain w residue 344 ASP Chi-restraints excluded: chain w residue 365 ILE Chi-restraints excluded: chain x residue 79 MET Chi-restraints excluded: chain x residue 344 ASP Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain y residue 344 ASP Chi-restraints excluded: chain z residue 112 ASN Chi-restraints excluded: chain z residue 192 GLU Chi-restraints excluded: chain z residue 344 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 393 optimal weight: 8.9990 chunk 219 optimal weight: 3.9990 chunk 589 optimal weight: 7.9990 chunk 482 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 709 optimal weight: 8.9990 chunk 766 optimal weight: 6.9990 chunk 631 optimal weight: 5.9990 chunk 703 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 569 optimal weight: 5.9990 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 e 54 GLN h 80 GLN i 80 GLN k 54 GLN l 112 ASN m 80 GLN p 80 GLN q 54 GLN q 80 GLN r 54 GLN r 80 GLN s 80 GLN u 80 GLN x 54 GLN z 80 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 58942 Z= 0.345 Angle : 0.592 7.406 79950 Z= 0.302 Chirality : 0.044 0.134 9932 Planarity : 0.004 0.048 10582 Dihedral : 5.243 29.429 8450 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.61 % Allowed : 14.66 % Favored : 83.73 % 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: 2.48 (0.12), residues: 1872 sheet: 0.61 (0.13), residues: 1664 loop : -1.51 (0.09), residues: 4264 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE l 57 TYR 0.008 0.001 TYR i 39 ARG 0.002 0.000 ARG i 224 *********************** 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 699 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 594 time to evaluate : 4.959 Fit side-chains REVERT: z 192 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7476 (pm20) outliers start: 105 outliers final: 40 residues processed: 635 average time/residue: 1.8481 time to fit residues: 1416.3894 Evaluate side-chains 586 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 545 time to evaluate : 4.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 344 ASP Chi-restraints excluded: chain c residue 344 ASP Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain d residue 79 MET Chi-restraints excluded: chain d residue 112 ASN Chi-restraints excluded: chain d residue 344 ASP Chi-restraints excluded: chain e residue 112 ASN Chi-restraints excluded: chain f residue 79 MET Chi-restraints excluded: chain f residue 344 ASP Chi-restraints excluded: chain g residue 79 MET Chi-restraints excluded: chain h residue 344 ASP Chi-restraints excluded: chain i residue 112 ASN Chi-restraints excluded: chain i residue 344 ASP Chi-restraints excluded: chain j residue 112 ASN Chi-restraints excluded: chain j residue 344 ASP Chi-restraints excluded: chain k residue 344 ASP Chi-restraints excluded: chain l residue 112 ASN Chi-restraints excluded: chain l residue 344 ASP Chi-restraints excluded: chain m residue 344 ASP Chi-restraints excluded: chain n residue 344 ASP Chi-restraints excluded: chain p residue 344 ASP Chi-restraints excluded: chain p residue 365 ILE Chi-restraints excluded: chain q residue 79 MET Chi-restraints excluded: chain q residue 112 ASN Chi-restraints excluded: chain q residue 344 ASP Chi-restraints excluded: chain r residue 112 ASN Chi-restraints excluded: chain r residue 196 MET Chi-restraints excluded: chain r residue 344 ASP Chi-restraints excluded: chain t residue 79 MET Chi-restraints excluded: chain t residue 110 MET Chi-restraints excluded: chain t residue 365 ILE Chi-restraints excluded: chain u residue 344 ASP Chi-restraints excluded: chain v residue 178 GLN Chi-restraints excluded: chain v residue 344 ASP Chi-restraints excluded: chain w residue 79 MET Chi-restraints excluded: chain w residue 365 ILE Chi-restraints excluded: chain x residue 79 MET Chi-restraints excluded: chain x residue 344 ASP Chi-restraints excluded: chain y residue 344 ASP Chi-restraints excluded: chain z residue 192 GLU Chi-restraints excluded: chain z residue 344 ASP 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: 9.9990 chunk 368 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 338 optimal weight: 7.9990 chunk 476 optimal weight: 9.9990 chunk 712 optimal weight: 5.9990 chunk 753 optimal weight: 4.9990 chunk 372 optimal weight: 0.9990 chunk 674 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 d 54 GLN f 54 GLN g 54 GLN h 54 GLN i 54 GLN j 54 GLN m 78 ASN n 54 GLN o 54 GLN p 54 GLN s 54 GLN t 54 GLN u 54 GLN v 54 GLN z 54 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2218 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= 0.321 Angle : 0.581 6.687 79950 Z= 0.296 Chirality : 0.044 0.133 9932 Planarity : 0.004 0.048 10582 Dihedral : 5.159 30.269 8450 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.50 % Allowed : 16.23 % Favored : 82.27 % 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: -0.03 (0.09), residues: 7800 helix: 2.41 (0.12), residues: 1898 sheet: 0.59 (0.13), residues: 1664 loop : -1.51 (0.09), residues: 4238 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE h 57 TYR 0.006 0.001 TYR l 210 ARG 0.002 0.000 ARG i 224 *********************** 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 690 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 592 time to evaluate : 5.163 Fit side-chains REVERT: z 192 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7492 (pm20) outliers start: 98 outliers final: 47 residues processed: 631 average time/residue: 1.8826 time to fit residues: 1430.7547 Evaluate side-chains 589 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 541 time to evaluate : 5.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 344 ASP Chi-restraints excluded: chain c residue 344 ASP Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain d residue 112 ASN Chi-restraints excluded: chain d residue 344 ASP Chi-restraints excluded: chain e residue 112 ASN Chi-restraints excluded: chain f residue 79 MET Chi-restraints excluded: chain f residue 344 ASP Chi-restraints excluded: chain f residue 365 ILE Chi-restraints excluded: chain g residue 79 MET Chi-restraints excluded: chain g residue 110 MET Chi-restraints excluded: chain h residue 112 ASN Chi-restraints excluded: chain h residue 123 MET Chi-restraints excluded: chain h residue 344 ASP Chi-restraints excluded: chain h residue 365 ILE Chi-restraints excluded: chain i residue 112 ASN Chi-restraints excluded: chain i residue 123 MET Chi-restraints excluded: chain i residue 344 ASP Chi-restraints excluded: chain i residue 365 ILE Chi-restraints excluded: chain j residue 112 ASN Chi-restraints excluded: chain j residue 344 ASP Chi-restraints excluded: chain k residue 344 ASP Chi-restraints excluded: chain l residue 344 ASP Chi-restraints excluded: chain o residue 344 ASP Chi-restraints excluded: chain p residue 344 ASP Chi-restraints excluded: chain p residue 365 ILE Chi-restraints excluded: chain q residue 112 ASN Chi-restraints excluded: chain q residue 344 ASP Chi-restraints excluded: chain r residue 112 ASN Chi-restraints excluded: chain r residue 196 MET Chi-restraints excluded: chain s residue 344 ASP Chi-restraints excluded: chain s residue 365 ILE Chi-restraints excluded: chain t residue 79 MET Chi-restraints excluded: chain t residue 110 MET Chi-restraints excluded: chain t residue 365 ILE Chi-restraints excluded: chain u residue 123 MET Chi-restraints excluded: chain u residue 344 ASP Chi-restraints excluded: chain u residue 365 ILE Chi-restraints excluded: chain v residue 178 GLN Chi-restraints excluded: chain v residue 344 ASP Chi-restraints excluded: chain w residue 344 ASP Chi-restraints excluded: chain w residue 365 ILE Chi-restraints excluded: chain x residue 344 ASP Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain y residue 344 ASP Chi-restraints excluded: chain z residue 112 ASN Chi-restraints excluded: chain z residue 192 GLU Chi-restraints excluded: chain z residue 365 ILE 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: 9.9990 chunk 10 optimal weight: 2.9990 chunk 561 optimal weight: 10.0000 chunk 311 optimal weight: 9.9990 chunk 643 optimal weight: 9.9990 chunk 521 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 384 optimal weight: 0.0870 chunk 676 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 78 ASN l 78 ASN m 54 GLN r 78 ASN z 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.004 0.028 58942 Z= 0.248 Angle : 0.551 9.171 79950 Z= 0.281 Chirality : 0.043 0.131 9932 Planarity : 0.004 0.048 10582 Dihedral : 4.965 27.981 8450 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.53 % Allowed : 16.90 % Favored : 81.57 % 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: 0.00 (0.10), residues: 7800 helix: 2.44 (0.12), residues: 1898 sheet: 0.11 (0.12), residues: 1872 loop : -1.31 (0.09), residues: 4030 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE h 57 TYR 0.005 0.001 TYR i 39 ARG 0.002 0.000 ARG e 21 *********************** 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 679 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 579 time to evaluate : 5.024 Fit side-chains REVERT: z 192 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7474 (pm20) outliers start: 100 outliers final: 42 residues processed: 621 average time/residue: 1.8649 time to fit residues: 1395.0412 Evaluate side-chains 582 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 539 time to evaluate : 4.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 344 ASP Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain d residue 112 ASN Chi-restraints excluded: chain d residue 344 ASP Chi-restraints excluded: chain e residue 112 ASN Chi-restraints excluded: chain f residue 365 ILE Chi-restraints excluded: chain g residue 110 MET Chi-restraints excluded: chain g residue 365 ILE Chi-restraints excluded: chain h residue 112 ASN Chi-restraints excluded: chain h residue 123 MET Chi-restraints excluded: chain h residue 344 ASP Chi-restraints excluded: chain i residue 112 ASN Chi-restraints excluded: chain i residue 123 MET Chi-restraints excluded: chain i residue 344 ASP Chi-restraints excluded: chain j residue 112 ASN Chi-restraints excluded: chain j residue 344 ASP Chi-restraints excluded: chain k residue 344 ASP Chi-restraints excluded: chain l residue 344 ASP Chi-restraints excluded: chain m residue 344 ASP Chi-restraints excluded: chain o residue 344 ASP Chi-restraints excluded: chain p residue 365 ILE Chi-restraints excluded: chain q residue 112 ASN Chi-restraints excluded: chain q residue 344 ASP Chi-restraints excluded: chain q residue 365 ILE Chi-restraints excluded: chain r residue 112 ASN Chi-restraints excluded: chain r residue 196 MET Chi-restraints excluded: chain s residue 344 ASP Chi-restraints excluded: chain s residue 365 ILE Chi-restraints excluded: chain t residue 110 MET Chi-restraints excluded: chain t residue 365 ILE Chi-restraints excluded: chain u residue 123 MET Chi-restraints excluded: chain u residue 344 ASP Chi-restraints excluded: chain u residue 365 ILE Chi-restraints excluded: chain v residue 123 MET Chi-restraints excluded: chain w residue 344 ASP Chi-restraints excluded: chain w residue 365 ILE Chi-restraints excluded: chain x residue 344 ASP Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain y residue 344 ASP Chi-restraints excluded: chain z residue 112 ASN Chi-restraints excluded: chain z residue 192 GLU Chi-restraints excluded: chain z residue 344 ASP Chi-restraints excluded: chain z residue 365 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 253 optimal weight: 1.9990 chunk 678 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 chunk 442 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 754 optimal weight: 10.0000 chunk 626 optimal weight: 10.0000 chunk 349 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 396 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 54 GLN l 112 ASN w 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 58942 Z= 0.477 Angle : 0.656 8.934 79950 Z= 0.334 Chirality : 0.045 0.140 9932 Planarity : 0.004 0.049 10582 Dihedral : 5.404 30.197 8450 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.05 % Allowed : 17.55 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.09), residues: 7800 helix: 2.35 (0.12), residues: 1898 sheet: 0.14 (0.12), residues: 1794 loop : -1.45 (0.09), residues: 4108 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE i 57 TYR 0.009 0.002 TYR y 210 ARG 0.002 0.000 ARG h 32 *********************** 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 729 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 595 time to evaluate : 4.993 Fit side-chains outliers start: 134 outliers final: 54 residues processed: 658 average time/residue: 1.8654 time to fit residues: 1479.2158 Evaluate side-chains 600 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 546 time to evaluate : 4.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 344 ASP Chi-restraints excluded: chain b residue 344 ASP Chi-restraints excluded: chain c residue 344 ASP Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain d residue 112 ASN Chi-restraints excluded: chain d residue 344 ASP Chi-restraints excluded: chain d residue 365 ILE Chi-restraints excluded: chain e residue 112 ASN Chi-restraints excluded: chain e residue 365 ILE Chi-restraints excluded: chain f residue 344 ASP Chi-restraints excluded: chain f residue 365 ILE Chi-restraints excluded: chain g residue 110 MET Chi-restraints excluded: chain g residue 365 ILE Chi-restraints excluded: chain h residue 112 ASN Chi-restraints excluded: chain h residue 344 ASP Chi-restraints excluded: chain h residue 365 ILE Chi-restraints excluded: chain i residue 112 ASN Chi-restraints excluded: chain i residue 123 MET Chi-restraints excluded: chain i residue 344 ASP Chi-restraints excluded: chain j residue 112 ASN Chi-restraints excluded: chain j residue 344 ASP Chi-restraints excluded: chain k residue 344 ASP Chi-restraints excluded: chain l residue 112 ASN Chi-restraints excluded: chain l residue 344 ASP Chi-restraints excluded: chain m residue 344 ASP Chi-restraints excluded: chain m residue 365 ILE Chi-restraints excluded: chain n residue 344 ASP Chi-restraints excluded: chain n residue 365 ILE Chi-restraints excluded: chain o residue 344 ASP Chi-restraints excluded: chain p residue 344 ASP Chi-restraints excluded: chain p residue 365 ILE Chi-restraints excluded: chain q residue 112 ASN Chi-restraints excluded: chain q residue 344 ASP Chi-restraints excluded: chain q residue 365 ILE Chi-restraints excluded: chain r residue 112 ASN Chi-restraints excluded: chain r residue 196 MET Chi-restraints excluded: chain r residue 365 ILE Chi-restraints excluded: chain s residue 344 ASP Chi-restraints excluded: chain s residue 365 ILE Chi-restraints excluded: chain t residue 110 MET Chi-restraints excluded: chain t residue 365 ILE Chi-restraints excluded: chain u residue 112 ASN Chi-restraints excluded: chain u residue 344 ASP Chi-restraints excluded: chain u residue 365 ILE Chi-restraints excluded: chain v residue 123 MET Chi-restraints excluded: chain v residue 344 ASP Chi-restraints excluded: chain w residue 344 ASP Chi-restraints excluded: chain w residue 365 ILE Chi-restraints excluded: chain x residue 344 ASP Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain y residue 344 ASP Chi-restraints excluded: chain y residue 365 ILE Chi-restraints excluded: chain z residue 112 ASN Chi-restraints excluded: chain z residue 344 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 727 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 429 optimal weight: 0.8980 chunk 551 optimal weight: 6.9990 chunk 427 optimal weight: 3.9990 chunk 635 optimal weight: 5.9990 chunk 421 optimal weight: 10.0000 chunk 751 optimal weight: 4.9990 chunk 470 optimal weight: 0.9990 chunk 458 optimal weight: 1.9990 chunk 347 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 161 ASN r 161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2505 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= 0.221 Angle : 0.557 8.195 79950 Z= 0.285 Chirality : 0.042 0.136 9932 Planarity : 0.004 0.049 10582 Dihedral : 4.965 27.569 8450 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.72 % Allowed : 18.07 % Favored : 80.22 % 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: -0.04 (0.10), residues: 7800 helix: 2.44 (0.12), residues: 1898 sheet: -0.28 (0.12), residues: 2002 loop : -1.16 (0.10), residues: 3900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE l 57 TYR 0.004 0.001 TYR k 39 ARG 0.002 0.000 ARG i 224 *********************** 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 693 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 581 time to evaluate : 4.936 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: s 123 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7373 (ttt) outliers start: 112 outliers final: 53 residues processed: 650 average time/residue: 1.7841 time to fit residues: 1411.3929 Evaluate side-chains 590 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 536 time to evaluate : 5.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 46 ASP Chi-restraints excluded: chain b residue 344 ASP Chi-restraints excluded: chain c residue 344 ASP Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain d residue 112 ASN Chi-restraints excluded: chain d residue 344 ASP Chi-restraints excluded: chain d residue 365 ILE Chi-restraints excluded: chain e residue 104 ASP Chi-restraints excluded: chain e residue 112 ASN Chi-restraints excluded: chain e residue 365 ILE Chi-restraints excluded: chain f residue 46 ASP Chi-restraints excluded: chain f residue 344 ASP Chi-restraints excluded: chain f residue 365 ILE Chi-restraints excluded: chain g residue 110 MET Chi-restraints excluded: chain g residue 365 ILE Chi-restraints excluded: chain h residue 112 ASN Chi-restraints excluded: chain h residue 344 ASP Chi-restraints excluded: chain h residue 365 ILE Chi-restraints excluded: chain i residue 112 ASN Chi-restraints excluded: chain i residue 123 MET Chi-restraints excluded: chain j residue 112 ASN Chi-restraints excluded: chain j residue 344 ASP Chi-restraints excluded: chain k residue 46 ASP Chi-restraints excluded: chain k residue 344 ASP Chi-restraints excluded: chain l residue 46 ASP Chi-restraints excluded: chain m residue 344 ASP Chi-restraints excluded: chain m residue 365 ILE Chi-restraints excluded: chain o residue 46 ASP Chi-restraints excluded: chain o residue 344 ASP Chi-restraints excluded: chain p residue 344 ASP Chi-restraints excluded: chain p residue 365 ILE Chi-restraints excluded: chain q residue 112 ASN Chi-restraints excluded: chain q residue 344 ASP Chi-restraints excluded: chain q residue 365 ILE Chi-restraints excluded: chain r residue 104 ASP Chi-restraints excluded: chain r residue 112 ASN Chi-restraints excluded: chain r residue 196 MET Chi-restraints excluded: chain r residue 365 ILE Chi-restraints excluded: chain s residue 46 ASP Chi-restraints excluded: chain s residue 123 MET Chi-restraints excluded: chain s residue 365 ILE Chi-restraints excluded: chain t residue 46 ASP Chi-restraints excluded: chain t residue 110 MET Chi-restraints excluded: chain t residue 365 ILE Chi-restraints excluded: chain u residue 344 ASP Chi-restraints excluded: chain v residue 123 MET Chi-restraints excluded: chain w residue 127 LYS Chi-restraints excluded: chain w residue 344 ASP Chi-restraints excluded: chain x residue 46 ASP Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain y residue 344 ASP Chi-restraints excluded: chain y residue 365 ILE Chi-restraints excluded: chain z residue 344 ASP Chi-restraints excluded: chain z residue 365 ILE 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: 3.9990 chunk 449 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 477 optimal weight: 4.9990 chunk 512 optimal weight: 9.9990 chunk 371 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 590 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 161 ASN l 112 ASN o 161 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 58942 Z= 0.301 Angle : 0.593 8.392 79950 Z= 0.302 Chirality : 0.043 0.134 9932 Planarity : 0.004 0.049 10582 Dihedral : 5.061 28.069 8450 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.87 % Allowed : 18.17 % Favored : 79.96 % 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: -0.05 (0.10), residues: 7800 helix: 2.36 (0.12), residues: 1898 sheet: -0.29 (0.12), residues: 2002 loop : -1.12 (0.10), residues: 3900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE i 57 TYR 0.006 0.001 TYR d 210 ARG 0.002 0.000 ARG p 21 *********************** 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 710 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 588 time to evaluate : 7.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 61 residues processed: 660 average time/residue: 1.8080 time to fit residues: 1448.9370 Evaluate side-chains 594 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 533 time to evaluate : 4.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 46 ASP Chi-restraints excluded: chain b residue 344 ASP Chi-restraints excluded: chain c residue 344 ASP Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain d residue 112 ASN Chi-restraints excluded: chain d residue 344 ASP Chi-restraints excluded: chain d residue 365 ILE Chi-restraints excluded: chain e residue 46 ASP Chi-restraints excluded: chain e residue 104 ASP Chi-restraints excluded: chain e residue 112 ASN Chi-restraints excluded: chain e residue 365 ILE Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 344 ASP Chi-restraints excluded: chain f residue 365 ILE Chi-restraints excluded: chain g residue 110 MET Chi-restraints excluded: chain h residue 112 ASN Chi-restraints excluded: chain h residue 344 ASP Chi-restraints excluded: chain h residue 365 ILE Chi-restraints excluded: chain i residue 112 ASN Chi-restraints excluded: chain i residue 123 MET Chi-restraints excluded: chain i residue 344 ASP Chi-restraints excluded: chain j residue 46 ASP Chi-restraints excluded: chain j residue 112 ASN Chi-restraints excluded: chain j residue 344 ASP Chi-restraints excluded: chain k residue 46 ASP Chi-restraints excluded: chain k residue 196 MET Chi-restraints excluded: chain k residue 344 ASP Chi-restraints excluded: chain l residue 46 ASP Chi-restraints excluded: chain l residue 344 ASP Chi-restraints excluded: chain m residue 365 ILE Chi-restraints excluded: chain n residue 365 ILE Chi-restraints excluded: chain o residue 46 ASP Chi-restraints excluded: chain o residue 344 ASP Chi-restraints excluded: chain p residue 344 ASP Chi-restraints excluded: chain p residue 365 ILE Chi-restraints excluded: chain q residue 112 ASN Chi-restraints excluded: chain q residue 344 ASP Chi-restraints excluded: chain q residue 365 ILE Chi-restraints excluded: chain r residue 46 ASP Chi-restraints excluded: chain r residue 104 ASP Chi-restraints excluded: chain r residue 112 ASN Chi-restraints excluded: chain r residue 196 MET Chi-restraints excluded: chain r residue 365 ILE Chi-restraints excluded: chain s residue 196 MET Chi-restraints excluded: chain s residue 344 ASP Chi-restraints excluded: chain s residue 365 ILE Chi-restraints excluded: chain t residue 110 MET Chi-restraints excluded: chain t residue 365 ILE Chi-restraints excluded: chain u residue 344 ASP Chi-restraints excluded: chain u residue 365 ILE Chi-restraints excluded: chain v residue 123 MET Chi-restraints excluded: chain w residue 127 LYS Chi-restraints excluded: chain w residue 344 ASP Chi-restraints excluded: chain w residue 365 ILE Chi-restraints excluded: chain x residue 46 ASP Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain y residue 46 ASP Chi-restraints excluded: chain y residue 344 ASP Chi-restraints excluded: chain y residue 365 ILE Chi-restraints excluded: chain z residue 112 ASN Chi-restraints excluded: chain z residue 365 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 683 optimal weight: 7.9990 chunk 720 optimal weight: 6.9990 chunk 657 optimal weight: 7.9990 chunk 700 optimal weight: 1.9990 chunk 421 optimal weight: 7.9990 chunk 305 optimal weight: 7.9990 chunk 550 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 633 optimal weight: 8.9990 chunk 662 optimal weight: 9.9990 chunk 698 optimal weight: 0.7980 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 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: 0.7943 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 58942 Z= 0.260 Angle : 0.591 11.846 79950 Z= 0.301 Chirality : 0.042 0.130 9932 Planarity : 0.004 0.049 10582 Dihedral : 4.998 27.661 8450 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.72 % Allowed : 18.60 % Favored : 79.68 % 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: 2.38 (0.12), residues: 1898 sheet: -0.31 (0.12), residues: 2002 loop : -1.06 (0.10), residues: 3900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE o 57 TYR 0.008 0.001 TYR l 210 ARG 0.001 0.000 ARG x 21 *********************** 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 688 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 576 time to evaluate : 5.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 64 residues processed: 638 average time/residue: 1.8969 time to fit residues: 1476.7295 Evaluate side-chains 602 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 538 time to evaluate : 5.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 365 ILE Chi-restraints excluded: chain b residue 46 ASP Chi-restraints excluded: chain b residue 344 ASP Chi-restraints excluded: chain c residue 344 ASP Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain d residue 112 ASN Chi-restraints excluded: chain d residue 344 ASP Chi-restraints excluded: chain e residue 46 ASP Chi-restraints excluded: chain e residue 104 ASP Chi-restraints excluded: chain e residue 112 ASN Chi-restraints excluded: chain e residue 365 ILE Chi-restraints excluded: chain f residue 112 ASN Chi-restraints excluded: chain f residue 344 ASP Chi-restraints excluded: chain f residue 365 ILE Chi-restraints excluded: chain g residue 365 ILE Chi-restraints excluded: chain h residue 112 ASN Chi-restraints excluded: chain h residue 344 ASP Chi-restraints excluded: chain h residue 365 ILE Chi-restraints excluded: chain i residue 112 ASN Chi-restraints excluded: chain i residue 123 MET Chi-restraints excluded: chain j residue 46 ASP Chi-restraints excluded: chain j residue 112 ASN Chi-restraints excluded: chain j residue 344 ASP Chi-restraints excluded: chain k residue 46 ASP Chi-restraints excluded: chain k residue 196 MET Chi-restraints excluded: chain k residue 344 ASP Chi-restraints excluded: chain l residue 46 ASP Chi-restraints excluded: chain l residue 161 ASN Chi-restraints excluded: chain l residue 344 ASP Chi-restraints excluded: chain m residue 344 ASP Chi-restraints excluded: chain m residue 365 ILE Chi-restraints excluded: chain o residue 46 ASP Chi-restraints excluded: chain o residue 344 ASP Chi-restraints excluded: chain p residue 344 ASP Chi-restraints excluded: chain p residue 365 ILE Chi-restraints excluded: chain q residue 112 ASN Chi-restraints excluded: chain q residue 344 ASP Chi-restraints excluded: chain q residue 365 ILE Chi-restraints excluded: chain r residue 46 ASP Chi-restraints excluded: chain r residue 104 ASP Chi-restraints excluded: chain r residue 112 ASN Chi-restraints excluded: chain r residue 196 MET Chi-restraints excluded: chain r residue 365 ILE Chi-restraints excluded: chain s residue 112 ASN Chi-restraints excluded: chain s residue 196 MET Chi-restraints excluded: chain s residue 344 ASP Chi-restraints excluded: chain t residue 110 MET Chi-restraints excluded: chain t residue 365 ILE Chi-restraints excluded: chain u residue 344 ASP Chi-restraints excluded: chain u residue 365 ILE Chi-restraints excluded: chain v residue 123 MET Chi-restraints excluded: chain w residue 127 LYS Chi-restraints excluded: chain w residue 344 ASP Chi-restraints excluded: chain w residue 365 ILE Chi-restraints excluded: chain x residue 46 ASP Chi-restraints excluded: chain x residue 196 MET Chi-restraints excluded: chain x residue 344 ASP Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain y residue 46 ASP Chi-restraints excluded: chain y residue 344 ASP Chi-restraints excluded: chain y residue 365 ILE Chi-restraints excluded: chain z residue 112 ASN Chi-restraints excluded: chain z residue 344 ASP Chi-restraints excluded: chain z residue 365 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 460 optimal weight: 10.0000 chunk 740 optimal weight: 10.0000 chunk 452 optimal weight: 2.9990 chunk 351 optimal weight: 9.9990 chunk 514 optimal weight: 5.9990 chunk 777 optimal weight: 0.9980 chunk 715 optimal weight: 1.9990 chunk 618 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 477 optimal weight: 1.9990 chunk 379 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** a 161 ASN b 161 ASN ** c 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 161 ASN l 161 ASN n 161 ASN o 161 ASN s 161 ASN ** t 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 161 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 58942 Z= 0.223 Angle : 0.581 12.340 79950 Z= 0.295 Chirality : 0.042 0.183 9932 Planarity : 0.004 0.049 10582 Dihedral : 4.890 28.508 8450 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.20 % Allowed : 19.20 % Favored : 79.60 % 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: 2.39 (0.12), residues: 1898 sheet: -0.26 (0.12), residues: 1898 loop : -0.98 (0.10), residues: 4004 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE h 57 TYR 0.006 0.001 TYR l 210 ARG 0.001 0.000 ARG k 164 ********************** 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 652 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 574 time to evaluate : 4.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 53 residues processed: 621 average time/residue: 1.8592 time to fit residues: 1404.4521 Evaluate side-chains 597 residues out of total 6526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 544 time to evaluate : 4.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 365 ILE Chi-restraints excluded: chain b residue 46 ASP Chi-restraints excluded: chain b residue 344 ASP Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain d residue 112 ASN Chi-restraints excluded: chain d residue 344 ASP Chi-restraints excluded: chain e residue 46 ASP Chi-restraints excluded: chain e residue 104 ASP Chi-restraints excluded: chain e residue 112 ASN Chi-restraints excluded: chain e residue 365 ILE Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 365 ILE Chi-restraints excluded: chain g residue 110 MET Chi-restraints excluded: chain g residue 365 ILE Chi-restraints excluded: chain h residue 112 ASN Chi-restraints excluded: chain h residue 344 ASP Chi-restraints excluded: chain h residue 365 ILE Chi-restraints excluded: chain i residue 112 ASN Chi-restraints excluded: chain i residue 344 ASP Chi-restraints excluded: chain j residue 46 ASP Chi-restraints excluded: chain j residue 112 ASN Chi-restraints excluded: chain k residue 46 ASP Chi-restraints excluded: chain l residue 46 ASP Chi-restraints excluded: chain l residue 161 ASN Chi-restraints excluded: chain l residue 196 MET Chi-restraints excluded: chain m residue 365 ILE Chi-restraints excluded: chain o residue 46 ASP Chi-restraints excluded: chain o residue 344 ASP Chi-restraints excluded: chain p residue 365 ILE Chi-restraints excluded: chain q residue 112 ASN Chi-restraints excluded: chain q residue 344 ASP Chi-restraints excluded: chain q residue 365 ILE Chi-restraints excluded: chain r residue 46 ASP Chi-restraints excluded: chain r residue 104 ASP Chi-restraints excluded: chain r residue 112 ASN Chi-restraints excluded: chain r residue 196 MET Chi-restraints excluded: chain r residue 365 ILE Chi-restraints excluded: chain s residue 196 MET Chi-restraints excluded: chain s residue 344 ASP Chi-restraints excluded: chain t residue 110 MET Chi-restraints excluded: chain t residue 365 ILE Chi-restraints excluded: chain u residue 344 ASP Chi-restraints excluded: chain v residue 123 MET Chi-restraints excluded: chain w residue 127 LYS Chi-restraints excluded: chain w residue 344 ASP Chi-restraints excluded: chain x residue 46 ASP Chi-restraints excluded: chain x residue 196 MET Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain y residue 46 ASP Chi-restraints excluded: chain y residue 344 ASP Chi-restraints excluded: chain y residue 365 ILE Chi-restraints excluded: chain z residue 112 ASN Chi-restraints excluded: chain z residue 365 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 491 optimal weight: 6.9990 chunk 659 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 570 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 619 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 636 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.053131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.043188 restraints weight = 200140.182| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.34 r_work: 0.2665 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 58942 Z= 0.391 Angle : 0.653 10.176 79950 Z= 0.335 Chirality : 0.044 0.180 9932 Planarity : 0.004 0.050 10582 Dihedral : 5.240 29.420 8450 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.23 % Allowed : 19.35 % Favored : 79.42 % 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: -0.03 (0.10), residues: 7800 helix: 2.33 (0.12), residues: 1898 sheet: -0.33 (0.12), residues: 1898 loop : -1.03 (0.10), residues: 4004 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE o 57 TYR 0.010 0.001 TYR l 210 ARG 0.002 0.000 ARG v 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19745.87 seconds wall clock time: 343 minutes 45.78 seconds (20625.78 seconds total)