Starting phenix.real_space_refine (version: dev) on Tue Dec 20 14:49:13 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et2_31296/12_2022/7et2_31296.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et2_31296/12_2022/7et2_31296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et2_31296/12_2022/7et2_31296.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et2_31296/12_2022/7et2_31296.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et2_31296/12_2022/7et2_31296.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7et2_31296/12_2022/7et2_31296.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.007 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 89": "OD1" <-> "OD2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ASP 160": "OD1" <-> "OD2" Residue "A ASP 169": "OD1" <-> "OD2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A ARG 630": "NH1" <-> "NH2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B ASP 160": "OD1" <-> "OD2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 280": "OD1" <-> "OD2" Residue "B PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B ASP 505": "OD1" <-> "OD2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B GLU 515": "OE1" <-> "OE2" Residue "B GLU 536": "OE1" <-> "OE2" Residue "B GLU 595": "OE1" <-> "OE2" Residue "B ARG 617": "NH1" <-> "NH2" Residue "B ARG 630": "NH1" <-> "NH2" Residue "B ARG 631": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ASP 169": "OD1" <-> "OD2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C ARG 199": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C GLU 245": "OE1" <-> "OE2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C ASP 299": "OD1" <-> "OD2" Residue "C GLU 490": "OE1" <-> "OE2" Residue "C GLU 498": "OE1" <-> "OE2" Residue "C ASP 505": "OD1" <-> "OD2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C GLU 536": "OE1" <-> "OE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "C GLU 574": "OE1" <-> "OE2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C GLU 620": "OE1" <-> "OE2" Residue "C ARG 630": "NH1" <-> "NH2" Residue "C ARG 631": "NH1" <-> "NH2" Residue "D ASP 89": "OD1" <-> "OD2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D ASP 176": "OD1" <-> "OD2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D ARG 234": "NH1" <-> "NH2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D GLU 490": "OE1" <-> "OE2" Residue "D GLU 498": "OE1" <-> "OE2" Residue "D ARG 510": "NH1" <-> "NH2" Residue "D GLU 515": "OE1" <-> "OE2" Residue "D GLU 574": "OE1" <-> "OE2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D GLU 620": "OE1" <-> "OE2" Residue "D ARG 630": "NH1" <-> "NH2" Residue "D ARG 631": "NH1" <-> "NH2" Residue "G ASP 89": "OD1" <-> "OD2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G ASP 160": "OD1" <-> "OD2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G ARG 199": "NH1" <-> "NH2" Residue "G GLU 233": "OE1" <-> "OE2" Residue "G ARG 234": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 280": "OD1" <-> "OD2" Residue "G PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 293": "OE1" <-> "OE2" Residue "G GLU 490": "OE1" <-> "OE2" Residue "G GLU 498": "OE1" <-> "OE2" Residue "G ASP 505": "OD1" <-> "OD2" Residue "G ARG 510": "NH1" <-> "NH2" Residue "G GLU 515": "OE1" <-> "OE2" Residue "G GLU 536": "OE1" <-> "OE2" Residue "G GLU 595": "OE1" <-> "OE2" Residue "G ARG 617": "NH1" <-> "NH2" Residue "G ARG 630": "NH1" <-> "NH2" Residue "G ARG 631": "NH1" <-> "NH2" Residue "J ARG 159": "NH1" <-> "NH2" Residue "J ASP 169": "OD1" <-> "OD2" Residue "J GLU 198": "OE1" <-> "OE2" Residue "J ARG 199": "NH1" <-> "NH2" Residue "J ARG 234": "NH1" <-> "NH2" Residue "J GLU 245": "OE1" <-> "OE2" Residue "J ARG 253": "NH1" <-> "NH2" Residue "J TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 293": "OE1" <-> "OE2" Residue "J ASP 299": "OD1" <-> "OD2" Residue "J GLU 490": "OE1" <-> "OE2" Residue "J GLU 498": "OE1" <-> "OE2" Residue "J ASP 505": "OD1" <-> "OD2" Residue "J ARG 510": "NH1" <-> "NH2" Residue "J GLU 515": "OE1" <-> "OE2" Residue "J GLU 536": "OE1" <-> "OE2" Residue "J GLU 544": "OE1" <-> "OE2" Residue "J GLU 574": "OE1" <-> "OE2" Residue "J ARG 617": "NH1" <-> "NH2" Residue "J GLU 620": "OE1" <-> "OE2" Residue "J ARG 630": "NH1" <-> "NH2" Residue "J ARG 631": "NH1" <-> "NH2" Residue "E ASP 89": "OD1" <-> "OD2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E ASP 160": "OD1" <-> "OD2" Residue "E ASP 169": "OD1" <-> "OD2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E ARG 199": "NH1" <-> "NH2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E ARG 234": "NH1" <-> "NH2" Residue "E GLU 245": "OE1" <-> "OE2" Residue "E ARG 253": "NH1" <-> "NH2" Residue "E TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 278": "OE1" <-> "OE2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "E GLU 490": "OE1" <-> "OE2" Residue "E GLU 498": "OE1" <-> "OE2" Residue "E ARG 510": "NH1" <-> "NH2" Residue "E GLU 515": "OE1" <-> "OE2" Residue "E GLU 574": "OE1" <-> "OE2" Residue "E GLU 595": "OE1" <-> "OE2" Residue "E ARG 617": "NH1" <-> "NH2" Residue "E GLU 620": "OE1" <-> "OE2" Residue "E ARG 630": "NH1" <-> "NH2" Residue "E ARG 631": "NH1" <-> "NH2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "H ARG 159": "NH1" <-> "NH2" Residue "H ASP 160": "OD1" <-> "OD2" Residue "H ASP 169": "OD1" <-> "OD2" Residue "H ARG 199": "NH1" <-> "NH2" Residue "H GLU 233": "OE1" <-> "OE2" Residue "H ARG 234": "NH1" <-> "NH2" Residue "H ARG 253": "NH1" <-> "NH2" Residue "H TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 280": "OD1" <-> "OD2" Residue "H PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 293": "OE1" <-> "OE2" Residue "H GLU 490": "OE1" <-> "OE2" Residue "H GLU 498": "OE1" <-> "OE2" Residue "H ASP 505": "OD1" <-> "OD2" Residue "H ARG 510": "NH1" <-> "NH2" Residue "H GLU 515": "OE1" <-> "OE2" Residue "H GLU 536": "OE1" <-> "OE2" Residue "H GLU 595": "OE1" <-> "OE2" Residue "H ARG 617": "NH1" <-> "NH2" Residue "H ARG 630": "NH1" <-> "NH2" Residue "H ARG 631": "NH1" <-> "NH2" Residue "K ARG 159": "NH1" <-> "NH2" Residue "K ASP 169": "OD1" <-> "OD2" Residue "K GLU 198": "OE1" <-> "OE2" Residue "K ARG 199": "NH1" <-> "NH2" Residue "K ARG 234": "NH1" <-> "NH2" Residue "K ARG 253": "NH1" <-> "NH2" Residue "K TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 293": "OE1" <-> "OE2" Residue "K ASP 299": "OD1" <-> "OD2" Residue "K GLU 490": "OE1" <-> "OE2" Residue "K GLU 498": "OE1" <-> "OE2" Residue "K ASP 505": "OD1" <-> "OD2" Residue "K ARG 510": "NH1" <-> "NH2" Residue "K GLU 515": "OE1" <-> "OE2" Residue "K GLU 536": "OE1" <-> "OE2" Residue "K GLU 544": "OE1" <-> "OE2" Residue "K GLU 574": "OE1" <-> "OE2" Residue "K ARG 617": "NH1" <-> "NH2" Residue "K GLU 620": "OE1" <-> "OE2" Residue "K ARG 630": "NH1" <-> "NH2" Residue "K ARG 631": "NH1" <-> "NH2" Residue "F ASP 89": "OD1" <-> "OD2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ASP 160": "OD1" <-> "OD2" Residue "F ASP 169": "OD1" <-> "OD2" Residue "F ASP 176": "OD1" <-> "OD2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F ARG 234": "NH1" <-> "NH2" Residue "F GLU 245": "OE1" <-> "OE2" Residue "F ARG 253": "NH1" <-> "NH2" Residue "F TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F GLU 490": "OE1" <-> "OE2" Residue "F GLU 498": "OE1" <-> "OE2" Residue "F ARG 510": "NH1" <-> "NH2" Residue "F GLU 515": "OE1" <-> "OE2" Residue "F GLU 574": "OE1" <-> "OE2" Residue "F GLU 595": "OE1" <-> "OE2" Residue "F ARG 617": "NH1" <-> "NH2" Residue "F GLU 620": "OE1" <-> "OE2" Residue "F ARG 630": "NH1" <-> "NH2" Residue "F ARG 631": "NH1" <-> "NH2" Residue "I ASP 89": "OD1" <-> "OD2" Residue "I ARG 159": "NH1" <-> "NH2" Residue "I ASP 160": "OD1" <-> "OD2" Residue "I ASP 169": "OD1" <-> "OD2" Residue "I ARG 199": "NH1" <-> "NH2" Residue "I GLU 233": "OE1" <-> "OE2" Residue "I ARG 234": "NH1" <-> "NH2" Residue "I ARG 253": "NH1" <-> "NH2" Residue "I TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 280": "OD1" <-> "OD2" Residue "I PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 293": "OE1" <-> "OE2" Residue "I GLU 490": "OE1" <-> "OE2" Residue "I GLU 498": "OE1" <-> "OE2" Residue "I ASP 505": "OD1" <-> "OD2" Residue "I ARG 510": "NH1" <-> "NH2" Residue "I GLU 515": "OE1" <-> "OE2" Residue "I GLU 536": "OE1" <-> "OE2" Residue "I GLU 595": "OE1" <-> "OE2" Residue "I ARG 617": "NH1" <-> "NH2" Residue "I ARG 630": "NH1" <-> "NH2" Residue "I ARG 631": "NH1" <-> "NH2" Residue "L ARG 159": "NH1" <-> "NH2" Residue "L ASP 169": "OD1" <-> "OD2" Residue "L GLU 198": "OE1" <-> "OE2" Residue "L ARG 199": "NH1" <-> "NH2" Residue "L ARG 234": "NH1" <-> "NH2" Residue "L ARG 253": "NH1" <-> "NH2" Residue "L TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 293": "OE1" <-> "OE2" Residue "L ASP 299": "OD1" <-> "OD2" Residue "L GLU 490": "OE1" <-> "OE2" Residue "L GLU 498": "OE1" <-> "OE2" Residue "L ASP 505": "OD1" <-> "OD2" Residue "L ARG 510": "NH1" <-> "NH2" Residue "L GLU 515": "OE1" <-> "OE2" Residue "L GLU 536": "OE1" <-> "OE2" Residue "L GLU 544": "OE1" <-> "OE2" Residue "L GLU 574": "OE1" <-> "OE2" Residue "L ARG 617": "NH1" <-> "NH2" Residue "L GLU 620": "OE1" <-> "OE2" Residue "L ARG 630": "NH1" <-> "NH2" Residue "L ARG 631": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 38880 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "B" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "C" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "D" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "G" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "J" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "E" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "H" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "K" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "F" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "I" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "L" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Time building chain proxies: 20.78, per 1000 atoms: 0.53 Number of scatterers: 38880 At special positions: 0 Unit cell: (167.375, 167.375, 144.625, 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 144 16.00 O 6888 8.00 N 6972 7.00 C 24876 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: 14.85 Conformation dependent library (CDL) restraints added in 5.8 seconds 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9240 Finding SS restraints... Secondary structure from input PDB file: 248 helices and 44 sheets defined 57.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 63 through 70 Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 92 through 106 removed outlier: 4.326A pdb=" N THR A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 removed outlier: 4.297A pdb=" N VAL A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 164 removed outlier: 4.204A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 179 removed outlier: 4.350A pdb=" N GLY A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 205 removed outlier: 3.951A pdb=" N GLU A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARG A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 removed outlier: 4.291A pdb=" N ARG A 209 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 211 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 224 removed outlier: 4.477A pdb=" N GLN A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 235 removed outlier: 3.560A pdb=" N LEU A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 311 removed outlier: 3.713A pdb=" N ASP A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS A 304 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.728A pdb=" N TYR A 492 " --> pdb=" O ALA A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 507 removed outlier: 4.129A pdb=" N ARG A 501 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP A 505 " --> pdb=" O ARG A 501 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 551 removed outlier: 4.084A pdb=" N GLN A 541 " --> pdb=" O ARG A 537 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG A 549 " --> pdb=" O ASN A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 561 No H-bonds generated for 'chain 'A' and resid 559 through 561' Processing helix chain 'A' and resid 571 through 582 removed outlier: 4.167A pdb=" N LEU A 578 " --> pdb=" O GLU A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 595 through 600 removed outlier: 3.774A pdb=" N GLN A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 600 " --> pdb=" O ALA A 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 600' Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.662A pdb=" N ASP A 612 " --> pdb=" O ALA A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 630 removed outlier: 3.802A pdb=" N LEU A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 627 " --> pdb=" O CYS A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'B' and resid 65 through 70 Processing helix chain 'B' and resid 80 through 83 Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 92 through 106 removed outlier: 4.293A pdb=" N THR B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 removed outlier: 4.070A pdb=" N VAL B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 164 removed outlier: 4.268A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 164 " --> pdb=" O ASP B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 179 removed outlier: 4.274A pdb=" N GLY B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 205 removed outlier: 4.000A pdb=" N GLU B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 removed outlier: 4.223A pdb=" N ARG B 209 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 211 " --> pdb=" O GLN B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 291 through 311 removed outlier: 3.829A pdb=" N ASP B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B 311 " --> pdb=" O ILE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 493 removed outlier: 3.815A pdb=" N TYR B 492 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 507 removed outlier: 3.950A pdb=" N ARG B 501 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 504 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP B 505 " --> pdb=" O ARG B 501 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 551 removed outlier: 4.185A pdb=" N GLN B 541 " --> pdb=" O ARG B 537 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN B 545 " --> pdb=" O GLN B 541 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG B 549 " --> pdb=" O ASN B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.886A pdb=" N ALA B 562 " --> pdb=" O HIS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 584 removed outlier: 4.184A pdb=" N LEU B 578 " --> pdb=" O GLU B 574 " (cutoff:3.500A) Proline residue: B 579 - end of helix Processing helix chain 'B' and resid 595 through 600 removed outlier: 3.598A pdb=" N GLN B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 600 " --> pdb=" O ALA B 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 595 through 600' Processing helix chain 'B' and resid 604 through 611 Processing helix chain 'B' and resid 615 through 630 removed outlier: 3.900A pdb=" N LEU B 621 " --> pdb=" O ARG B 617 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 627 " --> pdb=" O CYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'C' and resid 63 through 70 Processing helix chain 'C' and resid 80 through 83 Processing helix chain 'C' and resid 84 through 89 Processing helix chain 'C' and resid 92 through 106 removed outlier: 4.311A pdb=" N THR C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 120 removed outlier: 4.154A pdb=" N VAL C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 164 removed outlier: 4.174A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP C 160 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN C 164 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 179 removed outlier: 4.302A pdb=" N GLY C 172 " --> pdb=" O ASN C 168 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL C 179 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 205 removed outlier: 3.930A pdb=" N GLU C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 removed outlier: 4.218A pdb=" N ARG C 209 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.696A pdb=" N LEU C 228 " --> pdb=" O ASN C 224 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 311 removed outlier: 3.841A pdb=" N ASP C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 493 removed outlier: 3.801A pdb=" N TYR C 492 " --> pdb=" O ALA C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 507 removed outlier: 3.920A pdb=" N ARG C 501 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 504 " --> pdb=" O VAL C 500 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 505 " --> pdb=" O ARG C 501 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 551 removed outlier: 3.536A pdb=" N GLU C 536 " --> pdb=" O THR C 532 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG C 537 " --> pdb=" O GLU C 533 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE C 538 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN C 541 " --> pdb=" O ARG C 537 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ARG C 549 " --> pdb=" O ASN C 545 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C 551 " --> pdb=" O TYR C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 561 No H-bonds generated for 'chain 'C' and resid 559 through 561' Processing helix chain 'C' and resid 569 through 584 removed outlier: 3.931A pdb=" N VAL C 573 " --> pdb=" O SER C 569 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU C 574 " --> pdb=" O ASN C 570 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU C 578 " --> pdb=" O GLU C 574 " (cutoff:3.500A) Proline residue: C 579 - end of helix removed outlier: 3.511A pdb=" N HIS C 583 " --> pdb=" O PRO C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 600 removed outlier: 3.793A pdb=" N GLN C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 600 " --> pdb=" O ALA C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 613 removed outlier: 4.353A pdb=" N ALA C 607 " --> pdb=" O GLY C 603 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 630 removed outlier: 3.845A pdb=" N LEU C 621 " --> pdb=" O ARG C 617 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS C 627 " --> pdb=" O CYS C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 635 Processing helix chain 'D' and resid 63 through 70 Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 92 through 106 removed outlier: 4.326A pdb=" N THR D 104 " --> pdb=" O GLY D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 120 removed outlier: 4.297A pdb=" N VAL D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU D 116 " --> pdb=" O ARG D 112 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU D 117 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 164 removed outlier: 4.204A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 179 removed outlier: 4.345A pdb=" N GLY D 172 " --> pdb=" O ASN D 168 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR D 174 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL D 179 " --> pdb=" O VAL D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 removed outlier: 3.964A pdb=" N GLU D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ARG D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG D 204 " --> pdb=" O ALA D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 211 removed outlier: 4.294A pdb=" N ARG D 209 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR D 211 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 224 removed outlier: 4.475A pdb=" N GLN D 218 " --> pdb=" O HIS D 214 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP D 219 " --> pdb=" O PRO D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 235 removed outlier: 3.561A pdb=" N LEU D 228 " --> pdb=" O ASN D 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG D 234 " --> pdb=" O GLN D 230 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 311 removed outlier: 3.711A pdb=" N ASP D 299 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS D 304 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 493 removed outlier: 3.727A pdb=" N TYR D 492 " --> pdb=" O ALA D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 507 removed outlier: 4.129A pdb=" N ARG D 501 " --> pdb=" O LEU D 497 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 504 " --> pdb=" O VAL D 500 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP D 505 " --> pdb=" O ARG D 501 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA D 507 " --> pdb=" O ALA D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 551 removed outlier: 4.085A pdb=" N GLN D 541 " --> pdb=" O ARG D 537 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG D 549 " --> pdb=" O ASN D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 561 No H-bonds generated for 'chain 'D' and resid 559 through 561' Processing helix chain 'D' and resid 571 through 582 removed outlier: 4.213A pdb=" N LEU D 578 " --> pdb=" O GLU D 574 " (cutoff:3.500A) Proline residue: D 579 - end of helix Processing helix chain 'D' and resid 595 through 600 removed outlier: 3.704A pdb=" N GLN D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 600 " --> pdb=" O ALA D 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 595 through 600' Processing helix chain 'D' and resid 604 through 612 removed outlier: 3.661A pdb=" N ASP D 612 " --> pdb=" O ALA D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 630 removed outlier: 3.794A pdb=" N LEU D 621 " --> pdb=" O ARG D 617 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS D 627 " --> pdb=" O CYS D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 635 Processing helix chain 'G' and resid 63 through 70 Processing helix chain 'G' and resid 80 through 83 Processing helix chain 'G' and resid 84 through 89 Processing helix chain 'G' and resid 92 through 106 removed outlier: 4.293A pdb=" N THR G 104 " --> pdb=" O GLY G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 120 removed outlier: 4.069A pdb=" N VAL G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU G 116 " --> pdb=" O ARG G 112 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU G 117 " --> pdb=" O ARG G 113 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP G 118 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 164 removed outlier: 4.268A pdb=" N ALA G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU G 155 " --> pdb=" O GLN G 151 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA G 157 " --> pdb=" O GLY G 153 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP G 160 " --> pdb=" O GLY G 156 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE G 161 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU G 162 " --> pdb=" O LEU G 158 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN G 164 " --> pdb=" O ASP G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 179 removed outlier: 4.274A pdb=" N GLY G 172 " --> pdb=" O ASN G 168 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR G 174 " --> pdb=" O ASP G 170 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL G 179 " --> pdb=" O VAL G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 205 removed outlier: 3.999A pdb=" N GLU G 198 " --> pdb=" O SER G 194 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG G 199 " --> pdb=" O GLU G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 211 removed outlier: 4.223A pdb=" N ARG G 209 " --> pdb=" O ALA G 206 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR G 211 " --> pdb=" O GLN G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 224 Processing helix chain 'G' and resid 224 through 231 Processing helix chain 'G' and resid 291 through 311 removed outlier: 3.833A pdb=" N ASP G 299 " --> pdb=" O ILE G 295 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS G 304 " --> pdb=" O GLY G 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G 310 " --> pdb=" O LYS G 306 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU G 311 " --> pdb=" O ILE G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 493 removed outlier: 3.815A pdb=" N TYR G 492 " --> pdb=" O ALA G 489 " (cutoff:3.500A) Processing helix chain 'G' and resid 495 through 507 removed outlier: 3.952A pdb=" N ARG G 501 " --> pdb=" O LEU G 497 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG G 504 " --> pdb=" O VAL G 500 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP G 505 " --> pdb=" O ARG G 501 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA G 507 " --> pdb=" O ALA G 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 551 removed outlier: 3.913A pdb=" N GLU G 536 " --> pdb=" O THR G 532 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG G 537 " --> pdb=" O GLU G 533 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE G 538 " --> pdb=" O SER G 534 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN G 541 " --> pdb=" O ARG G 537 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN G 545 " --> pdb=" O GLN G 541 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ARG G 549 " --> pdb=" O ASN G 545 " (cutoff:3.500A) Processing helix chain 'G' and resid 558 through 562 removed outlier: 3.887A pdb=" N ALA G 562 " --> pdb=" O HIS G 559 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 584 removed outlier: 4.173A pdb=" N LEU G 578 " --> pdb=" O GLU G 574 " (cutoff:3.500A) Proline residue: G 579 - end of helix Processing helix chain 'G' and resid 595 through 600 removed outlier: 3.595A pdb=" N GLN G 599 " --> pdb=" O GLU G 595 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 600 " --> pdb=" O ALA G 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 595 through 600' Processing helix chain 'G' and resid 604 through 611 Processing helix chain 'G' and resid 615 through 630 removed outlier: 3.901A pdb=" N LEU G 621 " --> pdb=" O ARG G 617 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS G 627 " --> pdb=" O CYS G 623 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 635 Processing helix chain 'J' and resid 63 through 70 Processing helix chain 'J' and resid 80 through 83 Processing helix chain 'J' and resid 84 through 89 Processing helix chain 'J' and resid 92 through 106 removed outlier: 4.313A pdb=" N THR J 104 " --> pdb=" O GLY J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 120 removed outlier: 4.154A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU J 116 " --> pdb=" O ARG J 112 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU J 117 " --> pdb=" O ARG J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 164 removed outlier: 4.172A pdb=" N ALA J 144 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU J 155 " --> pdb=" O GLN J 151 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP J 160 " --> pdb=" O GLY J 156 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE J 161 " --> pdb=" O ALA J 157 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU J 162 " --> pdb=" O LEU J 158 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN J 164 " --> pdb=" O ASP J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 179 removed outlier: 4.298A pdb=" N GLY J 172 " --> pdb=" O ASN J 168 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR J 174 " --> pdb=" O ASP J 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL J 179 " --> pdb=" O VAL J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 192 through 205 removed outlier: 3.931A pdb=" N GLU J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 211 removed outlier: 4.218A pdb=" N ARG J 209 " --> pdb=" O ALA J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 224 Processing helix chain 'J' and resid 224 through 232 removed outlier: 3.692A pdb=" N LEU J 228 " --> pdb=" O ASN J 224 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 291 through 311 removed outlier: 3.842A pdb=" N ASP J 299 " --> pdb=" O ILE J 295 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS J 304 " --> pdb=" O GLY J 300 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU J 311 " --> pdb=" O ILE J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 489 through 493 removed outlier: 3.801A pdb=" N TYR J 492 " --> pdb=" O ALA J 489 " (cutoff:3.500A) Processing helix chain 'J' and resid 495 through 507 removed outlier: 3.919A pdb=" N ARG J 501 " --> pdb=" O LEU J 497 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG J 504 " --> pdb=" O VAL J 500 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP J 505 " --> pdb=" O ARG J 501 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA J 507 " --> pdb=" O ALA J 503 " (cutoff:3.500A) Processing helix chain 'J' and resid 532 through 551 removed outlier: 3.535A pdb=" N GLU J 536 " --> pdb=" O THR J 532 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG J 537 " --> pdb=" O GLU J 533 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE J 538 " --> pdb=" O SER J 534 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN J 541 " --> pdb=" O ARG J 537 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN J 545 " --> pdb=" O GLN J 541 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ARG J 549 " --> pdb=" O ASN J 545 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE J 551 " --> pdb=" O TYR J 547 " (cutoff:3.500A) Processing helix chain 'J' and resid 559 through 561 No H-bonds generated for 'chain 'J' and resid 559 through 561' Processing helix chain 'J' and resid 569 through 584 removed outlier: 3.899A pdb=" N VAL J 573 " --> pdb=" O SER J 569 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU J 574 " --> pdb=" O ASN J 570 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU J 578 " --> pdb=" O GLU J 574 " (cutoff:3.500A) Proline residue: J 579 - end of helix removed outlier: 3.512A pdb=" N HIS J 583 " --> pdb=" O PRO J 579 " (cutoff:3.500A) Processing helix chain 'J' and resid 594 through 600 removed outlier: 3.797A pdb=" N GLN J 599 " --> pdb=" O GLU J 595 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU J 600 " --> pdb=" O ALA J 596 " (cutoff:3.500A) Processing helix chain 'J' and resid 603 through 613 removed outlier: 4.350A pdb=" N ALA J 607 " --> pdb=" O GLY J 603 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP J 612 " --> pdb=" O ALA J 608 " (cutoff:3.500A) Processing helix chain 'J' and resid 615 through 630 removed outlier: 3.844A pdb=" N LEU J 621 " --> pdb=" O ARG J 617 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS J 627 " --> pdb=" O CYS J 623 " (cutoff:3.500A) Processing helix chain 'J' and resid 631 through 635 Processing helix chain 'E' and resid 63 through 70 Processing helix chain 'E' and resid 84 through 89 Processing helix chain 'E' and resid 92 through 106 removed outlier: 4.326A pdb=" N THR E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 120 removed outlier: 4.297A pdb=" N VAL E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU E 117 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 164 removed outlier: 4.204A pdb=" N ALA E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP E 160 " --> pdb=" O GLY E 156 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 179 removed outlier: 4.348A pdb=" N GLY E 172 " --> pdb=" O ASN E 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR E 174 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL E 179 " --> pdb=" O VAL E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 205 removed outlier: 3.962A pdb=" N GLU E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 211 removed outlier: 4.294A pdb=" N ARG E 209 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR E 211 " --> pdb=" O GLN E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 224 removed outlier: 4.475A pdb=" N GLN E 218 " --> pdb=" O HIS E 214 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP E 219 " --> pdb=" O PRO E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 235 removed outlier: 3.561A pdb=" N LEU E 228 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA E 232 " --> pdb=" O LEU E 228 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG E 234 " --> pdb=" O GLN E 230 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU E 235 " --> pdb=" O VAL E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 311 removed outlier: 3.714A pdb=" N ASP E 299 " --> pdb=" O ILE E 295 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS E 304 " --> pdb=" O GLY E 300 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU E 311 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 493 removed outlier: 3.728A pdb=" N TYR E 492 " --> pdb=" O ALA E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 507 removed outlier: 4.128A pdb=" N ARG E 501 " --> pdb=" O LEU E 497 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG E 504 " --> pdb=" O VAL E 500 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP E 505 " --> pdb=" O ARG E 501 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA E 507 " --> pdb=" O ALA E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 551 removed outlier: 4.083A pdb=" N GLN E 541 " --> pdb=" O ARG E 537 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN E 545 " --> pdb=" O GLN E 541 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE E 548 " --> pdb=" O GLU E 544 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG E 549 " --> pdb=" O ASN E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 561 No H-bonds generated for 'chain 'E' and resid 559 through 561' Processing helix chain 'E' and resid 571 through 582 removed outlier: 4.210A pdb=" N LEU E 578 " --> pdb=" O GLU E 574 " (cutoff:3.500A) Proline residue: E 579 - end of helix Processing helix chain 'E' and resid 595 through 600 removed outlier: 3.773A pdb=" N GLN E 599 " --> pdb=" O GLU E 595 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 600 " --> pdb=" O ALA E 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 595 through 600' Processing helix chain 'E' and resid 604 through 612 removed outlier: 3.662A pdb=" N ASP E 612 " --> pdb=" O ALA E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 630 removed outlier: 3.801A pdb=" N LEU E 621 " --> pdb=" O ARG E 617 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS E 627 " --> pdb=" O CYS E 623 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 635 Processing helix chain 'H' and resid 65 through 70 Processing helix chain 'H' and resid 80 through 83 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'H' and resid 92 through 106 removed outlier: 4.296A pdb=" N THR H 104 " --> pdb=" O GLY H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 120 removed outlier: 4.069A pdb=" N VAL H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU H 116 " --> pdb=" O ARG H 112 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP H 118 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 164 removed outlier: 4.269A pdb=" N ALA H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU H 155 " --> pdb=" O GLN H 151 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA H 157 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP H 160 " --> pdb=" O GLY H 156 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE H 161 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU H 162 " --> pdb=" O LEU H 158 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN H 164 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 179 removed outlier: 4.280A pdb=" N GLY H 172 " --> pdb=" O ASN H 168 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR H 174 " --> pdb=" O ASP H 170 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL H 179 " --> pdb=" O VAL H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 205 removed outlier: 4.002A pdb=" N GLU H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 211 removed outlier: 4.223A pdb=" N ARG H 209 " --> pdb=" O ALA H 206 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 211 " --> pdb=" O GLN H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 224 Processing helix chain 'H' and resid 224 through 231 Processing helix chain 'H' and resid 291 through 311 removed outlier: 3.835A pdb=" N ASP H 299 " --> pdb=" O ILE H 295 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS H 304 " --> pdb=" O GLY H 300 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU H 310 " --> pdb=" O LYS H 306 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU H 311 " --> pdb=" O ILE H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 489 through 493 removed outlier: 3.815A pdb=" N TYR H 492 " --> pdb=" O ALA H 489 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 507 removed outlier: 3.952A pdb=" N ARG H 501 " --> pdb=" O LEU H 497 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG H 504 " --> pdb=" O VAL H 500 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP H 505 " --> pdb=" O ARG H 501 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA H 507 " --> pdb=" O ALA H 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 535 through 551 removed outlier: 4.185A pdb=" N GLN H 541 " --> pdb=" O ARG H 537 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN H 545 " --> pdb=" O GLN H 541 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG H 549 " --> pdb=" O ASN H 545 " (cutoff:3.500A) Processing helix chain 'H' and resid 558 through 562 removed outlier: 3.892A pdb=" N ALA H 562 " --> pdb=" O HIS H 559 " (cutoff:3.500A) Processing helix chain 'H' and resid 571 through 584 removed outlier: 4.173A pdb=" N LEU H 578 " --> pdb=" O GLU H 574 " (cutoff:3.500A) Proline residue: H 579 - end of helix Processing helix chain 'H' and resid 595 through 600 removed outlier: 3.599A pdb=" N GLN H 599 " --> pdb=" O GLU H 595 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU H 600 " --> pdb=" O ALA H 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 595 through 600' Processing helix chain 'H' and resid 604 through 611 Processing helix chain 'H' and resid 615 through 630 removed outlier: 3.900A pdb=" N LEU H 621 " --> pdb=" O ARG H 617 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS H 627 " --> pdb=" O CYS H 623 " (cutoff:3.500A) Processing helix chain 'H' and resid 631 through 635 Processing helix chain 'K' and resid 63 through 70 Processing helix chain 'K' and resid 80 through 83 Processing helix chain 'K' and resid 84 through 89 Processing helix chain 'K' and resid 92 through 106 removed outlier: 4.295A pdb=" N THR K 104 " --> pdb=" O GLY K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 120 removed outlier: 4.154A pdb=" N VAL K 114 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU K 116 " --> pdb=" O ARG K 112 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU K 117 " --> pdb=" O ARG K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 164 removed outlier: 4.173A pdb=" N ALA K 144 " --> pdb=" O LEU K 140 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER K 149 " --> pdb=" O SER K 145 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU K 155 " --> pdb=" O GLN K 151 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA K 157 " --> pdb=" O GLY K 153 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP K 160 " --> pdb=" O GLY K 156 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE K 161 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU K 162 " --> pdb=" O LEU K 158 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN K 164 " --> pdb=" O ASP K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 179 removed outlier: 4.301A pdb=" N GLY K 172 " --> pdb=" O ASN K 168 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR K 174 " --> pdb=" O ASP K 170 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL K 179 " --> pdb=" O VAL K 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 205 removed outlier: 3.929A pdb=" N GLU K 198 " --> pdb=" O SER K 194 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG K 199 " --> pdb=" O GLU K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 211 removed outlier: 4.218A pdb=" N ARG K 209 " --> pdb=" O ALA K 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 224 Processing helix chain 'K' and resid 224 through 232 removed outlier: 3.693A pdb=" N LEU K 228 " --> pdb=" O ASN K 224 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA K 232 " --> pdb=" O LEU K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 311 removed outlier: 3.845A pdb=" N ASP K 299 " --> pdb=" O ILE K 295 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS K 304 " --> pdb=" O GLY K 300 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU K 311 " --> pdb=" O ILE K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 489 through 493 removed outlier: 3.800A pdb=" N TYR K 492 " --> pdb=" O ALA K 489 " (cutoff:3.500A) Processing helix chain 'K' and resid 495 through 507 removed outlier: 3.917A pdb=" N ARG K 501 " --> pdb=" O LEU K 497 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG K 504 " --> pdb=" O VAL K 500 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP K 505 " --> pdb=" O ARG K 501 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA K 507 " --> pdb=" O ALA K 503 " (cutoff:3.500A) Processing helix chain 'K' and resid 532 through 551 removed outlier: 3.535A pdb=" N GLU K 536 " --> pdb=" O THR K 532 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG K 537 " --> pdb=" O GLU K 533 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE K 538 " --> pdb=" O SER K 534 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN K 541 " --> pdb=" O ARG K 537 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN K 545 " --> pdb=" O GLN K 541 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG K 549 " --> pdb=" O ASN K 545 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE K 551 " --> pdb=" O TYR K 547 " (cutoff:3.500A) Processing helix chain 'K' and resid 559 through 561 No H-bonds generated for 'chain 'K' and resid 559 through 561' Processing helix chain 'K' and resid 569 through 584 removed outlier: 3.933A pdb=" N VAL K 573 " --> pdb=" O SER K 569 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU K 574 " --> pdb=" O ASN K 570 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU K 578 " --> pdb=" O GLU K 574 " (cutoff:3.500A) Proline residue: K 579 - end of helix removed outlier: 3.513A pdb=" N HIS K 583 " --> pdb=" O PRO K 579 " (cutoff:3.500A) Processing helix chain 'K' and resid 594 through 600 removed outlier: 3.797A pdb=" N GLN K 599 " --> pdb=" O GLU K 595 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU K 600 " --> pdb=" O ALA K 596 " (cutoff:3.500A) Processing helix chain 'K' and resid 603 through 613 removed outlier: 4.350A pdb=" N ALA K 607 " --> pdb=" O GLY K 603 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP K 612 " --> pdb=" O ALA K 608 " (cutoff:3.500A) Processing helix chain 'K' and resid 615 through 630 removed outlier: 3.844A pdb=" N LEU K 621 " --> pdb=" O ARG K 617 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS K 627 " --> pdb=" O CYS K 623 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 635 Processing helix chain 'F' and resid 63 through 70 Processing helix chain 'F' and resid 84 through 89 Processing helix chain 'F' and resid 92 through 106 removed outlier: 4.326A pdb=" N THR F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 120 removed outlier: 4.297A pdb=" N VAL F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU F 116 " --> pdb=" O ARG F 112 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP F 118 " --> pdb=" O VAL F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 164 removed outlier: 4.204A pdb=" N ALA F 144 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 155 " --> pdb=" O GLN F 151 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP F 160 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU F 162 " --> pdb=" O LEU F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 179 removed outlier: 4.351A pdb=" N GLY F 172 " --> pdb=" O ASN F 168 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL F 179 " --> pdb=" O VAL F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 205 removed outlier: 3.951A pdb=" N GLU F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARG F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 211 removed outlier: 4.291A pdb=" N ARG F 209 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR F 211 " --> pdb=" O GLN F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 224 removed outlier: 4.475A pdb=" N GLN F 218 " --> pdb=" O HIS F 214 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP F 219 " --> pdb=" O PRO F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 235 removed outlier: 3.561A pdb=" N LEU F 228 " --> pdb=" O ASN F 224 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG F 234 " --> pdb=" O GLN F 230 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU F 235 " --> pdb=" O VAL F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 311 removed outlier: 3.710A pdb=" N ASP F 299 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS F 304 " --> pdb=" O GLY F 300 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU F 311 " --> pdb=" O ILE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 493 removed outlier: 3.727A pdb=" N TYR F 492 " --> pdb=" O ALA F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 507 removed outlier: 4.129A pdb=" N ARG F 501 " --> pdb=" O LEU F 497 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG F 504 " --> pdb=" O VAL F 500 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP F 505 " --> pdb=" O ARG F 501 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA F 507 " --> pdb=" O ALA F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 551 removed outlier: 4.076A pdb=" N GLN F 541 " --> pdb=" O ARG F 537 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN F 545 " --> pdb=" O GLN F 541 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE F 548 " --> pdb=" O GLU F 544 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ARG F 549 " --> pdb=" O ASN F 545 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE F 551 " --> pdb=" O TYR F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 561 No H-bonds generated for 'chain 'F' and resid 559 through 561' Processing helix chain 'F' and resid 571 through 582 removed outlier: 4.200A pdb=" N LEU F 578 " --> pdb=" O GLU F 574 " (cutoff:3.500A) Proline residue: F 579 - end of helix Processing helix chain 'F' and resid 595 through 600 removed outlier: 3.767A pdb=" N GLN F 599 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 600 " --> pdb=" O ALA F 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 595 through 600' Processing helix chain 'F' and resid 604 through 612 removed outlier: 3.659A pdb=" N ASP F 612 " --> pdb=" O ALA F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 630 removed outlier: 3.794A pdb=" N LEU F 621 " --> pdb=" O ARG F 617 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS F 627 " --> pdb=" O CYS F 623 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 635 Processing helix chain 'I' and resid 63 through 70 Processing helix chain 'I' and resid 80 through 83 Processing helix chain 'I' and resid 84 through 89 Processing helix chain 'I' and resid 92 through 106 removed outlier: 4.294A pdb=" N THR I 104 " --> pdb=" O GLY I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 120 removed outlier: 4.070A pdb=" N VAL I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU I 116 " --> pdb=" O ARG I 112 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU I 117 " --> pdb=" O ARG I 113 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 164 removed outlier: 4.268A pdb=" N ALA I 144 " --> pdb=" O LEU I 140 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA I 157 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP I 160 " --> pdb=" O GLY I 156 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN I 164 " --> pdb=" O ASP I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 179 removed outlier: 4.275A pdb=" N GLY I 172 " --> pdb=" O ASN I 168 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR I 174 " --> pdb=" O ASP I 170 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL I 179 " --> pdb=" O VAL I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 205 removed outlier: 4.000A pdb=" N GLU I 198 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG I 199 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 211 removed outlier: 4.223A pdb=" N ARG I 209 " --> pdb=" O ALA I 206 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR I 211 " --> pdb=" O GLN I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'I' and resid 224 through 231 Processing helix chain 'I' and resid 291 through 311 removed outlier: 3.836A pdb=" N ASP I 299 " --> pdb=" O ILE I 295 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS I 304 " --> pdb=" O GLY I 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU I 310 " --> pdb=" O LYS I 306 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU I 311 " --> pdb=" O ILE I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 489 through 493 removed outlier: 3.815A pdb=" N TYR I 492 " --> pdb=" O ALA I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 507 removed outlier: 3.951A pdb=" N ARG I 501 " --> pdb=" O LEU I 497 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG I 504 " --> pdb=" O VAL I 500 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP I 505 " --> pdb=" O ARG I 501 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA I 507 " --> pdb=" O ALA I 503 " (cutoff:3.500A) Processing helix chain 'I' and resid 532 through 551 removed outlier: 3.915A pdb=" N GLU I 536 " --> pdb=" O THR I 532 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG I 537 " --> pdb=" O GLU I 533 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE I 538 " --> pdb=" O SER I 534 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN I 541 " --> pdb=" O ARG I 537 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN I 545 " --> pdb=" O GLN I 541 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG I 549 " --> pdb=" O ASN I 545 " (cutoff:3.500A) Processing helix chain 'I' and resid 558 through 562 removed outlier: 3.892A pdb=" N ALA I 562 " --> pdb=" O HIS I 559 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 584 removed outlier: 4.174A pdb=" N LEU I 578 " --> pdb=" O GLU I 574 " (cutoff:3.500A) Proline residue: I 579 - end of helix Processing helix chain 'I' and resid 595 through 600 removed outlier: 3.598A pdb=" N GLN I 599 " --> pdb=" O GLU I 595 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU I 600 " --> pdb=" O ALA I 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 595 through 600' Processing helix chain 'I' and resid 604 through 611 Processing helix chain 'I' and resid 615 through 630 removed outlier: 3.900A pdb=" N LEU I 621 " --> pdb=" O ARG I 617 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS I 627 " --> pdb=" O CYS I 623 " (cutoff:3.500A) Processing helix chain 'I' and resid 631 through 635 Processing helix chain 'L' and resid 63 through 70 Processing helix chain 'L' and resid 80 through 83 Processing helix chain 'L' and resid 84 through 89 Processing helix chain 'L' and resid 92 through 106 removed outlier: 4.312A pdb=" N THR L 104 " --> pdb=" O GLY L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 120 removed outlier: 4.154A pdb=" N VAL L 114 " --> pdb=" O THR L 110 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU L 116 " --> pdb=" O ARG L 112 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 164 removed outlier: 4.174A pdb=" N ALA L 144 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER L 149 " --> pdb=" O SER L 145 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU L 155 " --> pdb=" O GLN L 151 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA L 157 " --> pdb=" O GLY L 153 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP L 160 " --> pdb=" O GLY L 156 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE L 161 " --> pdb=" O ALA L 157 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU L 162 " --> pdb=" O LEU L 158 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN L 164 " --> pdb=" O ASP L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 179 removed outlier: 4.295A pdb=" N GLY L 172 " --> pdb=" O ASN L 168 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR L 174 " --> pdb=" O ASP L 170 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL L 179 " --> pdb=" O VAL L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 205 removed outlier: 3.928A pdb=" N GLU L 198 " --> pdb=" O SER L 194 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG L 199 " --> pdb=" O GLU L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 211 removed outlier: 4.217A pdb=" N ARG L 209 " --> pdb=" O ALA L 206 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 224 Processing helix chain 'L' and resid 224 through 232 removed outlier: 3.690A pdb=" N LEU L 228 " --> pdb=" O ASN L 224 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 311 removed outlier: 3.840A pdb=" N ASP L 299 " --> pdb=" O ILE L 295 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS L 304 " --> pdb=" O GLY L 300 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU L 311 " --> pdb=" O ILE L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 489 through 493 removed outlier: 3.800A pdb=" N TYR L 492 " --> pdb=" O ALA L 489 " (cutoff:3.500A) Processing helix chain 'L' and resid 495 through 507 removed outlier: 3.920A pdb=" N ARG L 501 " --> pdb=" O LEU L 497 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG L 504 " --> pdb=" O VAL L 500 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP L 505 " --> pdb=" O ARG L 501 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA L 507 " --> pdb=" O ALA L 503 " (cutoff:3.500A) Processing helix chain 'L' and resid 532 through 551 removed outlier: 3.536A pdb=" N GLU L 536 " --> pdb=" O THR L 532 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG L 537 " --> pdb=" O GLU L 533 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE L 538 " --> pdb=" O SER L 534 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN L 541 " --> pdb=" O ARG L 537 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN L 545 " --> pdb=" O GLN L 541 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG L 549 " --> pdb=" O ASN L 545 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE L 551 " --> pdb=" O TYR L 547 " (cutoff:3.500A) Processing helix chain 'L' and resid 559 through 561 No H-bonds generated for 'chain 'L' and resid 559 through 561' Processing helix chain 'L' and resid 569 through 584 removed outlier: 3.930A pdb=" N VAL L 573 " --> pdb=" O SER L 569 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU L 574 " --> pdb=" O ASN L 570 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU L 578 " --> pdb=" O GLU L 574 " (cutoff:3.500A) Proline residue: L 579 - end of helix removed outlier: 3.510A pdb=" N HIS L 583 " --> pdb=" O PRO L 579 " (cutoff:3.500A) Processing helix chain 'L' and resid 594 through 600 removed outlier: 3.795A pdb=" N GLN L 599 " --> pdb=" O GLU L 595 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU L 600 " --> pdb=" O ALA L 596 " (cutoff:3.500A) Processing helix chain 'L' and resid 603 through 613 removed outlier: 4.370A pdb=" N ALA L 607 " --> pdb=" O GLY L 603 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP L 612 " --> pdb=" O ALA L 608 " (cutoff:3.500A) Processing helix chain 'L' and resid 615 through 630 removed outlier: 3.845A pdb=" N LEU L 621 " --> pdb=" O ARG L 617 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS L 627 " --> pdb=" O CYS L 623 " (cutoff:3.500A) Processing helix chain 'L' and resid 631 through 635 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.556A pdb=" N ARG A 247 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 259 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 185 removed outlier: 4.018A pdb=" N VAL A 184 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 269 " --> pdb=" O VAL A 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.874A pdb=" N LEU A 512 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 522 through 525 removed outlier: 3.832A pdb=" N LEU L 512 " --> pdb=" O VAL L 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 554 through 557 removed outlier: 4.132A pdb=" N LEU A 556 " --> pdb=" O ALA A 565 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA A 565 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 57 removed outlier: 3.704A pdb=" N ARG B 247 " --> pdb=" O GLN B 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 183 through 185 removed outlier: 4.087A pdb=" N VAL B 184 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR B 269 " --> pdb=" O VAL B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 512 through 513 removed outlier: 3.846A pdb=" N LEU B 512 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 320 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 317 " --> pdb=" O PHE C 524 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 57 removed outlier: 3.831A pdb=" N ARG C 247 " --> pdb=" O GLN C 260 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 259 " --> pdb=" O ILE C 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 183 through 185 removed outlier: 4.132A pdb=" N VAL C 184 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 269 " --> pdb=" O VAL C 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 512 through 513 removed outlier: 3.833A pdb=" N LEU C 512 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 554 through 557 removed outlier: 4.125A pdb=" N LEU C 556 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA C 565 " --> pdb=" O LEU C 556 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 56 through 57 removed outlier: 3.560A pdb=" N ARG D 247 " --> pdb=" O GLN D 260 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA D 259 " --> pdb=" O ILE D 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 183 through 185 removed outlier: 4.016A pdb=" N VAL D 184 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR D 269 " --> pdb=" O VAL D 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 512 through 513 removed outlier: 3.872A pdb=" N LEU D 512 " --> pdb=" O VAL D 318 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 554 through 557 removed outlier: 4.131A pdb=" N LEU D 556 " --> pdb=" O ALA D 565 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA D 565 " --> pdb=" O LEU D 556 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 56 through 57 removed outlier: 3.696A pdb=" N ARG G 247 " --> pdb=" O GLN G 260 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 183 through 185 removed outlier: 4.088A pdb=" N VAL G 184 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR G 269 " --> pdb=" O VAL G 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 512 through 513 removed outlier: 3.843A pdb=" N LEU G 512 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR G 320 " --> pdb=" O LEU G 512 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS G 317 " --> pdb=" O PHE J 524 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 56 through 57 removed outlier: 3.831A pdb=" N ARG J 247 " --> pdb=" O GLN J 260 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA J 259 " --> pdb=" O ILE J 266 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 183 through 185 removed outlier: 4.131A pdb=" N VAL J 184 " --> pdb=" O TYR J 269 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR J 269 " --> pdb=" O VAL J 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'J' and resid 512 through 513 removed outlier: 3.834A pdb=" N LEU J 512 " --> pdb=" O VAL J 318 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 554 through 557 removed outlier: 4.124A pdb=" N LEU J 556 " --> pdb=" O ALA J 565 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA J 565 " --> pdb=" O LEU J 556 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 56 through 57 removed outlier: 3.559A pdb=" N ARG E 247 " --> pdb=" O GLN E 260 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA E 259 " --> pdb=" O ILE E 266 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 183 through 185 removed outlier: 4.015A pdb=" N VAL E 184 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR E 269 " --> pdb=" O VAL E 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 512 through 513 removed outlier: 3.875A pdb=" N LEU E 512 " --> pdb=" O VAL E 318 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 554 through 557 removed outlier: 4.133A pdb=" N LEU E 556 " --> pdb=" O ALA E 565 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA E 565 " --> pdb=" O LEU E 556 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 56 through 57 removed outlier: 3.699A pdb=" N ARG H 247 " --> pdb=" O GLN H 260 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 183 through 185 removed outlier: 4.087A pdb=" N VAL H 184 " --> pdb=" O TYR H 269 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR H 269 " --> pdb=" O VAL H 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'H' and resid 512 through 513 removed outlier: 3.845A pdb=" N LEU H 512 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR H 320 " --> pdb=" O LEU H 512 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS H 317 " --> pdb=" O PHE K 524 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 56 through 57 removed outlier: 3.832A pdb=" N ARG K 247 " --> pdb=" O GLN K 260 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA K 259 " --> pdb=" O ILE K 266 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 183 through 185 removed outlier: 4.131A pdb=" N VAL K 184 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR K 269 " --> pdb=" O VAL K 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'K' and resid 512 through 513 removed outlier: 3.832A pdb=" N LEU K 512 " --> pdb=" O VAL K 318 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 554 through 557 removed outlier: 4.127A pdb=" N LEU K 556 " --> pdb=" O ALA K 565 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ALA K 565 " --> pdb=" O LEU K 556 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 56 through 57 removed outlier: 3.559A pdb=" N ARG F 247 " --> pdb=" O GLN F 260 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA F 259 " --> pdb=" O ILE F 266 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 183 through 185 removed outlier: 4.016A pdb=" N VAL F 184 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR F 269 " --> pdb=" O VAL F 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 512 through 513 removed outlier: 3.873A pdb=" N LEU F 512 " --> pdb=" O VAL F 318 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 554 through 557 removed outlier: 3.515A pdb=" N ARG F 554 " --> pdb=" O VAL F 567 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU F 556 " --> pdb=" O ALA F 565 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA F 565 " --> pdb=" O LEU F 556 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 56 through 57 removed outlier: 3.696A pdb=" N ARG I 247 " --> pdb=" O GLN I 260 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 183 through 185 removed outlier: 4.086A pdb=" N VAL I 184 " --> pdb=" O TYR I 269 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR I 269 " --> pdb=" O VAL I 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'I' and resid 512 through 513 removed outlier: 3.845A pdb=" N LEU I 512 " --> pdb=" O VAL I 318 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR I 320 " --> pdb=" O LEU I 512 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS I 317 " --> pdb=" O PHE L 524 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 56 through 57 removed outlier: 3.831A pdb=" N ARG L 247 " --> pdb=" O GLN L 260 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA L 259 " --> pdb=" O ILE L 266 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 183 through 185 removed outlier: 4.129A pdb=" N VAL L 184 " --> pdb=" O TYR L 269 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR L 269 " --> pdb=" O VAL L 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'L' and resid 554 through 557 removed outlier: 4.129A pdb=" N LEU L 556 " --> pdb=" O ALA L 565 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA L 565 " --> pdb=" O LEU L 556 " (cutoff:3.500A) 1410 hydrogen bonds defined for protein. 3909 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: 13.37 Time building geometry restraints manager: 16.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12908 1.34 - 1.46: 8259 1.46 - 1.58: 18325 1.58 - 1.70: 0 1.70 - 1.81: 180 Bond restraints: 39672 Sorted by residual: bond pdb=" C PHE D 314 " pdb=" N PRO D 315 " ideal model delta sigma weight residual 1.337 1.314 0.023 1.24e-02 6.50e+03 3.50e+00 bond pdb=" C PHE A 314 " pdb=" N PRO A 315 " ideal model delta sigma weight residual 1.337 1.314 0.023 1.24e-02 6.50e+03 3.50e+00 bond pdb=" C PHE E 314 " pdb=" N PRO E 315 " ideal model delta sigma weight residual 1.337 1.315 0.022 1.24e-02 6.50e+03 3.28e+00 bond pdb=" C PHE F 314 " pdb=" N PRO F 315 " ideal model delta sigma weight residual 1.337 1.315 0.022 1.24e-02 6.50e+03 3.28e+00 bond pdb=" C LEU L 590 " pdb=" N ASP L 591 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.35e-02 5.49e+03 3.12e+00 ... (remaining 39667 not shown) Histogram of bond angle deviations from ideal: 99.88 - 107.04: 1028 107.04 - 114.20: 22585 114.20 - 121.36: 20581 121.36 - 128.52: 9362 128.52 - 135.68: 264 Bond angle restraints: 53820 Sorted by residual: angle pdb=" N VAL L 92 " pdb=" CA VAL L 92 " pdb=" C VAL L 92 " ideal model delta sigma weight residual 112.12 105.21 6.91 8.40e-01 1.42e+00 6.76e+01 angle pdb=" N VAL K 92 " pdb=" CA VAL K 92 " pdb=" C VAL K 92 " ideal model delta sigma weight residual 112.12 105.52 6.60 8.40e-01 1.42e+00 6.18e+01 angle pdb=" N VAL J 92 " pdb=" CA VAL J 92 " pdb=" C VAL J 92 " ideal model delta sigma weight residual 112.12 105.53 6.59 8.40e-01 1.42e+00 6.16e+01 angle pdb=" N VAL C 92 " pdb=" CA VAL C 92 " pdb=" C VAL C 92 " ideal model delta sigma weight residual 112.12 105.54 6.58 8.40e-01 1.42e+00 6.13e+01 angle pdb=" N VAL E 92 " pdb=" CA VAL E 92 " pdb=" C VAL E 92 " ideal model delta sigma weight residual 112.12 105.72 6.40 8.40e-01 1.42e+00 5.80e+01 ... (remaining 53815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 20972 17.98 - 35.97: 2363 35.97 - 53.95: 488 53.95 - 71.94: 105 71.94 - 89.92: 48 Dihedral angle restraints: 23976 sinusoidal: 9756 harmonic: 14220 Sorted by residual: dihedral pdb=" CA LEU B 587 " pdb=" C LEU B 587 " pdb=" N GLY B 588 " pdb=" CA GLY B 588 " ideal model delta harmonic sigma weight residual 180.00 154.21 25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA LEU H 587 " pdb=" C LEU H 587 " pdb=" N GLY H 588 " pdb=" CA GLY H 588 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA LEU G 587 " pdb=" C LEU G 587 " pdb=" N GLY G 588 " pdb=" CA GLY G 588 " ideal model delta harmonic sigma weight residual 180.00 154.26 25.74 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 23973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4394 0.055 - 0.109: 1342 0.109 - 0.164: 378 0.164 - 0.218: 43 0.218 - 0.273: 11 Chirality restraints: 6168 Sorted by residual: chirality pdb=" CG LEU J 70 " pdb=" CB LEU J 70 " pdb=" CD1 LEU J 70 " pdb=" CD2 LEU J 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CG LEU C 70 " pdb=" CB LEU C 70 " pdb=" CD1 LEU C 70 " pdb=" CD2 LEU C 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CG LEU K 70 " pdb=" CB LEU K 70 " pdb=" CD1 LEU K 70 " pdb=" CD2 LEU K 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 6165 not shown) Planarity restraints: 6888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 286 " -0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO H 287 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO H 287 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO H 287 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 573 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C VAL B 573 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL B 573 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU B 574 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 286 " 0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO B 287 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " 0.044 5.00e-02 4.00e+02 ... (remaining 6885 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 10697 2.81 - 3.33: 35325 3.33 - 3.85: 62774 3.85 - 4.38: 69906 4.38 - 4.90: 118021 Nonbonded interactions: 296723 Sorted by model distance: nonbonded pdb=" O PRO C 90 " pdb=" OH TYR D 571 " model vdw 2.282 2.440 nonbonded pdb=" OG1 THR A 320 " pdb=" OD2 ASP B 516 " model vdw 2.282 2.440 nonbonded pdb=" OG1 THR D 320 " pdb=" OD2 ASP G 516 " model vdw 2.282 2.440 nonbonded pdb=" OG1 THR F 320 " pdb=" OD2 ASP I 516 " model vdw 2.282 2.440 nonbonded pdb=" O PRO K 90 " pdb=" OH TYR F 571 " model vdw 2.282 2.440 ... (remaining 296718 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 24876 2.51 5 N 6972 2.21 5 O 6888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 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: 0.030 Extract box with map and model: 4.540 Check model and map are aligned: 0.570 Convert atoms to be neutral: 0.280 Process input model: 93.650 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 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 : 0.006 0.063 39672 Z= 0.365 Angle : 1.043 13.171 53820 Z= 0.562 Chirality : 0.057 0.273 6168 Planarity : 0.008 0.082 6888 Dihedral : 16.252 89.922 14736 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.41 % 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: -4.80 (0.09), residues: 4740 helix: -3.92 (0.06), residues: 2148 sheet: -2.30 (0.41), residues: 120 loop : -2.49 (0.11), residues: 2472 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2310 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 2293 time to evaluate : 4.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 2297 average time/residue: 0.5373 time to fit residues: 1975.6726 Evaluate side-chains 2082 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2077 time to evaluate : 4.075 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4102 time to fit residues: 10.6297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 4.9990 chunk 363 optimal weight: 7.9990 chunk 201 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 245 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 376 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 280 optimal weight: 9.9990 chunk 435 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 137 GLN ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS A 309 GLN B 72 HIS B 214 HIS B 260 GLN B 304 HIS B 541 GLN B 545 ASN C 72 HIS ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 HIS C 137 GLN C 242 ASN C 304 HIS ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN D 72 HIS D 137 GLN D 304 HIS ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN G 214 HIS G 260 GLN G 304 HIS G 541 GLN J 72 HIS ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 HIS J 137 GLN J 242 ASN J 304 HIS ** J 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 632 GLN E 72 HIS E 137 GLN E 304 HIS E 632 GLN H 72 HIS H 214 HIS H 260 GLN H 304 HIS H 541 GLN K 72 HIS ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 HIS K 137 GLN K 242 ASN K 304 HIS ** K 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 632 GLN F 72 HIS ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN F 304 HIS F 309 GLN I 72 HIS I 214 HIS I 260 GLN I 304 HIS I 541 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 HIS L 137 GLN L 242 ASN L 304 HIS ** L 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 632 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 39672 Z= 0.231 Angle : 0.684 7.446 53820 Z= 0.348 Chirality : 0.042 0.158 6168 Planarity : 0.006 0.054 6888 Dihedral : 5.790 20.100 5424 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.43 % 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: -3.60 (0.11), residues: 4740 helix: -2.66 (0.09), residues: 2292 sheet: -2.29 (0.37), residues: 120 loop : -2.01 (0.12), residues: 2328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2231 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 2213 time to evaluate : 4.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 2222 average time/residue: 0.5278 time to fit residues: 1898.9596 Evaluate side-chains 2013 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2009 time to evaluate : 4.771 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3566 time to fit residues: 9.3100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 0.2980 chunk 135 optimal weight: 6.9990 chunk 362 optimal weight: 9.9990 chunk 296 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 436 optimal weight: 0.0870 chunk 471 optimal weight: 6.9990 chunk 388 optimal weight: 30.0000 chunk 433 optimal weight: 7.9990 chunk 148 optimal weight: 30.0000 chunk 350 optimal weight: 4.9990 overall best weight: 3.6764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 632 GLN B 137 GLN B 260 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN D 137 GLN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 632 GLN G 72 HIS G 137 GLN G 260 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN J 632 GLN E 137 GLN ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 632 GLN H 137 GLN H 260 GLN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** K 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 632 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 632 GLN I 85 GLN I 137 GLN I 260 GLN I 545 ASN L 72 HIS ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN ** L 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 632 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 39672 Z= 0.219 Angle : 0.661 8.934 53820 Z= 0.329 Chirality : 0.042 0.136 6168 Planarity : 0.005 0.051 6888 Dihedral : 5.463 19.604 5424 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.26 % 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: -2.87 (0.11), residues: 4740 helix: -2.02 (0.10), residues: 2316 sheet: -1.77 (0.40), residues: 120 loop : -1.68 (0.13), residues: 2304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2182 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2171 time to evaluate : 4.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 0 residues processed: 2175 average time/residue: 0.5158 time to fit residues: 1790.8110 Evaluate side-chains 1996 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1996 time to evaluate : 4.695 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.5314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 8.9990 chunk 328 optimal weight: 8.9990 chunk 226 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 208 optimal weight: 8.9990 chunk 293 optimal weight: 20.0000 chunk 438 optimal weight: 10.0000 chunk 463 optimal weight: 10.0000 chunk 228 optimal weight: 7.9990 chunk 415 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 309 GLN B 96 GLN B 168 ASN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN D 137 GLN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN ** J 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 632 GLN E 137 GLN ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 632 GLN H 85 GLN H 168 ASN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** K 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 632 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN F 137 GLN F 309 GLN I 85 GLN I 96 GLN I 137 GLN I 168 ASN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN ** L 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 632 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 39672 Z= 0.332 Angle : 0.722 7.604 53820 Z= 0.366 Chirality : 0.044 0.141 6168 Planarity : 0.006 0.059 6888 Dihedral : 5.667 21.008 5424 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 0.22 % 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: -2.42 (0.12), residues: 4740 helix: -1.51 (0.10), residues: 2292 sheet: -1.58 (0.43), residues: 120 loop : -1.63 (0.14), residues: 2328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2175 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 2166 time to evaluate : 4.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 0 residues processed: 2169 average time/residue: 0.5277 time to fit residues: 1851.5897 Evaluate side-chains 1965 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1965 time to evaluate : 4.988 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.7070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 4.9990 chunk 263 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 345 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 395 optimal weight: 9.9990 chunk 320 optimal weight: 10.9990 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 416 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 85 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 632 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN ** J 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 632 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 632 GLN H 218 GLN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** K 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 632 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN I 137 GLN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN L 632 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 39672 Z= 0.279 Angle : 0.702 7.156 53820 Z= 0.350 Chirality : 0.043 0.139 6168 Planarity : 0.005 0.048 6888 Dihedral : 5.547 21.934 5424 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.14 % 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: -2.22 (0.12), residues: 4740 helix: -1.35 (0.10), residues: 2304 sheet: -1.25 (0.45), residues: 120 loop : -1.53 (0.14), residues: 2316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2198 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 2192 time to evaluate : 4.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 2194 average time/residue: 0.5012 time to fit residues: 1771.1482 Evaluate side-chains 1965 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1965 time to evaluate : 4.684 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 0.5980 chunk 417 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 272 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 464 optimal weight: 1.9990 chunk 385 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 305 GLN B 96 GLN B 137 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN D 137 GLN ** G 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN ** J 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 632 GLN E 137 GLN E 632 GLN ** H 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** K 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 632 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN L 137 GLN ** L 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 632 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 39672 Z= 0.176 Angle : 0.662 7.868 53820 Z= 0.322 Chirality : 0.042 0.136 6168 Planarity : 0.005 0.045 6888 Dihedral : 5.175 18.265 5424 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.19 % 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: -2.11 (0.12), residues: 4740 helix: -1.31 (0.10), residues: 2280 sheet: -1.02 (0.45), residues: 120 loop : -1.42 (0.14), residues: 2340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2191 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2183 time to evaluate : 4.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 2189 average time/residue: 0.5096 time to fit residues: 1798.8459 Evaluate side-chains 2003 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2003 time to evaluate : 4.595 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.7550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 264 optimal weight: 0.4980 chunk 339 optimal weight: 9.9990 chunk 262 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 chunk 462 optimal weight: 20.0000 chunk 289 optimal weight: 20.0000 chunk 282 optimal weight: 20.0000 chunk 213 optimal weight: 0.0980 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 265 HIS A 305 GLN B 137 GLN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN D 265 HIS D 309 GLN G 85 GLN ** G 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN ** J 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 632 GLN E 137 GLN E 265 HIS E 305 GLN E 632 GLN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** K 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 632 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 HIS ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN ** I 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN ** L 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 632 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 39672 Z= 0.305 Angle : 0.743 8.342 53820 Z= 0.369 Chirality : 0.044 0.139 6168 Planarity : 0.006 0.067 6888 Dihedral : 5.541 20.665 5424 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.17 % 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: -2.14 (0.12), residues: 4740 helix: -1.23 (0.10), residues: 2328 sheet: -2.36 (0.29), residues: 240 loop : -1.39 (0.14), residues: 2172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2134 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2127 time to evaluate : 4.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 2133 average time/residue: 0.5060 time to fit residues: 1745.8870 Evaluate side-chains 1942 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1942 time to evaluate : 4.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 0.0270 chunk 184 optimal weight: 9.9990 chunk 276 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 294 optimal weight: 20.0000 chunk 315 optimal weight: 0.1980 chunk 228 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 363 optimal weight: 6.9990 overall best weight: 3.4444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 HIS ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN ** G 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN ** J 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 632 GLN E 137 GLN E 632 GLN ** H 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** K 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 632 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN ** L 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 632 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 39672 Z= 0.213 Angle : 0.703 10.054 53820 Z= 0.342 Chirality : 0.043 0.144 6168 Planarity : 0.005 0.066 6888 Dihedral : 5.302 20.276 5424 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.14 % 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: -1.93 (0.12), residues: 4740 helix: -1.04 (0.10), residues: 2364 sheet: -2.24 (0.29), residues: 240 loop : -1.31 (0.14), residues: 2136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2140 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 2134 time to evaluate : 4.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 2138 average time/residue: 0.5103 time to fit residues: 1763.6267 Evaluate side-chains 1974 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1974 time to evaluate : 4.530 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.3737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 0.0570 chunk 443 optimal weight: 5.9990 chunk 404 optimal weight: 9.9990 chunk 431 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 chunk 187 optimal weight: 0.9990 chunk 338 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 389 optimal weight: 6.9990 chunk 407 optimal weight: 6.9990 chunk 429 optimal weight: 5.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 85 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN C 137 GLN C 632 GLN D 137 GLN D 305 GLN D 309 GLN ** G 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 HIS ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN J 545 ASN J 632 GLN E 137 GLN E 265 HIS E 305 GLN E 632 GLN H 137 GLN ** H 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 583 HIS ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** K 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 GLN K 632 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 583 HIS ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN L 309 GLN L 632 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 39672 Z= 0.188 Angle : 0.696 9.272 53820 Z= 0.337 Chirality : 0.042 0.140 6168 Planarity : 0.005 0.074 6888 Dihedral : 5.162 23.411 5424 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 0.19 % 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: -1.72 (0.12), residues: 4740 helix: -0.93 (0.10), residues: 2364 sheet: -0.47 (0.46), residues: 120 loop : -1.32 (0.14), residues: 2256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2163 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2155 time to evaluate : 4.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 2161 average time/residue: 0.5122 time to fit residues: 1790.2377 Evaluate side-chains 1987 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1987 time to evaluate : 4.415 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.1902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 1.9990 chunk 455 optimal weight: 5.9990 chunk 278 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 316 optimal weight: 8.9990 chunk 478 optimal weight: 2.9990 chunk 440 optimal weight: 0.0270 chunk 380 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 294 optimal weight: 9.9990 chunk 233 optimal weight: 0.9990 overall best weight: 1.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 214 HIS C 527 GLN C 632 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN ** J 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 527 GLN J 632 GLN E 137 GLN E 305 GLN E 632 GLN H 137 GLN ** H 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN K 214 HIS ** K 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 527 GLN K 632 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 HIS ** L 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 632 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 39672 Z= 0.174 Angle : 0.697 8.892 53820 Z= 0.335 Chirality : 0.042 0.151 6168 Planarity : 0.005 0.071 6888 Dihedral : 4.998 22.760 5424 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.22 % 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: -1.77 (0.12), residues: 4740 helix: -0.92 (0.10), residues: 2424 sheet: -0.30 (0.46), residues: 120 loop : -1.41 (0.14), residues: 2196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2169 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 2160 time to evaluate : 4.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 0 residues processed: 2164 average time/residue: 0.5066 time to fit residues: 1783.4433 Evaluate side-chains 1987 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1987 time to evaluate : 4.345 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 9.9990 chunk 405 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 351 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 105 optimal weight: 0.4980 chunk 381 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 391 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 265 HIS ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 309 GLN C 632 GLN D 265 HIS D 305 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN ** G 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN ** J 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 632 GLN E 137 GLN E 265 HIS ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** K 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 632 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 HIS ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN ** L 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 527 GLN L 632 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.169365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.142479 restraints weight = 68791.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.147080 restraints weight = 39032.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.150149 restraints weight = 25616.615| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 39672 Z= 0.190 Angle : 0.700 12.703 53820 Z= 0.339 Chirality : 0.042 0.210 6168 Planarity : 0.005 0.066 6888 Dihedral : 5.030 25.099 5424 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.22 % 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: -1.71 (0.12), residues: 4740 helix: -0.86 (0.10), residues: 2388 sheet: -0.14 (0.46), residues: 120 loop : -1.42 (0.14), residues: 2232 =============================================================================== Job complete usr+sys time: 20978.31 seconds wall clock time: 366 minutes 58.25 seconds (22018.25 seconds total)