Starting phenix.real_space_refine on Tue Mar 26 00:14:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc2_33112/03_2024/7xc2_33112_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc2_33112/03_2024/7xc2_33112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc2_33112/03_2024/7xc2_33112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc2_33112/03_2024/7xc2_33112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc2_33112/03_2024/7xc2_33112_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc2_33112/03_2024/7xc2_33112_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 240 5.16 5 C 33300 2.51 5 N 8745 2.21 5 O 9770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 39": "OE1" <-> "OE2" Residue "C PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 446": "NH1" <-> "NH2" Residue "C ASP 492": "OD1" <-> "OD2" Residue "C ASP 591": "OD1" <-> "OD2" Residue "C TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 613": "OD1" <-> "OD2" Residue "C TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 697": "NH1" <-> "NH2" Residue "C ARG 745": "NH1" <-> "NH2" Residue "C TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 175": "OD1" <-> "OD2" Residue "D PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D ASP 291": "OD1" <-> "OD2" Residue "D TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D ASP 328": "OD1" <-> "OD2" Residue "D ARG 373": "NH1" <-> "NH2" Residue "D PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 419": "OD1" <-> "OD2" Residue "D ARG 427": "NH1" <-> "NH2" Residue "D GLU 481": "OE1" <-> "OE2" Residue "D PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A ASP 492": "OD1" <-> "OD2" Residue "A ASP 591": "OD1" <-> "OD2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 613": "OD1" <-> "OD2" Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 697": "NH1" <-> "NH2" Residue "A ARG 745": "NH1" <-> "NH2" Residue "A TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 419": "OD1" <-> "OD2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 446": "NH1" <-> "NH2" Residue "E ASP 492": "OD1" <-> "OD2" Residue "E ASP 591": "OD1" <-> "OD2" Residue "E TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 613": "OD1" <-> "OD2" Residue "E TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 697": "NH1" <-> "NH2" Residue "E ARG 745": "NH1" <-> "NH2" Residue "E TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 175": "OD1" <-> "OD2" Residue "F PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "F ASP 291": "OD1" <-> "OD2" Residue "F TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "F ASP 328": "OD1" <-> "OD2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "F PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 419": "OD1" <-> "OD2" Residue "F ARG 427": "NH1" <-> "NH2" Residue "F GLU 481": "OE1" <-> "OE2" Residue "F PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 344": "NH1" <-> "NH2" Residue "G TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 446": "NH1" <-> "NH2" Residue "G ASP 492": "OD1" <-> "OD2" Residue "G ASP 591": "OD1" <-> "OD2" Residue "G TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 613": "OD1" <-> "OD2" Residue "G TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 697": "NH1" <-> "NH2" Residue "G ARG 745": "NH1" <-> "NH2" Residue "G TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 175": "OD1" <-> "OD2" Residue "H PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 236": "OE1" <-> "OE2" Residue "H ASP 291": "OD1" <-> "OD2" Residue "H TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 325": "OE1" <-> "OE2" Residue "H ASP 328": "OD1" <-> "OD2" Residue "H ARG 373": "NH1" <-> "NH2" Residue "H PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 419": "OD1" <-> "OD2" Residue "H ARG 427": "NH1" <-> "NH2" Residue "H GLU 481": "OE1" <-> "OE2" Residue "H PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 39": "OE1" <-> "OE2" Residue "I PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 446": "NH1" <-> "NH2" Residue "I ASP 492": "OD1" <-> "OD2" Residue "I ASP 591": "OD1" <-> "OD2" Residue "I TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 613": "OD1" <-> "OD2" Residue "I TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 697": "NH1" <-> "NH2" Residue "I ARG 745": "NH1" <-> "NH2" Residue "I TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 175": "OD1" <-> "OD2" Residue "J PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 236": "OE1" <-> "OE2" Residue "J ASP 291": "OD1" <-> "OD2" Residue "J TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 325": "OE1" <-> "OE2" Residue "J ASP 328": "OD1" <-> "OD2" Residue "J ARG 373": "NH1" <-> "NH2" Residue "J PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 419": "OD1" <-> "OD2" Residue "J ARG 427": "NH1" <-> "NH2" Residue "J GLU 481": "OE1" <-> "OE2" Residue "J PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 52070 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 6852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6852 Classifications: {'peptide': 858} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 823} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3531 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 6852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6852 Classifications: {'peptide': 858} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 823} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3531 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 6852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6852 Classifications: {'peptide': 858} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 823} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3531 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 6852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6852 Classifications: {'peptide': 858} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 823} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3531 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 6852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6852 Classifications: {'peptide': 858} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 823} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3531 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.42, per 1000 atoms: 0.49 Number of scatterers: 52070 At special positions: 0 Unit cell: (249.7, 246.4, 110, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 240 16.00 P 15 15.00 O 9770 8.00 N 8745 7.00 C 33300 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: 19.06 Conformation dependent library (CDL) restraints added in 8.6 seconds 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12310 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 265 helices and 25 sheets defined 50.5% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.40 Creating SS restraints... Processing helix chain 'C' and resid 23 through 52 removed outlier: 3.947A pdb=" N LYS C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 86 Processing helix chain 'C' and resid 114 through 141 removed outlier: 3.859A pdb=" N TYR C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 162 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 206 through 220 removed outlier: 5.653A pdb=" N VAL C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 246 Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 261 through 271 Processing helix chain 'C' and resid 287 through 297 removed outlier: 4.486A pdb=" N CYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE C 297 " --> pdb=" O ILE C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 319 Processing helix chain 'C' and resid 334 through 345 Processing helix chain 'C' and resid 354 through 367 removed outlier: 4.764A pdb=" N LYS C 358 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 359 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 382 Processing helix chain 'C' and resid 390 through 398 Processing helix chain 'C' and resid 408 through 422 removed outlier: 3.974A pdb=" N PHE C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 437 removed outlier: 3.671A pdb=" N LYS C 429 " --> pdb=" O SER C 426 " (cutoff:3.500A) Proline residue: C 430 - end of helix removed outlier: 3.870A pdb=" N TYR C 434 " --> pdb=" O CYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 456 Processing helix chain 'C' and resid 468 through 481 Processing helix chain 'C' and resid 503 through 516 removed outlier: 4.004A pdb=" N GLU C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 570 Processing helix chain 'C' and resid 618 through 620 No H-bonds generated for 'chain 'C' and resid 618 through 620' Processing helix chain 'C' and resid 639 through 643 Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 681 through 689 removed outlier: 4.137A pdb=" N GLY C 688 " --> pdb=" O VAL C 684 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG C 689 " --> pdb=" O LYS C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 763 through 765 No H-bonds generated for 'chain 'C' and resid 763 through 765' Processing helix chain 'C' and resid 788 through 792 Processing helix chain 'C' and resid 805 through 808 No H-bonds generated for 'chain 'C' and resid 805 through 808' Processing helix chain 'C' and resid 861 through 864 Processing helix chain 'C' and resid 893 through 908 removed outlier: 3.661A pdb=" N GLU C 898 " --> pdb=" O GLU C 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 151 removed outlier: 3.736A pdb=" N ASP D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 157 removed outlier: 4.206A pdb=" N GLN D 157 " --> pdb=" O PHE D 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 153 through 157' Processing helix chain 'D' and resid 161 through 164 Processing helix chain 'D' and resid 175 through 202 removed outlier: 3.715A pdb=" N LEU D 199 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 225 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 253 through 275 Processing helix chain 'D' and resid 282 through 288 Processing helix chain 'D' and resid 291 through 316 removed outlier: 3.855A pdb=" N ALA D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASP D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER D 312 " --> pdb=" O LYS D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 removed outlier: 3.533A pdb=" N MET D 327 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP D 328 " --> pdb=" O GLU D 325 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 329 " --> pdb=" O MET D 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 324 through 329' Processing helix chain 'D' and resid 331 through 346 removed outlier: 3.721A pdb=" N SER D 334 " --> pdb=" O TRP D 331 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N HIS D 335 " --> pdb=" O GLN D 332 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR D 336 " --> pdb=" O PHE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 364 removed outlier: 3.536A pdb=" N GLY D 360 " --> pdb=" O TRP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 391 removed outlier: 3.659A pdb=" N ALA D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU D 385 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 396 Processing helix chain 'D' and resid 401 through 418 Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 448 through 454 removed outlier: 4.100A pdb=" N LEU D 452 " --> pdb=" O PHE D 448 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS D 453 " --> pdb=" O THR D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 483 removed outlier: 3.822A pdb=" N GLU D 481 " --> pdb=" O HIS D 477 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER D 482 " --> pdb=" O ARG D 478 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS D 483 " --> pdb=" O PHE D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 529 removed outlier: 4.206A pdb=" N VAL D 516 " --> pdb=" O LYS D 512 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU D 528 " --> pdb=" O SER D 524 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG D 529 " --> pdb=" O THR D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 560 removed outlier: 3.690A pdb=" N GLN D 538 " --> pdb=" O ASN D 534 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU D 539 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS D 540 " --> pdb=" O ILE D 536 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASP D 542 " --> pdb=" O GLN D 538 " (cutoff:3.500A) Proline residue: D 543 - end of helix Proline residue: D 556 - end of helix Processing helix chain 'A' and resid 23 through 52 removed outlier: 3.947A pdb=" N LYS A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 86 Processing helix chain 'A' and resid 114 through 141 removed outlier: 3.858A pdb=" N TYR A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 162 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 171 through 182 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 206 through 220 removed outlier: 5.653A pdb=" N VAL A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 287 through 297 removed outlier: 4.486A pdb=" N CYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 319 Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 354 through 367 removed outlier: 4.763A pdb=" N LYS A 358 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 359 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 382 Processing helix chain 'A' and resid 390 through 398 Processing helix chain 'A' and resid 408 through 422 removed outlier: 3.974A pdb=" N PHE A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.672A pdb=" N LYS A 429 " --> pdb=" O SER A 426 " (cutoff:3.500A) Proline residue: A 430 - end of helix removed outlier: 3.871A pdb=" N TYR A 434 " --> pdb=" O CYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 468 through 481 Processing helix chain 'A' and resid 503 through 516 removed outlier: 4.004A pdb=" N GLU A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 570 Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 639 through 643 Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 681 through 689 removed outlier: 4.137A pdb=" N GLY A 688 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG A 689 " --> pdb=" O LYS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'A' and resid 788 through 792 Processing helix chain 'A' and resid 805 through 808 No H-bonds generated for 'chain 'A' and resid 805 through 808' Processing helix chain 'A' and resid 861 through 864 Processing helix chain 'A' and resid 893 through 908 removed outlier: 3.661A pdb=" N GLU A 898 " --> pdb=" O GLU A 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 removed outlier: 3.736A pdb=" N ASP B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 157 removed outlier: 4.206A pdb=" N GLN B 157 " --> pdb=" O PHE B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 153 through 157' Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 175 through 202 removed outlier: 3.715A pdb=" N LEU B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 225 Processing helix chain 'B' and resid 230 through 244 Processing helix chain 'B' and resid 253 through 275 Processing helix chain 'B' and resid 282 through 288 Processing helix chain 'B' and resid 291 through 316 removed outlier: 3.855A pdb=" N ALA B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASP B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 329 removed outlier: 3.533A pdb=" N MET B 327 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP B 328 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 329 " --> pdb=" O MET B 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 324 through 329' Processing helix chain 'B' and resid 331 through 346 removed outlier: 3.721A pdb=" N SER B 334 " --> pdb=" O TRP B 331 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS B 335 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR B 336 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 364 removed outlier: 3.536A pdb=" N GLY B 360 " --> pdb=" O TRP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 391 removed outlier: 3.658A pdb=" N ALA B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 396 Processing helix chain 'B' and resid 401 through 418 Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 448 through 454 removed outlier: 4.099A pdb=" N LEU B 452 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 483 removed outlier: 3.822A pdb=" N GLU B 481 " --> pdb=" O HIS B 477 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER B 482 " --> pdb=" O ARG B 478 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS B 483 " --> pdb=" O PHE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 529 removed outlier: 4.206A pdb=" N VAL B 516 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG B 529 " --> pdb=" O THR B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 560 removed outlier: 3.690A pdb=" N GLN B 538 " --> pdb=" O ASN B 534 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS B 540 " --> pdb=" O ILE B 536 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASP B 542 " --> pdb=" O GLN B 538 " (cutoff:3.500A) Proline residue: B 543 - end of helix Proline residue: B 556 - end of helix Processing helix chain 'E' and resid 23 through 52 removed outlier: 3.947A pdb=" N LYS E 52 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 86 Processing helix chain 'E' and resid 114 through 141 removed outlier: 3.859A pdb=" N TYR E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 162 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 171 through 182 Processing helix chain 'E' and resid 188 through 190 No H-bonds generated for 'chain 'E' and resid 188 through 190' Processing helix chain 'E' and resid 206 through 220 removed outlier: 5.652A pdb=" N VAL E 219 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 246 Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 261 through 271 Processing helix chain 'E' and resid 287 through 297 removed outlier: 4.486A pdb=" N CYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 319 Processing helix chain 'E' and resid 334 through 345 Processing helix chain 'E' and resid 354 through 367 removed outlier: 4.764A pdb=" N LYS E 358 " --> pdb=" O GLU E 355 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL E 359 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 382 Processing helix chain 'E' and resid 390 through 398 Processing helix chain 'E' and resid 408 through 422 removed outlier: 3.973A pdb=" N PHE E 419 " --> pdb=" O LYS E 415 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER E 420 " --> pdb=" O ILE E 416 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR E 421 " --> pdb=" O LEU E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 437 removed outlier: 3.671A pdb=" N LYS E 429 " --> pdb=" O SER E 426 " (cutoff:3.500A) Proline residue: E 430 - end of helix removed outlier: 3.870A pdb=" N TYR E 434 " --> pdb=" O CYS E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 456 Processing helix chain 'E' and resid 468 through 481 Processing helix chain 'E' and resid 503 through 516 removed outlier: 4.004A pdb=" N GLU E 516 " --> pdb=" O LEU E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 570 Processing helix chain 'E' and resid 618 through 620 No H-bonds generated for 'chain 'E' and resid 618 through 620' Processing helix chain 'E' and resid 639 through 643 Processing helix chain 'E' and resid 662 through 664 No H-bonds generated for 'chain 'E' and resid 662 through 664' Processing helix chain 'E' and resid 681 through 689 removed outlier: 4.137A pdb=" N GLY E 688 " --> pdb=" O VAL E 684 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG E 689 " --> pdb=" O LYS E 685 " (cutoff:3.500A) Processing helix chain 'E' and resid 708 through 716 Processing helix chain 'E' and resid 763 through 765 No H-bonds generated for 'chain 'E' and resid 763 through 765' Processing helix chain 'E' and resid 788 through 792 Processing helix chain 'E' and resid 805 through 808 No H-bonds generated for 'chain 'E' and resid 805 through 808' Processing helix chain 'E' and resid 861 through 864 Processing helix chain 'E' and resid 893 through 908 removed outlier: 3.661A pdb=" N GLU E 898 " --> pdb=" O GLU E 894 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 151 removed outlier: 3.736A pdb=" N ASP F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 157 removed outlier: 4.207A pdb=" N GLN F 157 " --> pdb=" O PHE F 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 153 through 157' Processing helix chain 'F' and resid 161 through 164 Processing helix chain 'F' and resid 175 through 202 removed outlier: 3.716A pdb=" N LEU F 199 " --> pdb=" O ASP F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 225 Processing helix chain 'F' and resid 230 through 244 Processing helix chain 'F' and resid 253 through 275 Processing helix chain 'F' and resid 282 through 288 Processing helix chain 'F' and resid 291 through 316 removed outlier: 3.855A pdb=" N ALA F 298 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS F 299 " --> pdb=" O LYS F 295 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR F 305 " --> pdb=" O LYS F 301 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASP F 311 " --> pdb=" O MET F 307 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 329 removed outlier: 3.532A pdb=" N MET F 327 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP F 328 " --> pdb=" O GLU F 325 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 329 " --> pdb=" O MET F 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 324 through 329' Processing helix chain 'F' and resid 331 through 346 removed outlier: 3.721A pdb=" N SER F 334 " --> pdb=" O TRP F 331 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS F 335 " --> pdb=" O GLN F 332 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR F 336 " --> pdb=" O PHE F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 364 removed outlier: 3.536A pdb=" N GLY F 360 " --> pdb=" O TRP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 391 removed outlier: 3.658A pdb=" N ALA F 384 " --> pdb=" O GLY F 380 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 385 " --> pdb=" O ARG F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 396 Processing helix chain 'F' and resid 401 through 418 Processing helix chain 'F' and resid 424 through 440 Processing helix chain 'F' and resid 448 through 454 removed outlier: 4.100A pdb=" N LEU F 452 " --> pdb=" O PHE F 448 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS F 453 " --> pdb=" O THR F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 483 removed outlier: 3.822A pdb=" N GLU F 481 " --> pdb=" O HIS F 477 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER F 482 " --> pdb=" O ARG F 478 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS F 483 " --> pdb=" O PHE F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 529 removed outlier: 4.206A pdb=" N VAL F 516 " --> pdb=" O LYS F 512 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU F 528 " --> pdb=" O SER F 524 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG F 529 " --> pdb=" O THR F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 560 removed outlier: 3.690A pdb=" N GLN F 538 " --> pdb=" O ASN F 534 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU F 539 " --> pdb=" O SER F 535 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS F 540 " --> pdb=" O ILE F 536 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP F 542 " --> pdb=" O GLN F 538 " (cutoff:3.500A) Proline residue: F 543 - end of helix Proline residue: F 556 - end of helix Processing helix chain 'G' and resid 23 through 52 removed outlier: 3.947A pdb=" N LYS G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 86 Processing helix chain 'G' and resid 114 through 141 removed outlier: 3.859A pdb=" N TYR G 141 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 162 Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 171 through 182 Processing helix chain 'G' and resid 188 through 190 No H-bonds generated for 'chain 'G' and resid 188 through 190' Processing helix chain 'G' and resid 206 through 220 removed outlier: 5.653A pdb=" N VAL G 219 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN G 220 " --> pdb=" O LYS G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 246 Processing helix chain 'G' and resid 254 through 256 No H-bonds generated for 'chain 'G' and resid 254 through 256' Processing helix chain 'G' and resid 261 through 271 Processing helix chain 'G' and resid 287 through 297 removed outlier: 4.487A pdb=" N CYS G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA G 296 " --> pdb=" O LEU G 292 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE G 297 " --> pdb=" O ILE G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 319 Processing helix chain 'G' and resid 334 through 345 Processing helix chain 'G' and resid 354 through 367 removed outlier: 4.763A pdb=" N LYS G 358 " --> pdb=" O GLU G 355 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL G 359 " --> pdb=" O LEU G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 371 through 382 Processing helix chain 'G' and resid 390 through 398 Processing helix chain 'G' and resid 408 through 422 removed outlier: 3.973A pdb=" N PHE G 419 " --> pdb=" O LYS G 415 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER G 420 " --> pdb=" O ILE G 416 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR G 421 " --> pdb=" O LEU G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 437 removed outlier: 3.671A pdb=" N LYS G 429 " --> pdb=" O SER G 426 " (cutoff:3.500A) Proline residue: G 430 - end of helix removed outlier: 3.870A pdb=" N TYR G 434 " --> pdb=" O CYS G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 456 Processing helix chain 'G' and resid 468 through 481 Processing helix chain 'G' and resid 503 through 516 removed outlier: 4.004A pdb=" N GLU G 516 " --> pdb=" O LEU G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 567 through 570 Processing helix chain 'G' and resid 618 through 620 No H-bonds generated for 'chain 'G' and resid 618 through 620' Processing helix chain 'G' and resid 639 through 643 Processing helix chain 'G' and resid 662 through 664 No H-bonds generated for 'chain 'G' and resid 662 through 664' Processing helix chain 'G' and resid 681 through 689 removed outlier: 4.137A pdb=" N GLY G 688 " --> pdb=" O VAL G 684 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG G 689 " --> pdb=" O LYS G 685 " (cutoff:3.500A) Processing helix chain 'G' and resid 708 through 716 Processing helix chain 'G' and resid 763 through 765 No H-bonds generated for 'chain 'G' and resid 763 through 765' Processing helix chain 'G' and resid 788 through 792 Processing helix chain 'G' and resid 805 through 808 No H-bonds generated for 'chain 'G' and resid 805 through 808' Processing helix chain 'G' and resid 861 through 864 Processing helix chain 'G' and resid 893 through 908 removed outlier: 3.662A pdb=" N GLU G 898 " --> pdb=" O GLU G 894 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 151 removed outlier: 3.736A pdb=" N ASP H 144 " --> pdb=" O SER H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 157 removed outlier: 4.206A pdb=" N GLN H 157 " --> pdb=" O PHE H 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 153 through 157' Processing helix chain 'H' and resid 161 through 164 Processing helix chain 'H' and resid 175 through 202 removed outlier: 3.716A pdb=" N LEU H 199 " --> pdb=" O ASP H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 225 Processing helix chain 'H' and resid 230 through 244 Processing helix chain 'H' and resid 253 through 275 Processing helix chain 'H' and resid 282 through 288 Processing helix chain 'H' and resid 291 through 316 removed outlier: 3.854A pdb=" N ALA H 298 " --> pdb=" O LEU H 294 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS H 299 " --> pdb=" O LYS H 295 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR H 305 " --> pdb=" O LYS H 301 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASP H 311 " --> pdb=" O MET H 307 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER H 312 " --> pdb=" O LYS H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 329 removed outlier: 3.532A pdb=" N MET H 327 " --> pdb=" O THR H 324 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP H 328 " --> pdb=" O GLU H 325 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU H 329 " --> pdb=" O MET H 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 324 through 329' Processing helix chain 'H' and resid 331 through 346 removed outlier: 3.721A pdb=" N SER H 334 " --> pdb=" O TRP H 331 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS H 335 " --> pdb=" O GLN H 332 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR H 336 " --> pdb=" O PHE H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 364 removed outlier: 3.536A pdb=" N GLY H 360 " --> pdb=" O TRP H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 391 removed outlier: 3.658A pdb=" N ALA H 384 " --> pdb=" O GLY H 380 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU H 385 " --> pdb=" O ARG H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 396 Processing helix chain 'H' and resid 401 through 418 Processing helix chain 'H' and resid 424 through 440 Processing helix chain 'H' and resid 448 through 454 removed outlier: 4.100A pdb=" N LEU H 452 " --> pdb=" O PHE H 448 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS H 453 " --> pdb=" O THR H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 483 removed outlier: 3.822A pdb=" N GLU H 481 " --> pdb=" O HIS H 477 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER H 482 " --> pdb=" O ARG H 478 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS H 483 " --> pdb=" O PHE H 479 " (cutoff:3.500A) Processing helix chain 'H' and resid 511 through 529 removed outlier: 4.206A pdb=" N VAL H 516 " --> pdb=" O LYS H 512 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU H 528 " --> pdb=" O SER H 524 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG H 529 " --> pdb=" O THR H 525 " (cutoff:3.500A) Processing helix chain 'H' and resid 534 through 560 removed outlier: 3.689A pdb=" N GLN H 538 " --> pdb=" O ASN H 534 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU H 539 " --> pdb=" O SER H 535 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS H 540 " --> pdb=" O ILE H 536 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP H 542 " --> pdb=" O GLN H 538 " (cutoff:3.500A) Proline residue: H 543 - end of helix Proline residue: H 556 - end of helix Processing helix chain 'I' and resid 23 through 52 removed outlier: 3.946A pdb=" N LYS I 52 " --> pdb=" O SER I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 86 Processing helix chain 'I' and resid 114 through 141 removed outlier: 3.859A pdb=" N TYR I 141 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 162 Processing helix chain 'I' and resid 165 through 167 No H-bonds generated for 'chain 'I' and resid 165 through 167' Processing helix chain 'I' and resid 171 through 182 Processing helix chain 'I' and resid 188 through 190 No H-bonds generated for 'chain 'I' and resid 188 through 190' Processing helix chain 'I' and resid 206 through 220 removed outlier: 5.653A pdb=" N VAL I 219 " --> pdb=" O ASP I 215 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN I 220 " --> pdb=" O LYS I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 246 Processing helix chain 'I' and resid 254 through 256 No H-bonds generated for 'chain 'I' and resid 254 through 256' Processing helix chain 'I' and resid 261 through 271 Processing helix chain 'I' and resid 287 through 297 removed outlier: 4.487A pdb=" N CYS I 295 " --> pdb=" O GLU I 291 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA I 296 " --> pdb=" O LEU I 292 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE I 297 " --> pdb=" O ILE I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 319 Processing helix chain 'I' and resid 334 through 345 Processing helix chain 'I' and resid 354 through 367 removed outlier: 4.763A pdb=" N LYS I 358 " --> pdb=" O GLU I 355 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL I 359 " --> pdb=" O LEU I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 371 through 382 Processing helix chain 'I' and resid 390 through 398 Processing helix chain 'I' and resid 408 through 422 removed outlier: 3.973A pdb=" N PHE I 419 " --> pdb=" O LYS I 415 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER I 420 " --> pdb=" O ILE I 416 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR I 421 " --> pdb=" O LEU I 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 426 through 437 removed outlier: 3.671A pdb=" N LYS I 429 " --> pdb=" O SER I 426 " (cutoff:3.500A) Proline residue: I 430 - end of helix removed outlier: 3.870A pdb=" N TYR I 434 " --> pdb=" O CYS I 431 " (cutoff:3.500A) Processing helix chain 'I' and resid 446 through 456 Processing helix chain 'I' and resid 468 through 481 Processing helix chain 'I' and resid 503 through 516 removed outlier: 4.004A pdb=" N GLU I 516 " --> pdb=" O LEU I 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 567 through 570 Processing helix chain 'I' and resid 618 through 620 No H-bonds generated for 'chain 'I' and resid 618 through 620' Processing helix chain 'I' and resid 639 through 643 Processing helix chain 'I' and resid 662 through 664 No H-bonds generated for 'chain 'I' and resid 662 through 664' Processing helix chain 'I' and resid 681 through 689 removed outlier: 4.137A pdb=" N GLY I 688 " --> pdb=" O VAL I 684 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG I 689 " --> pdb=" O LYS I 685 " (cutoff:3.500A) Processing helix chain 'I' and resid 708 through 716 Processing helix chain 'I' and resid 763 through 765 No H-bonds generated for 'chain 'I' and resid 763 through 765' Processing helix chain 'I' and resid 788 through 792 Processing helix chain 'I' and resid 805 through 808 No H-bonds generated for 'chain 'I' and resid 805 through 808' Processing helix chain 'I' and resid 861 through 864 Processing helix chain 'I' and resid 893 through 908 removed outlier: 3.662A pdb=" N GLU I 898 " --> pdb=" O GLU I 894 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 151 removed outlier: 3.736A pdb=" N ASP J 144 " --> pdb=" O SER J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 157 removed outlier: 4.206A pdb=" N GLN J 157 " --> pdb=" O PHE J 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 153 through 157' Processing helix chain 'J' and resid 161 through 164 Processing helix chain 'J' and resid 175 through 202 removed outlier: 3.715A pdb=" N LEU J 199 " --> pdb=" O ASP J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 225 Processing helix chain 'J' and resid 230 through 244 Processing helix chain 'J' and resid 253 through 275 Processing helix chain 'J' and resid 282 through 288 Processing helix chain 'J' and resid 291 through 316 removed outlier: 3.855A pdb=" N ALA J 298 " --> pdb=" O LEU J 294 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS J 299 " --> pdb=" O LYS J 295 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR J 305 " --> pdb=" O LYS J 301 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASP J 311 " --> pdb=" O MET J 307 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER J 312 " --> pdb=" O LYS J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 329 removed outlier: 3.532A pdb=" N MET J 327 " --> pdb=" O THR J 324 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP J 328 " --> pdb=" O GLU J 325 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU J 329 " --> pdb=" O MET J 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 324 through 329' Processing helix chain 'J' and resid 331 through 346 removed outlier: 3.721A pdb=" N SER J 334 " --> pdb=" O TRP J 331 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N HIS J 335 " --> pdb=" O GLN J 332 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR J 336 " --> pdb=" O PHE J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 348 through 364 removed outlier: 3.536A pdb=" N GLY J 360 " --> pdb=" O TRP J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 391 removed outlier: 3.658A pdb=" N ALA J 384 " --> pdb=" O GLY J 380 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU J 385 " --> pdb=" O ARG J 381 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 396 Processing helix chain 'J' and resid 401 through 418 Processing helix chain 'J' and resid 424 through 440 Processing helix chain 'J' and resid 448 through 454 removed outlier: 4.099A pdb=" N LEU J 452 " --> pdb=" O PHE J 448 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS J 453 " --> pdb=" O THR J 449 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 483 removed outlier: 3.822A pdb=" N GLU J 481 " --> pdb=" O HIS J 477 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER J 482 " --> pdb=" O ARG J 478 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS J 483 " --> pdb=" O PHE J 479 " (cutoff:3.500A) Processing helix chain 'J' and resid 511 through 529 removed outlier: 4.207A pdb=" N VAL J 516 " --> pdb=" O LYS J 512 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU J 528 " --> pdb=" O SER J 524 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG J 529 " --> pdb=" O THR J 525 " (cutoff:3.500A) Processing helix chain 'J' and resid 534 through 560 removed outlier: 3.690A pdb=" N GLN J 538 " --> pdb=" O ASN J 534 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU J 539 " --> pdb=" O SER J 535 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS J 540 " --> pdb=" O ILE J 536 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASP J 542 " --> pdb=" O GLN J 538 " (cutoff:3.500A) Proline residue: J 543 - end of helix Proline residue: J 556 - end of helix Processing sheet with id= A, first strand: chain 'C' and resid 326 through 328 removed outlier: 8.071A pdb=" N TYR C 327 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER C 197 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N CYS C 223 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N VAL C 280 " --> pdb=" O CYS C 223 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA C 225 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ASP C 282 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL C 227 " --> pdb=" O ASP C 282 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE C 284 " --> pdb=" O VAL C 227 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 486 through 488 Processing sheet with id= C, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.484A pdb=" N SER C 558 " --> pdb=" O LEU C 539 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE C 541 " --> pdb=" O SER C 558 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR C 560 " --> pdb=" O ILE C 541 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL C 581 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N VAL C 561 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP C 583 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR C 603 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR C 626 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU C 606 " --> pdb=" O THR C 626 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ASP C 628 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS C 649 " --> pdb=" O LEU C 627 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU C 629 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR C 651 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 723 through 725 removed outlier: 6.881A pdb=" N ARG C 748 " --> pdb=" O LEU C 724 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 778 through 780 removed outlier: 8.579A pdb=" N ILE C 802 " --> pdb=" O GLU C 831 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG C 833 " --> pdb=" O ILE C 802 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN C 804 " --> pdb=" O ARG C 833 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ILE C 835 " --> pdb=" O ASN C 804 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG C 854 " --> pdb=" O CYS C 832 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE C 834 " --> pdb=" O ARG C 854 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TRP C 856 " --> pdb=" O PHE C 834 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG C 881 " --> pdb=" O LEU C 855 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N PHE C 857 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL C 883 " --> pdb=" O PHE C 857 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N PHE C 859 " --> pdb=" O VAL C 883 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP C 885 " --> pdb=" O PHE C 859 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 326 through 328 removed outlier: 8.071A pdb=" N TYR A 327 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER A 197 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N CYS A 223 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL A 280 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA A 225 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASP A 282 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL A 227 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE A 284 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 486 through 488 Processing sheet with id= H, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.485A pdb=" N SER A 558 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE A 541 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR A 560 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 581 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N VAL A 561 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASP A 583 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR A 603 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR A 626 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU A 606 " --> pdb=" O THR A 626 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP A 628 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS A 649 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU A 629 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR A 651 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 723 through 725 removed outlier: 6.880A pdb=" N ARG A 748 " --> pdb=" O LEU A 724 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 778 through 780 removed outlier: 8.580A pdb=" N ILE A 802 " --> pdb=" O GLU A 831 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG A 833 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN A 804 " --> pdb=" O ARG A 833 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ILE A 835 " --> pdb=" O ASN A 804 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG A 854 " --> pdb=" O CYS A 832 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE A 834 " --> pdb=" O ARG A 854 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TRP A 856 " --> pdb=" O PHE A 834 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG A 881 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N PHE A 857 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 883 " --> pdb=" O PHE A 857 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N PHE A 859 " --> pdb=" O VAL A 883 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP A 885 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 326 through 328 removed outlier: 8.072A pdb=" N TYR E 327 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER E 197 " --> pdb=" O TYR E 327 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS E 223 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL E 280 " --> pdb=" O CYS E 223 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA E 225 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASP E 282 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL E 227 " --> pdb=" O ASP E 282 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE E 284 " --> pdb=" O VAL E 227 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 486 through 488 Processing sheet with id= M, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.484A pdb=" N SER E 558 " --> pdb=" O LEU E 539 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE E 541 " --> pdb=" O SER E 558 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR E 560 " --> pdb=" O ILE E 541 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL E 581 " --> pdb=" O VAL E 559 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL E 561 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASP E 583 " --> pdb=" O VAL E 561 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR E 603 " --> pdb=" O LEU E 582 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR E 626 " --> pdb=" O LEU E 604 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU E 606 " --> pdb=" O THR E 626 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ASP E 628 " --> pdb=" O LEU E 606 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS E 649 " --> pdb=" O LEU E 627 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU E 629 " --> pdb=" O CYS E 649 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR E 651 " --> pdb=" O LEU E 629 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 723 through 725 removed outlier: 6.880A pdb=" N ARG E 748 " --> pdb=" O LEU E 724 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 778 through 780 removed outlier: 8.580A pdb=" N ILE E 802 " --> pdb=" O GLU E 831 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG E 833 " --> pdb=" O ILE E 802 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN E 804 " --> pdb=" O ARG E 833 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE E 835 " --> pdb=" O ASN E 804 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG E 854 " --> pdb=" O CYS E 832 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE E 834 " --> pdb=" O ARG E 854 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP E 856 " --> pdb=" O PHE E 834 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG E 881 " --> pdb=" O LEU E 855 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N PHE E 857 " --> pdb=" O ARG E 881 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL E 883 " --> pdb=" O PHE E 857 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N PHE E 859 " --> pdb=" O VAL E 883 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP E 885 " --> pdb=" O PHE E 859 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 326 through 328 removed outlier: 8.072A pdb=" N TYR G 327 " --> pdb=" O THR G 195 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER G 197 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS G 223 " --> pdb=" O LEU G 278 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL G 280 " --> pdb=" O CYS G 223 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA G 225 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ASP G 282 " --> pdb=" O ALA G 225 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL G 227 " --> pdb=" O ASP G 282 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE G 284 " --> pdb=" O VAL G 227 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 486 through 488 Processing sheet with id= R, first strand: chain 'G' and resid 520 through 522 removed outlier: 6.485A pdb=" N SER G 558 " --> pdb=" O LEU G 539 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE G 541 " --> pdb=" O SER G 558 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR G 560 " --> pdb=" O ILE G 541 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL G 581 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL G 561 " --> pdb=" O VAL G 581 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASP G 583 " --> pdb=" O VAL G 561 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR G 603 " --> pdb=" O LEU G 582 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR G 626 " --> pdb=" O LEU G 604 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU G 606 " --> pdb=" O THR G 626 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP G 628 " --> pdb=" O LEU G 606 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS G 649 " --> pdb=" O LEU G 627 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU G 629 " --> pdb=" O CYS G 649 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR G 651 " --> pdb=" O LEU G 629 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 723 through 725 removed outlier: 6.881A pdb=" N ARG G 748 " --> pdb=" O LEU G 724 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'G' and resid 778 through 780 removed outlier: 8.580A pdb=" N ILE G 802 " --> pdb=" O GLU G 831 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG G 833 " --> pdb=" O ILE G 802 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN G 804 " --> pdb=" O ARG G 833 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE G 835 " --> pdb=" O ASN G 804 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG G 854 " --> pdb=" O CYS G 832 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE G 834 " --> pdb=" O ARG G 854 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TRP G 856 " --> pdb=" O PHE G 834 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG G 881 " --> pdb=" O LEU G 855 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N PHE G 857 " --> pdb=" O ARG G 881 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL G 883 " --> pdb=" O PHE G 857 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N PHE G 859 " --> pdb=" O VAL G 883 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP G 885 " --> pdb=" O PHE G 859 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 326 through 328 removed outlier: 8.072A pdb=" N TYR I 327 " --> pdb=" O THR I 195 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER I 197 " --> pdb=" O TYR I 327 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS I 223 " --> pdb=" O LEU I 278 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N VAL I 280 " --> pdb=" O CYS I 223 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA I 225 " --> pdb=" O VAL I 280 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASP I 282 " --> pdb=" O ALA I 225 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL I 227 " --> pdb=" O ASP I 282 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE I 284 " --> pdb=" O VAL I 227 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 486 through 488 Processing sheet with id= W, first strand: chain 'I' and resid 520 through 522 removed outlier: 6.485A pdb=" N SER I 558 " --> pdb=" O LEU I 539 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE I 541 " --> pdb=" O SER I 558 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR I 560 " --> pdb=" O ILE I 541 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL I 581 " --> pdb=" O VAL I 559 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL I 561 " --> pdb=" O VAL I 581 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASP I 583 " --> pdb=" O VAL I 561 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR I 603 " --> pdb=" O LEU I 582 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR I 626 " --> pdb=" O LEU I 604 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU I 606 " --> pdb=" O THR I 626 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP I 628 " --> pdb=" O LEU I 606 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS I 649 " --> pdb=" O LEU I 627 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU I 629 " --> pdb=" O CYS I 649 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR I 651 " --> pdb=" O LEU I 629 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 723 through 725 removed outlier: 6.881A pdb=" N ARG I 748 " --> pdb=" O LEU I 724 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'I' and resid 778 through 780 removed outlier: 8.581A pdb=" N ILE I 802 " --> pdb=" O GLU I 831 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG I 833 " --> pdb=" O ILE I 802 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN I 804 " --> pdb=" O ARG I 833 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ILE I 835 " --> pdb=" O ASN I 804 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG I 854 " --> pdb=" O CYS I 832 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE I 834 " --> pdb=" O ARG I 854 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TRP I 856 " --> pdb=" O PHE I 834 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG I 881 " --> pdb=" O LEU I 855 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N PHE I 857 " --> pdb=" O ARG I 881 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL I 883 " --> pdb=" O PHE I 857 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N PHE I 859 " --> pdb=" O VAL I 883 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP I 885 " --> pdb=" O PHE I 859 " (cutoff:3.500A) 2100 hydrogen bonds defined for protein. 5775 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: 22.29 Time building geometry restraints manager: 20.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11353 1.33 - 1.45: 10968 1.45 - 1.57: 30344 1.57 - 1.69: 35 1.69 - 1.81: 390 Bond restraints: 53090 Sorted by residual: bond pdb=" C4 ATP E1001 " pdb=" C5 ATP E1001 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.66e+01 bond pdb=" C4 ATP G1001 " pdb=" C5 ATP G1001 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.64e+01 bond pdb=" C4 ATP I1001 " pdb=" C5 ATP I1001 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.60e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.57e+01 bond pdb=" C4 ATP C1001 " pdb=" C5 ATP C1001 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.56e+01 ... (remaining 53085 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.46: 1293 106.46 - 113.86: 31075 113.86 - 121.25: 27188 121.25 - 128.65: 11750 128.65 - 136.05: 379 Bond angle restraints: 71685 Sorted by residual: angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 120.81 19.06 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PB ATP C1001 " pdb=" O3B ATP C1001 " pdb=" PG ATP C1001 " ideal model delta sigma weight residual 139.87 120.83 19.04 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PB ATP G1001 " pdb=" O3B ATP G1001 " pdb=" PG ATP G1001 " ideal model delta sigma weight residual 139.87 120.85 19.02 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PB ATP E1001 " pdb=" O3B ATP E1001 " pdb=" PG ATP E1001 " ideal model delta sigma weight residual 139.87 120.87 19.00 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PB ATP I1001 " pdb=" O3B ATP I1001 " pdb=" PG ATP I1001 " ideal model delta sigma weight residual 139.87 120.89 18.98 1.00e+00 1.00e+00 3.60e+02 ... (remaining 71680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 29403 16.79 - 33.57: 2528 33.57 - 50.36: 498 50.36 - 67.15: 61 67.15 - 83.94: 30 Dihedral angle restraints: 32520 sinusoidal: 13570 harmonic: 18950 Sorted by residual: dihedral pdb=" CA PHE E 346 " pdb=" C PHE E 346 " pdb=" N SER E 347 " pdb=" CA SER E 347 " ideal model delta harmonic sigma weight residual 180.00 -150.75 -29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA PHE C 346 " pdb=" C PHE C 346 " pdb=" N SER C 347 " pdb=" CA SER C 347 " ideal model delta harmonic sigma weight residual -180.00 -150.76 -29.24 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA PHE I 346 " pdb=" C PHE I 346 " pdb=" N SER I 347 " pdb=" CA SER I 347 " ideal model delta harmonic sigma weight residual -180.00 -150.76 -29.24 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 32517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 6895 0.065 - 0.129: 1112 0.129 - 0.194: 50 0.194 - 0.259: 8 0.259 - 0.323: 5 Chirality restraints: 8070 Sorted by residual: chirality pdb=" CB ILE F 536 " pdb=" CA ILE F 536 " pdb=" CG1 ILE F 536 " pdb=" CG2 ILE F 536 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB ILE D 536 " pdb=" CA ILE D 536 " pdb=" CG1 ILE D 536 " pdb=" CG2 ILE D 536 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE B 536 " pdb=" CA ILE B 536 " pdb=" CG1 ILE B 536 " pdb=" CG2 ILE B 536 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 8067 not shown) Planarity restraints: 9035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 441 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.13e+00 pdb=" C ASP A 441 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP A 441 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG A 442 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 441 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C ASP E 441 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP E 441 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG E 442 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 441 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C ASP C 441 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP C 441 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG C 442 " -0.013 2.00e-02 2.50e+03 ... (remaining 9032 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 870 2.65 - 3.22: 50450 3.22 - 3.78: 73754 3.78 - 4.34: 103534 4.34 - 4.90: 167834 Nonbonded interactions: 396442 Sorted by model distance: nonbonded pdb=" O HIS H 335 " pdb=" OG1 THR H 338 " model vdw 2.093 2.440 nonbonded pdb=" O HIS F 335 " pdb=" OG1 THR F 338 " model vdw 2.093 2.440 nonbonded pdb=" O HIS J 335 " pdb=" OG1 THR J 338 " model vdw 2.093 2.440 nonbonded pdb=" O HIS B 335 " pdb=" OG1 THR B 338 " model vdw 2.093 2.440 nonbonded pdb=" O HIS D 335 " pdb=" OG1 THR D 338 " model vdw 2.094 2.440 ... (remaining 396437 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 12.410 Check model and map are aligned: 0.710 Set scattering table: 0.430 Process input model: 129.250 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:14.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 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 : 0.007 0.068 53090 Z= 0.479 Angle : 0.832 19.058 71685 Z= 0.511 Chirality : 0.046 0.323 8070 Planarity : 0.004 0.046 9035 Dihedral : 12.950 83.937 20210 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.80 % Allowed : 5.07 % Favored : 93.13 % 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: -2.27 (0.10), residues: 6375 helix: -0.41 (0.08), residues: 3135 sheet: -2.03 (0.20), residues: 640 loop : -2.73 (0.11), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 639 HIS 0.006 0.001 HIS D 487 PHE 0.017 0.002 PHE G 346 TYR 0.015 0.002 TYR D 336 ARG 0.005 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 325 time to evaluate : 5.919 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: C 504 MET cc_start: 0.8529 (mmm) cc_final: 0.8305 (mmt) REVERT: E 360 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.8066 (p) REVERT: E 553 MET cc_start: 0.7342 (mtt) cc_final: 0.7098 (mtt) outliers start: 105 outliers final: 25 residues processed: 418 average time/residue: 1.9936 time to fit residues: 1007.9780 Evaluate side-chains 202 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 176 time to evaluate : 5.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain E residue 574 SER Chi-restraints excluded: chain E residue 590 SER Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 574 SER Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 349 SER Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 360 SER Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 421 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 540 optimal weight: 7.9990 chunk 485 optimal weight: 6.9990 chunk 269 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 327 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 501 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 305 optimal weight: 1.9990 chunk 373 optimal weight: 7.9990 chunk 581 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN C 191 HIS C 255 HIS C 412 GLN C 588 HIS C 729 ASN C 739 HIS ** C 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN D 271 HIS D 332 GLN D 346 ASN D 475 ASN D 477 HIS A 118 HIS A 130 GLN A 191 HIS A 255 HIS A 588 HIS A 729 ASN A 739 HIS ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS B 158 GLN B 271 HIS B 332 GLN B 346 ASN B 402 HIS B 475 ASN B 477 HIS E 130 GLN E 191 HIS E 255 HIS E 412 GLN E 588 HIS E 729 ASN E 739 HIS ** E 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 GLN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 HIS F 332 GLN F 346 ASN F 475 ASN F 477 HIS G 118 HIS G 130 GLN G 191 HIS G 255 HIS G 588 HIS G 729 ASN G 739 HIS ** G 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 GLN H 271 HIS H 332 GLN H 346 ASN H 475 ASN H 477 HIS I 118 HIS I 130 GLN I 191 HIS I 255 HIS I 588 HIS I 729 ASN I 739 HIS ** I 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 GLN ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 271 HIS J 332 GLN J 346 ASN J 475 ASN J 477 HIS Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 53090 Z= 0.246 Angle : 0.584 13.131 71685 Z= 0.303 Chirality : 0.042 0.148 8070 Planarity : 0.004 0.039 9035 Dihedral : 7.172 89.462 7161 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.59 % Allowed : 10.56 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.11), residues: 6375 helix: 0.88 (0.09), residues: 3095 sheet: -1.49 (0.21), residues: 615 loop : -2.23 (0.12), residues: 2665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 764 HIS 0.021 0.001 HIS E 739 PHE 0.011 0.001 PHE F 521 TYR 0.012 0.001 TYR E 162 ARG 0.010 0.001 ARG B 550 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 192 time to evaluate : 6.155 Fit side-chains REVERT: C 386 HIS cc_start: 0.5126 (OUTLIER) cc_final: 0.4856 (m-70) REVERT: C 504 MET cc_start: 0.8505 (mmm) cc_final: 0.8300 (mmt) REVERT: A 386 HIS cc_start: 0.5028 (OUTLIER) cc_final: 0.4795 (m-70) REVERT: B 136 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5978 (tmm) REVERT: B 327 MET cc_start: 0.6082 (mtm) cc_final: 0.5814 (mtp) REVERT: B 421 ASN cc_start: 0.6166 (OUTLIER) cc_final: 0.5718 (p0) REVERT: I 386 HIS cc_start: 0.5190 (OUTLIER) cc_final: 0.4920 (m-70) outliers start: 93 outliers final: 32 residues processed: 254 average time/residue: 1.5332 time to fit residues: 501.0140 Evaluate side-chains 213 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 176 time to evaluate : 6.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 386 HIS Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 563 SER Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 421 ASN Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 360 SER Chi-restraints excluded: chain I residue 386 HIS Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 707 MET Chi-restraints excluded: chain I residue 746 LEU Chi-restraints excluded: chain J residue 421 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 322 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 483 optimal weight: 9.9990 chunk 395 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 582 optimal weight: 5.9990 chunk 628 optimal weight: 10.0000 chunk 518 optimal weight: 7.9990 chunk 577 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 467 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 GLN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 HIS ** C 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN E 118 HIS ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 402 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 53090 Z= 0.362 Angle : 0.602 10.408 71685 Z= 0.313 Chirality : 0.043 0.148 8070 Planarity : 0.004 0.039 9035 Dihedral : 7.026 88.179 7127 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.42 % Allowed : 11.36 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.11), residues: 6375 helix: 1.04 (0.09), residues: 3130 sheet: -1.44 (0.22), residues: 600 loop : -2.16 (0.12), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 290 HIS 0.007 0.001 HIS E 600 PHE 0.015 0.001 PHE A 341 TYR 0.015 0.002 TYR E 214 ARG 0.006 0.001 ARG D 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 182 time to evaluate : 5.704 Fit side-chains revert: symmetry clash REVERT: C 386 HIS cc_start: 0.5168 (OUTLIER) cc_final: 0.4921 (m-70) REVERT: C 571 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6722 (pt) REVERT: A 181 MET cc_start: 0.8266 (ttm) cc_final: 0.7951 (ttm) REVERT: A 386 HIS cc_start: 0.4979 (OUTLIER) cc_final: 0.4734 (m-70) REVERT: I 386 HIS cc_start: 0.5165 (OUTLIER) cc_final: 0.4887 (m-70) outliers start: 141 outliers final: 50 residues processed: 287 average time/residue: 1.3765 time to fit residues: 518.6838 Evaluate side-chains 232 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 178 time to evaluate : 6.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 386 HIS Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 542 ASP Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain G residue 680 ASP Chi-restraints excluded: chain G residue 681 LEU Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 421 ASN Chi-restraints excluded: chain H residue 542 ASP Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 360 SER Chi-restraints excluded: chain I residue 386 HIS Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain J residue 406 LEU Chi-restraints excluded: chain J residue 421 ASN Chi-restraints excluded: chain J residue 542 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 575 optimal weight: 5.9990 chunk 437 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 277 optimal weight: 0.9990 chunk 390 optimal weight: 0.8980 chunk 584 optimal weight: 0.9990 chunk 618 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 553 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 GLN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 GLN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 53090 Z= 0.148 Angle : 0.517 14.276 71685 Z= 0.267 Chirality : 0.040 0.190 8070 Planarity : 0.003 0.038 9035 Dihedral : 6.651 88.541 7127 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.23 % Allowed : 12.36 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.11), residues: 6375 helix: 1.33 (0.10), residues: 3135 sheet: -1.23 (0.22), residues: 600 loop : -1.88 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 290 HIS 0.004 0.001 HIS J 394 PHE 0.012 0.001 PHE J 376 TYR 0.010 0.001 TYR C 654 ARG 0.006 0.000 ARG J 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 184 time to evaluate : 6.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 386 HIS cc_start: 0.4988 (OUTLIER) cc_final: 0.4764 (m-70) REVERT: C 504 MET cc_start: 0.8555 (mmt) cc_final: 0.8331 (mmt) outliers start: 130 outliers final: 54 residues processed: 279 average time/residue: 1.4948 time to fit residues: 541.6373 Evaluate side-chains 232 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 177 time to evaluate : 6.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 386 HIS Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 542 ASP Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain F residue 542 ASP Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 563 SER Chi-restraints excluded: chain G residue 680 ASP Chi-restraints excluded: chain H residue 421 ASN Chi-restraints excluded: chain H residue 542 ASP Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 746 LEU Chi-restraints excluded: chain I residue 918 ILE Chi-restraints excluded: chain J residue 421 ASN Chi-restraints excluded: chain J residue 542 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 515 optimal weight: 7.9990 chunk 351 optimal weight: 30.0000 chunk 8 optimal weight: 3.9990 chunk 460 optimal weight: 8.9990 chunk 255 optimal weight: 3.9990 chunk 527 optimal weight: 4.9990 chunk 427 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 315 optimal weight: 0.9990 chunk 555 optimal weight: 0.0870 chunk 156 optimal weight: 0.9980 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 GLN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 GLN F 172 GLN G 875 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 53090 Z= 0.194 Angle : 0.515 12.723 71685 Z= 0.265 Chirality : 0.040 0.162 8070 Planarity : 0.003 0.036 9035 Dihedral : 6.543 89.349 7126 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.94 % Allowed : 13.14 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.11), residues: 6375 helix: 1.41 (0.10), residues: 3145 sheet: -1.13 (0.22), residues: 600 loop : -1.82 (0.12), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 290 HIS 0.005 0.001 HIS J 394 PHE 0.009 0.001 PHE D 377 TYR 0.011 0.001 TYR E 214 ARG 0.004 0.000 ARG D 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 176 time to evaluate : 7.042 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.8261 (ttm) cc_final: 0.7997 (ttm) REVERT: A 680 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7253 (p0) REVERT: A 682 ASP cc_start: 0.5936 (OUTLIER) cc_final: 0.5657 (p0) REVERT: H 316 MET cc_start: 0.5274 (tpp) cc_final: 0.5037 (tpp) outliers start: 113 outliers final: 63 residues processed: 259 average time/residue: 1.4745 time to fit residues: 498.2359 Evaluate side-chains 241 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 176 time to evaluate : 6.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 542 ASP Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 707 MET Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain F residue 509 HIS Chi-restraints excluded: chain F residue 542 ASP Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 563 SER Chi-restraints excluded: chain G residue 680 ASP Chi-restraints excluded: chain G residue 681 LEU Chi-restraints excluded: chain H residue 421 ASN Chi-restraints excluded: chain H residue 542 ASP Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 682 ASP Chi-restraints excluded: chain I residue 918 ILE Chi-restraints excluded: chain J residue 421 ASN Chi-restraints excluded: chain J residue 509 HIS Chi-restraints excluded: chain J residue 542 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 208 optimal weight: 0.0020 chunk 557 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 363 optimal weight: 10.0000 chunk 152 optimal weight: 0.8980 chunk 619 optimal weight: 9.9990 chunk 514 optimal weight: 3.9990 chunk 286 optimal weight: 0.8980 chunk 51 optimal weight: 0.0970 chunk 204 optimal weight: 0.1980 chunk 325 optimal weight: 5.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 GLN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 GLN ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 875 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 53090 Z= 0.119 Angle : 0.491 12.557 71685 Z= 0.250 Chirality : 0.039 0.138 8070 Planarity : 0.003 0.043 9035 Dihedral : 6.196 89.269 7126 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.70 % Allowed : 14.31 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.11), residues: 6375 helix: 1.52 (0.10), residues: 3185 sheet: -0.95 (0.23), residues: 600 loop : -1.78 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 65 HIS 0.004 0.000 HIS J 394 PHE 0.014 0.001 PHE J 376 TYR 0.012 0.001 TYR F 456 ARG 0.004 0.000 ARG J 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 183 time to evaluate : 5.795 Fit side-chains revert: symmetry clash REVERT: A 680 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.7150 (p0) REVERT: H 316 MET cc_start: 0.5041 (tpp) cc_final: 0.4788 (tpp) outliers start: 99 outliers final: 45 residues processed: 261 average time/residue: 1.4515 time to fit residues: 492.3175 Evaluate side-chains 220 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 174 time to evaluate : 6.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 542 ASP Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain F residue 509 HIS Chi-restraints excluded: chain F residue 542 ASP Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 563 SER Chi-restraints excluded: chain G residue 680 ASP Chi-restraints excluded: chain G residue 707 MET Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 421 ASN Chi-restraints excluded: chain H residue 542 ASP Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 918 ILE Chi-restraints excluded: chain J residue 509 HIS Chi-restraints excluded: chain J residue 542 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 597 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 352 optimal weight: 5.9990 chunk 452 optimal weight: 0.0010 chunk 350 optimal weight: 5.9990 chunk 521 optimal weight: 1.9990 chunk 345 optimal weight: 8.9990 chunk 616 optimal weight: 10.0000 chunk 386 optimal weight: 2.9990 chunk 376 optimal weight: 40.0000 chunk 284 optimal weight: 2.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 GLN A 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 53090 Z= 0.267 Angle : 0.541 12.372 71685 Z= 0.276 Chirality : 0.041 0.144 8070 Planarity : 0.003 0.044 9035 Dihedral : 6.374 89.653 7123 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.95 % Allowed : 14.53 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.11), residues: 6375 helix: 1.56 (0.10), residues: 3150 sheet: -0.92 (0.22), residues: 600 loop : -1.69 (0.12), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 290 HIS 0.005 0.001 HIS F 394 PHE 0.012 0.001 PHE H 377 TYR 0.018 0.001 TYR F 456 ARG 0.003 0.000 ARG C 552 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 175 time to evaluate : 5.755 Fit side-chains revert: symmetry clash REVERT: H 505 ILE cc_start: 0.5476 (OUTLIER) cc_final: 0.5120 (mp) outliers start: 114 outliers final: 67 residues processed: 266 average time/residue: 1.4565 time to fit residues: 502.8748 Evaluate side-chains 243 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 175 time to evaluate : 6.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 707 MET Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 283 ASP Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 542 ASP Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 682 ASP Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain F residue 509 HIS Chi-restraints excluded: chain F residue 542 ASP Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 680 ASP Chi-restraints excluded: chain G residue 707 MET Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 421 ASN Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 509 HIS Chi-restraints excluded: chain H residue 542 ASP Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 712 GLU Chi-restraints excluded: chain I residue 918 ILE Chi-restraints excluded: chain J residue 283 ASP Chi-restraints excluded: chain J residue 509 HIS Chi-restraints excluded: chain J residue 542 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 381 optimal weight: 20.0000 chunk 246 optimal weight: 8.9990 chunk 368 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 121 optimal weight: 0.0370 chunk 119 optimal weight: 8.9990 chunk 392 optimal weight: 0.9980 chunk 420 optimal weight: 0.0770 chunk 304 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 484 optimal weight: 7.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 53090 Z= 0.121 Angle : 0.492 11.771 71685 Z= 0.248 Chirality : 0.039 0.135 8070 Planarity : 0.003 0.046 9035 Dihedral : 6.126 87.761 7123 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.51 % Allowed : 15.12 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.11), residues: 6375 helix: 1.63 (0.10), residues: 3190 sheet: -0.80 (0.23), residues: 600 loop : -1.62 (0.12), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 65 HIS 0.004 0.000 HIS F 394 PHE 0.010 0.001 PHE J 559 TYR 0.010 0.001 TYR I 214 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 179 time to evaluate : 4.980 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 52 residues processed: 256 average time/residue: 1.4873 time to fit residues: 492.4922 Evaluate side-chains 225 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 173 time to evaluate : 5.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 283 ASP Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 542 ASP Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 682 ASP Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 509 HIS Chi-restraints excluded: chain F residue 542 ASP Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 680 ASP Chi-restraints excluded: chain G residue 707 MET Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 421 ASN Chi-restraints excluded: chain H residue 542 ASP Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 918 ILE Chi-restraints excluded: chain J residue 283 ASP Chi-restraints excluded: chain J residue 509 HIS Chi-restraints excluded: chain J residue 542 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 561 optimal weight: 0.9980 chunk 590 optimal weight: 10.0000 chunk 539 optimal weight: 0.9980 chunk 574 optimal weight: 3.9990 chunk 345 optimal weight: 20.0000 chunk 250 optimal weight: 7.9990 chunk 451 optimal weight: 0.2980 chunk 176 optimal weight: 2.9990 chunk 519 optimal weight: 2.9990 chunk 543 optimal weight: 0.6980 chunk 572 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 432 HIS A 412 GLN ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 53090 Z= 0.121 Angle : 0.497 15.254 71685 Z= 0.248 Chirality : 0.039 0.181 8070 Planarity : 0.003 0.046 9035 Dihedral : 5.961 88.203 7120 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.11 % Allowed : 15.68 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.11), residues: 6375 helix: 1.74 (0.10), residues: 3190 sheet: -0.55 (0.24), residues: 575 loop : -1.60 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 290 HIS 0.004 0.000 HIS F 394 PHE 0.013 0.001 PHE F 559 TYR 0.009 0.001 TYR F 456 ARG 0.003 0.000 ARG D 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 180 time to evaluate : 6.324 Fit side-chains revert: symmetry clash REVERT: H 316 MET cc_start: 0.4853 (tpp) cc_final: 0.4561 (ttp) REVERT: H 505 ILE cc_start: 0.5389 (OUTLIER) cc_final: 0.5071 (mp) outliers start: 65 outliers final: 45 residues processed: 236 average time/residue: 1.5203 time to fit residues: 463.0146 Evaluate side-chains 219 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 4.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 283 ASP Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 542 ASP Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 682 ASP Chi-restraints excluded: chain F residue 509 HIS Chi-restraints excluded: chain F residue 542 ASP Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 680 ASP Chi-restraints excluded: chain G residue 707 MET Chi-restraints excluded: chain G residue 758 PHE Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 542 ASP Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 918 ILE Chi-restraints excluded: chain J residue 283 ASP Chi-restraints excluded: chain J residue 509 HIS Chi-restraints excluded: chain J residue 536 ILE Chi-restraints excluded: chain J residue 542 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 377 optimal weight: 0.3980 chunk 607 optimal weight: 0.0370 chunk 371 optimal weight: 0.5980 chunk 288 optimal weight: 1.9990 chunk 422 optimal weight: 0.8980 chunk 637 optimal weight: 0.8980 chunk 586 optimal weight: 10.0000 chunk 507 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 392 optimal weight: 5.9990 chunk 311 optimal weight: 10.0000 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 53090 Z= 0.119 Angle : 0.492 12.605 71685 Z= 0.245 Chirality : 0.039 0.192 8070 Planarity : 0.003 0.045 9035 Dihedral : 5.842 87.822 7120 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.03 % Allowed : 15.89 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.11), residues: 6375 helix: 1.80 (0.10), residues: 3190 sheet: -0.48 (0.24), residues: 575 loop : -1.54 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 290 HIS 0.004 0.000 HIS J 359 PHE 0.011 0.001 PHE F 376 TYR 0.011 0.001 TYR A 654 ARG 0.003 0.000 ARG B 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 180 time to evaluate : 6.029 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 46 residues processed: 233 average time/residue: 1.5348 time to fit residues: 469.4931 Evaluate side-chains 219 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 5.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain D residue 283 ASP Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 509 HIS Chi-restraints excluded: chain D residue 542 ASP Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 682 ASP Chi-restraints excluded: chain E residue 918 ILE Chi-restraints excluded: chain F residue 509 HIS Chi-restraints excluded: chain F residue 542 ASP Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 680 ASP Chi-restraints excluded: chain G residue 707 MET Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 542 ASP Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 918 ILE Chi-restraints excluded: chain J residue 283 ASP Chi-restraints excluded: chain J residue 509 HIS Chi-restraints excluded: chain J residue 542 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 403 optimal weight: 0.0170 chunk 540 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 468 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 141 optimal weight: 0.6980 chunk 508 optimal weight: 7.9990 chunk 212 optimal weight: 20.0000 chunk 522 optimal weight: 5.9990 chunk 64 optimal weight: 0.3980 chunk 93 optimal weight: 7.9990 overall best weight: 2.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.080248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.046440 restraints weight = 178090.519| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.56 r_work: 0.2686 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 53090 Z= 0.234 Angle : 0.542 12.045 71685 Z= 0.272 Chirality : 0.041 0.189 8070 Planarity : 0.003 0.045 9035 Dihedral : 6.102 86.862 7120 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.11 % Allowed : 15.94 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.11), residues: 6375 helix: 1.78 (0.10), residues: 3175 sheet: -0.67 (0.23), residues: 600 loop : -1.52 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 290 HIS 0.004 0.001 HIS F 394 PHE 0.017 0.001 PHE J 376 TYR 0.013 0.001 TYR E 162 ARG 0.003 0.000 ARG C 552 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11605.48 seconds wall clock time: 209 minutes 9.61 seconds (12549.61 seconds total)