Starting phenix.real_space_refine on Sat Feb 17 07:51:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt4_0967/02_2024/6lt4_0967_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt4_0967/02_2024/6lt4_0967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt4_0967/02_2024/6lt4_0967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt4_0967/02_2024/6lt4_0967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt4_0967/02_2024/6lt4_0967_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt4_0967/02_2024/6lt4_0967_updated.pdb" } resolution = 4.5 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 ------------------------------------------------------------------------------- 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= 0.009 sd= 0.045 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: 6 Type Number sf(0) Gaussians P 84 5.49 5 Mg 28 5.21 5 S 182 5.16 5 C 42350 2.51 5 N 12040 2.21 5 O 13748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 468": "OD1" <-> "OD2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 272": "OD1" <-> "OD2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 468": "OD1" <-> "OD2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 486": "OD1" <-> "OD2" Residue "B TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 272": "OD1" <-> "OD2" Residue "C GLU 331": "OE1" <-> "OE2" Residue "C PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 468": "OD1" <-> "OD2" Residue "C PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 486": "OD1" <-> "OD2" Residue "C TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 272": "OD1" <-> "OD2" Residue "D GLU 331": "OE1" <-> "OE2" Residue "D PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 468": "OD1" <-> "OD2" Residue "D PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 486": "OD1" <-> "OD2" Residue "D TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 654": "OE1" <-> "OE2" Residue "E PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 272": "OD1" <-> "OD2" Residue "E GLU 331": "OE1" <-> "OE2" Residue "E PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 468": "OD1" <-> "OD2" Residue "E PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 486": "OD1" <-> "OD2" Residue "E TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 654": "OE1" <-> "OE2" Residue "F PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 272": "OD1" <-> "OD2" Residue "F GLU 331": "OE1" <-> "OE2" Residue "F PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 468": "OD1" <-> "OD2" Residue "F PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 486": "OD1" <-> "OD2" Residue "F TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 654": "OE1" <-> "OE2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 272": "OD1" <-> "OD2" Residue "G GLU 331": "OE1" <-> "OE2" Residue "G PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 468": "OD1" <-> "OD2" Residue "G PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 486": "OD1" <-> "OD2" Residue "G TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 654": "OE1" <-> "OE2" Residue "H PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 272": "OD1" <-> "OD2" Residue "H GLU 331": "OE1" <-> "OE2" Residue "H PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 468": "OD1" <-> "OD2" Residue "H PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 486": "OD1" <-> "OD2" Residue "H TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 654": "OE1" <-> "OE2" Residue "I PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 272": "OD1" <-> "OD2" Residue "I GLU 331": "OE1" <-> "OE2" Residue "I PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 468": "OD1" <-> "OD2" Residue "I PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 486": "OD1" <-> "OD2" Residue "I TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 654": "OE1" <-> "OE2" Residue "J PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 272": "OD1" <-> "OD2" Residue "J GLU 331": "OE1" <-> "OE2" Residue "J PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 468": "OD1" <-> "OD2" Residue "J PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 486": "OD1" <-> "OD2" Residue "J TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 654": "OE1" <-> "OE2" Residue "K PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 272": "OD1" <-> "OD2" Residue "K GLU 331": "OE1" <-> "OE2" Residue "K PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 468": "OD1" <-> "OD2" Residue "K PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 486": "OD1" <-> "OD2" Residue "K TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 654": "OE1" <-> "OE2" Residue "L PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 272": "OD1" <-> "OD2" Residue "L GLU 331": "OE1" <-> "OE2" Residue "L PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 468": "OD1" <-> "OD2" Residue "L PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 486": "OD1" <-> "OD2" Residue "L TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 654": "OE1" <-> "OE2" Residue "M PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 272": "OD1" <-> "OD2" Residue "M GLU 331": "OE1" <-> "OE2" Residue "M PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 468": "OD1" <-> "OD2" Residue "M PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 486": "OD1" <-> "OD2" Residue "M TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 654": "OE1" <-> "OE2" Residue "N PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 272": "OD1" <-> "OD2" Residue "N GLU 331": "OE1" <-> "OE2" Residue "N PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 468": "OD1" <-> "OD2" Residue "N PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 486": "OD1" <-> "OD2" Residue "N TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 654": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68432 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "B" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "C" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "D" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "E" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "F" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "G" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "H" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "I" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "J" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "K" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "L" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "M" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "N" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 25.69, per 1000 atoms: 0.38 Number of scatterers: 68432 At special positions: 0 Unit cell: (165.2, 165.2, 226.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 182 16.00 P 84 15.00 Mg 28 11.99 O 13748 8.00 N 12040 7.00 C 42350 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: 22.61 Conformation dependent library (CDL) restraints added in 9.5 seconds 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16268 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 406 helices and 70 sheets defined 51.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.31 Creating SS restraints... Processing helix chain 'A' and resid 83 through 89 Processing helix chain 'A' and resid 99 through 109 removed outlier: 4.017A pdb=" N ALA A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 140 removed outlier: 4.366A pdb=" N VAL A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 167 through 180 removed outlier: 3.627A pdb=" N VAL A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 212 through 221 removed outlier: 5.256A pdb=" N LYS A 217 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 233 through 242 removed outlier: 4.506A pdb=" N LEU A 241 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 262 through 277 removed outlier: 4.639A pdb=" N ASP A 272 " --> pdb=" O GLN A 268 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 297 removed outlier: 3.616A pdb=" N GLN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 371 Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 436 Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 484 No H-bonds generated for 'chain 'A' and resid 481 through 484' Processing helix chain 'A' and resid 497 through 506 removed outlier: 3.858A pdb=" N VAL A 501 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 536 through 544 removed outlier: 3.905A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Proline residue: A 591 - end of helix Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 613 through 633 removed outlier: 4.091A pdb=" N SER A 616 " --> pdb=" O GLU A 613 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 617 " --> pdb=" O ASP A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 651 Processing helix chain 'A' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 89 Processing helix chain 'B' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 197 No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS B 217 " --> pdb=" O ASP B 214 " (cutoff:3.500A) Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU B 241 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 262 through 277 removed outlier: 4.639A pdb=" N ASP B 272 " --> pdb=" O GLN B 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 297 removed outlier: 3.616A pdb=" N GLN B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 319 Processing helix chain 'B' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 371 Processing helix chain 'B' and resid 380 through 391 Processing helix chain 'B' and resid 402 through 416 removed outlier: 3.644A pdb=" N LYS B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 416 " --> pdb=" O ARG B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 436 Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 484 No H-bonds generated for 'chain 'B' and resid 481 through 484' Processing helix chain 'B' and resid 497 through 506 removed outlier: 3.859A pdb=" N VAL B 501 " --> pdb=" O THR B 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 516 Processing helix chain 'B' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) Proline residue: B 591 - end of helix Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 613 through 633 removed outlier: 4.092A pdb=" N SER B 616 " --> pdb=" O GLU B 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS B 617 " --> pdb=" O ASP B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 651 Processing helix chain 'B' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL B 665 " --> pdb=" O LEU B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 89 Processing helix chain 'C' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL C 131 " --> pdb=" O LYS C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS C 217 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Proline residue: C 218 - end of helix Processing helix chain 'C' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU C 241 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 262 through 277 removed outlier: 4.639A pdb=" N ASP C 272 " --> pdb=" O GLN C 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 319 Processing helix chain 'C' and resid 325 through 346 removed outlier: 5.368A pdb=" N VAL C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 371 Processing helix chain 'C' and resid 380 through 391 Processing helix chain 'C' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS C 411 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 416 " --> pdb=" O ARG C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 Processing helix chain 'C' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 484 No H-bonds generated for 'chain 'C' and resid 481 through 484' Processing helix chain 'C' and resid 497 through 506 removed outlier: 3.858A pdb=" N VAL C 501 " --> pdb=" O THR C 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 516 Processing helix chain 'C' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) Proline residue: C 591 - end of helix Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'C' and resid 613 through 633 removed outlier: 4.090A pdb=" N SER C 616 " --> pdb=" O GLU C 613 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS C 617 " --> pdb=" O ASP C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 651 Processing helix chain 'C' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL C 665 " --> pdb=" O LEU C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 89 Processing helix chain 'D' and resid 99 through 109 removed outlier: 4.019A pdb=" N ALA D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER D 106 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU D 107 " --> pdb=" O GLN D 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 No H-bonds generated for 'chain 'D' and resid 194 through 197' Processing helix chain 'D' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS D 217 " --> pdb=" O ASP D 214 " (cutoff:3.500A) Proline residue: D 218 - end of helix Processing helix chain 'D' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU D 241 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 262 through 277 removed outlier: 4.639A pdb=" N ASP D 272 " --> pdb=" O GLN D 268 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 325 through 346 removed outlier: 5.366A pdb=" N VAL D 330 " --> pdb=" O ASP D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 371 Processing helix chain 'D' and resid 380 through 391 Processing helix chain 'D' and resid 402 through 416 removed outlier: 3.644A pdb=" N LYS D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS D 411 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 416 " --> pdb=" O ARG D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 436 Processing helix chain 'D' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU D 465 " --> pdb=" O LEU D 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA D 466 " --> pdb=" O ALA D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 484 No H-bonds generated for 'chain 'D' and resid 481 through 484' Processing helix chain 'D' and resid 497 through 506 removed outlier: 3.857A pdb=" N VAL D 501 " --> pdb=" O THR D 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 516 Processing helix chain 'D' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 592 removed outlier: 4.842A pdb=" N ARG D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) Proline residue: D 591 - end of helix Processing helix chain 'D' and resid 595 through 599 Processing helix chain 'D' and resid 613 through 633 removed outlier: 4.091A pdb=" N SER D 616 " --> pdb=" O GLU D 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS D 617 " --> pdb=" O ASP D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 651 Processing helix chain 'D' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL D 665 " --> pdb=" O LEU D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 89 Processing helix chain 'E' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER E 106 " --> pdb=" O ILE E 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL E 131 " --> pdb=" O LYS E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 147 No H-bonds generated for 'chain 'E' and resid 145 through 147' Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL E 178 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 197 No H-bonds generated for 'chain 'E' and resid 194 through 197' Processing helix chain 'E' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS E 217 " --> pdb=" O ASP E 214 " (cutoff:3.500A) Proline residue: E 218 - end of helix Processing helix chain 'E' and resid 233 through 242 removed outlier: 4.506A pdb=" N LEU E 241 " --> pdb=" O ARG E 237 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS E 242 " --> pdb=" O ASN E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 248 Processing helix chain 'E' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP E 272 " --> pdb=" O GLN E 268 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU E 273 " --> pdb=" O GLY E 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN E 276 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 297 removed outlier: 3.616A pdb=" N GLN E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 Processing helix chain 'E' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 371 Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 402 through 416 removed outlier: 3.644A pdb=" N LYS E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA E 410 " --> pdb=" O LEU E 406 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS E 411 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS E 416 " --> pdb=" O ARG E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 436 Processing helix chain 'E' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU E 465 " --> pdb=" O LEU E 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 481 through 484 No H-bonds generated for 'chain 'E' and resid 481 through 484' Processing helix chain 'E' and resid 497 through 506 removed outlier: 3.858A pdb=" N VAL E 501 " --> pdb=" O THR E 497 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY E 502 " --> pdb=" O ALA E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 516 Processing helix chain 'E' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL E 541 " --> pdb=" O LEU E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 592 removed outlier: 4.842A pdb=" N ARG E 588 " --> pdb=" O GLU E 584 " (cutoff:3.500A) Proline residue: E 591 - end of helix Processing helix chain 'E' and resid 595 through 599 Processing helix chain 'E' and resid 613 through 633 removed outlier: 4.090A pdb=" N SER E 616 " --> pdb=" O GLU E 613 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS E 617 " --> pdb=" O ASP E 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 651 Processing helix chain 'E' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL E 665 " --> pdb=" O LEU E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 678 removed outlier: 3.503A pdb=" N ASP E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 89 Processing helix chain 'F' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA F 105 " --> pdb=" O GLU F 101 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER F 106 " --> pdb=" O ILE F 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL F 131 " --> pdb=" O LYS F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 147 No H-bonds generated for 'chain 'F' and resid 145 through 147' Processing helix chain 'F' and resid 160 through 163 Processing helix chain 'F' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL F 178 " --> pdb=" O VAL F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 197 No H-bonds generated for 'chain 'F' and resid 194 through 197' Processing helix chain 'F' and resid 212 through 221 removed outlier: 5.256A pdb=" N LYS F 217 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Proline residue: F 218 - end of helix Processing helix chain 'F' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU F 241 " --> pdb=" O ARG F 237 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS F 242 " --> pdb=" O ASN F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 248 Processing helix chain 'F' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP F 272 " --> pdb=" O GLN F 268 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU F 273 " --> pdb=" O GLY F 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR F 274 " --> pdb=" O ILE F 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN F 275 " --> pdb=" O ARG F 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN F 276 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN F 296 " --> pdb=" O ASP F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL F 330 " --> pdb=" O ASP F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 371 Processing helix chain 'F' and resid 380 through 391 Processing helix chain 'F' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA F 410 " --> pdb=" O LEU F 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS F 411 " --> pdb=" O LYS F 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS F 416 " --> pdb=" O ARG F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 436 Processing helix chain 'F' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU F 465 " --> pdb=" O LEU F 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA F 466 " --> pdb=" O ALA F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 481 through 484 No H-bonds generated for 'chain 'F' and resid 481 through 484' Processing helix chain 'F' and resid 497 through 506 removed outlier: 3.858A pdb=" N VAL F 501 " --> pdb=" O THR F 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY F 502 " --> pdb=" O ALA F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 516 Processing helix chain 'F' and resid 536 through 544 removed outlier: 3.907A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) Proline residue: F 591 - end of helix Processing helix chain 'F' and resid 595 through 599 Processing helix chain 'F' and resid 613 through 633 removed outlier: 4.091A pdb=" N SER F 616 " --> pdb=" O GLU F 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS F 617 " --> pdb=" O ASP F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 651 Processing helix chain 'F' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL F 665 " --> pdb=" O LEU F 661 " (cutoff:3.500A) Processing helix chain 'F' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 89 Processing helix chain 'G' and resid 99 through 109 removed outlier: 4.019A pdb=" N ALA G 105 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER G 106 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU G 107 " --> pdb=" O GLN G 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE G 108 " --> pdb=" O GLU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 140 removed outlier: 4.366A pdb=" N VAL G 131 " --> pdb=" O LYS G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 147 No H-bonds generated for 'chain 'G' and resid 145 through 147' Processing helix chain 'G' and resid 160 through 163 Processing helix chain 'G' and resid 167 through 180 removed outlier: 3.627A pdb=" N VAL G 178 " --> pdb=" O VAL G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 197 No H-bonds generated for 'chain 'G' and resid 194 through 197' Processing helix chain 'G' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS G 217 " --> pdb=" O ASP G 214 " (cutoff:3.500A) Proline residue: G 218 - end of helix Processing helix chain 'G' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU G 241 " --> pdb=" O ARG G 237 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 248 Processing helix chain 'G' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP G 272 " --> pdb=" O GLN G 268 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU G 273 " --> pdb=" O GLY G 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR G 274 " --> pdb=" O ILE G 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN G 275 " --> pdb=" O ARG G 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN G 276 " --> pdb=" O ASP G 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS G 277 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN G 296 " --> pdb=" O ASP G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 319 Processing helix chain 'G' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL G 330 " --> pdb=" O ASP G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 371 Processing helix chain 'G' and resid 380 through 391 Processing helix chain 'G' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS G 407 " --> pdb=" O ILE G 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA G 410 " --> pdb=" O LEU G 406 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS G 411 " --> pdb=" O LYS G 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS G 416 " --> pdb=" O ARG G 412 " (cutoff:3.500A) Processing helix chain 'G' and resid 421 through 436 Processing helix chain 'G' and resid 460 through 470 removed outlier: 3.789A pdb=" N LEU G 465 " --> pdb=" O LEU G 461 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA G 466 " --> pdb=" O ALA G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 481 through 484 No H-bonds generated for 'chain 'G' and resid 481 through 484' Processing helix chain 'G' and resid 497 through 506 removed outlier: 3.859A pdb=" N VAL G 501 " --> pdb=" O THR G 497 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY G 502 " --> pdb=" O ALA G 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 516 Processing helix chain 'G' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL G 541 " --> pdb=" O LEU G 537 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 592 removed outlier: 4.842A pdb=" N ARG G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) Proline residue: G 591 - end of helix Processing helix chain 'G' and resid 595 through 599 Processing helix chain 'G' and resid 613 through 633 removed outlier: 4.091A pdb=" N SER G 616 " --> pdb=" O GLU G 613 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS G 617 " --> pdb=" O ASP G 614 " (cutoff:3.500A) Processing helix chain 'G' and resid 641 through 651 Processing helix chain 'G' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL G 665 " --> pdb=" O LEU G 661 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 678 removed outlier: 3.503A pdb=" N ASP G 675 " --> pdb=" O ASP G 671 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 89 Processing helix chain 'H' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA H 105 " --> pdb=" O GLU H 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER H 106 " --> pdb=" O ILE H 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU H 107 " --> pdb=" O GLN H 103 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE H 108 " --> pdb=" O GLU H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL H 131 " --> pdb=" O LYS H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing helix chain 'H' and resid 160 through 163 Processing helix chain 'H' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL H 178 " --> pdb=" O VAL H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 197 No H-bonds generated for 'chain 'H' and resid 194 through 197' Processing helix chain 'H' and resid 212 through 221 removed outlier: 5.256A pdb=" N LYS H 217 " --> pdb=" O ASP H 214 " (cutoff:3.500A) Proline residue: H 218 - end of helix Processing helix chain 'H' and resid 233 through 242 removed outlier: 4.506A pdb=" N LEU H 241 " --> pdb=" O ARG H 237 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS H 242 " --> pdb=" O ASN H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 248 Processing helix chain 'H' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP H 272 " --> pdb=" O GLN H 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU H 273 " --> pdb=" O GLY H 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR H 274 " --> pdb=" O ILE H 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN H 275 " --> pdb=" O ARG H 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN H 276 " --> pdb=" O ASP H 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS H 277 " --> pdb=" O LEU H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN H 296 " --> pdb=" O ASP H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 319 Processing helix chain 'H' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL H 330 " --> pdb=" O ASP H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 371 Processing helix chain 'H' and resid 380 through 391 Processing helix chain 'H' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS H 407 " --> pdb=" O ILE H 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA H 410 " --> pdb=" O LEU H 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS H 411 " --> pdb=" O LYS H 407 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS H 416 " --> pdb=" O ARG H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 421 through 436 Processing helix chain 'H' and resid 460 through 470 removed outlier: 3.789A pdb=" N LEU H 465 " --> pdb=" O LEU H 461 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA H 466 " --> pdb=" O ALA H 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 481 through 484 No H-bonds generated for 'chain 'H' and resid 481 through 484' Processing helix chain 'H' and resid 497 through 506 removed outlier: 3.858A pdb=" N VAL H 501 " --> pdb=" O THR H 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY H 502 " --> pdb=" O ALA H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 511 through 516 Processing helix chain 'H' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN H 540 " --> pdb=" O THR H 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL H 541 " --> pdb=" O LEU H 537 " (cutoff:3.500A) Processing helix chain 'H' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG H 588 " --> pdb=" O GLU H 584 " (cutoff:3.500A) Proline residue: H 591 - end of helix Processing helix chain 'H' and resid 595 through 599 Processing helix chain 'H' and resid 613 through 633 removed outlier: 4.090A pdb=" N SER H 616 " --> pdb=" O GLU H 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS H 617 " --> pdb=" O ASP H 614 " (cutoff:3.500A) Processing helix chain 'H' and resid 641 through 651 Processing helix chain 'H' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL H 665 " --> pdb=" O LEU H 661 " (cutoff:3.500A) Processing helix chain 'H' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP H 675 " --> pdb=" O ASP H 671 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 89 Processing helix chain 'I' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER I 106 " --> pdb=" O ILE I 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU I 107 " --> pdb=" O GLN I 103 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL I 131 " --> pdb=" O LYS I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 147 No H-bonds generated for 'chain 'I' and resid 145 through 147' Processing helix chain 'I' and resid 160 through 163 Processing helix chain 'I' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL I 178 " --> pdb=" O VAL I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 197 No H-bonds generated for 'chain 'I' and resid 194 through 197' Processing helix chain 'I' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS I 217 " --> pdb=" O ASP I 214 " (cutoff:3.500A) Proline residue: I 218 - end of helix Processing helix chain 'I' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU I 241 " --> pdb=" O ARG I 237 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS I 242 " --> pdb=" O ASN I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 244 through 248 Processing helix chain 'I' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP I 272 " --> pdb=" O GLN I 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU I 273 " --> pdb=" O GLY I 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR I 274 " --> pdb=" O ILE I 270 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN I 275 " --> pdb=" O ARG I 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN I 276 " --> pdb=" O ASP I 272 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS I 277 " --> pdb=" O LEU I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN I 296 " --> pdb=" O ASP I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 319 Processing helix chain 'I' and resid 325 through 346 removed outlier: 5.368A pdb=" N VAL I 330 " --> pdb=" O ASP I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 371 Processing helix chain 'I' and resid 380 through 391 Processing helix chain 'I' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS I 407 " --> pdb=" O ILE I 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA I 410 " --> pdb=" O LEU I 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS I 411 " --> pdb=" O LYS I 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS I 416 " --> pdb=" O ARG I 412 " (cutoff:3.500A) Processing helix chain 'I' and resid 421 through 436 Processing helix chain 'I' and resid 460 through 470 removed outlier: 3.789A pdb=" N LEU I 465 " --> pdb=" O LEU I 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA I 466 " --> pdb=" O ALA I 462 " (cutoff:3.500A) Processing helix chain 'I' and resid 481 through 484 No H-bonds generated for 'chain 'I' and resid 481 through 484' Processing helix chain 'I' and resid 497 through 506 removed outlier: 3.859A pdb=" N VAL I 501 " --> pdb=" O THR I 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY I 502 " --> pdb=" O ALA I 498 " (cutoff:3.500A) Processing helix chain 'I' and resid 511 through 516 Processing helix chain 'I' and resid 536 through 544 removed outlier: 3.905A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL I 541 " --> pdb=" O LEU I 537 " (cutoff:3.500A) Processing helix chain 'I' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG I 588 " --> pdb=" O GLU I 584 " (cutoff:3.500A) Proline residue: I 591 - end of helix Processing helix chain 'I' and resid 595 through 599 Processing helix chain 'I' and resid 613 through 633 removed outlier: 4.092A pdb=" N SER I 616 " --> pdb=" O GLU I 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS I 617 " --> pdb=" O ASP I 614 " (cutoff:3.500A) Processing helix chain 'I' and resid 641 through 651 Processing helix chain 'I' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL I 665 " --> pdb=" O LEU I 661 " (cutoff:3.500A) Processing helix chain 'I' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP I 675 " --> pdb=" O ASP I 671 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 89 Processing helix chain 'J' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA J 105 " --> pdb=" O GLU J 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER J 106 " --> pdb=" O ILE J 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU J 107 " --> pdb=" O GLN J 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL J 131 " --> pdb=" O LYS J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 147 No H-bonds generated for 'chain 'J' and resid 145 through 147' Processing helix chain 'J' and resid 160 through 163 Processing helix chain 'J' and resid 167 through 180 removed outlier: 3.627A pdb=" N VAL J 178 " --> pdb=" O VAL J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 197 No H-bonds generated for 'chain 'J' and resid 194 through 197' Processing helix chain 'J' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS J 217 " --> pdb=" O ASP J 214 " (cutoff:3.500A) Proline residue: J 218 - end of helix Processing helix chain 'J' and resid 233 through 242 removed outlier: 4.506A pdb=" N LEU J 241 " --> pdb=" O ARG J 237 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS J 242 " --> pdb=" O ASN J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 244 through 248 Processing helix chain 'J' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP J 272 " --> pdb=" O GLN J 268 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU J 273 " --> pdb=" O GLY J 269 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR J 274 " --> pdb=" O ILE J 270 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN J 275 " --> pdb=" O ARG J 271 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLN J 276 " --> pdb=" O ASP J 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS J 277 " --> pdb=" O LEU J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 297 removed outlier: 3.616A pdb=" N GLN J 296 " --> pdb=" O ASP J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 319 Processing helix chain 'J' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL J 330 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 371 Processing helix chain 'J' and resid 380 through 391 Processing helix chain 'J' and resid 402 through 416 removed outlier: 3.644A pdb=" N LYS J 407 " --> pdb=" O ILE J 403 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA J 410 " --> pdb=" O LEU J 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS J 411 " --> pdb=" O LYS J 407 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS J 416 " --> pdb=" O ARG J 412 " (cutoff:3.500A) Processing helix chain 'J' and resid 421 through 436 Processing helix chain 'J' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU J 465 " --> pdb=" O LEU J 461 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA J 466 " --> pdb=" O ALA J 462 " (cutoff:3.500A) Processing helix chain 'J' and resid 481 through 484 No H-bonds generated for 'chain 'J' and resid 481 through 484' Processing helix chain 'J' and resid 497 through 506 removed outlier: 3.858A pdb=" N VAL J 501 " --> pdb=" O THR J 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY J 502 " --> pdb=" O ALA J 498 " (cutoff:3.500A) Processing helix chain 'J' and resid 511 through 516 Processing helix chain 'J' and resid 536 through 544 removed outlier: 3.907A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL J 541 " --> pdb=" O LEU J 537 " (cutoff:3.500A) Processing helix chain 'J' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG J 588 " --> pdb=" O GLU J 584 " (cutoff:3.500A) Proline residue: J 591 - end of helix Processing helix chain 'J' and resid 595 through 599 Processing helix chain 'J' and resid 613 through 633 removed outlier: 4.091A pdb=" N SER J 616 " --> pdb=" O GLU J 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS J 617 " --> pdb=" O ASP J 614 " (cutoff:3.500A) Processing helix chain 'J' and resid 641 through 651 Processing helix chain 'J' and resid 659 through 666 removed outlier: 4.349A pdb=" N VAL J 665 " --> pdb=" O LEU J 661 " (cutoff:3.500A) Processing helix chain 'J' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP J 675 " --> pdb=" O ASP J 671 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 89 Processing helix chain 'K' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER K 106 " --> pdb=" O ILE K 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU K 107 " --> pdb=" O GLN K 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE K 108 " --> pdb=" O GLU K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL K 131 " --> pdb=" O LYS K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 147 No H-bonds generated for 'chain 'K' and resid 145 through 147' Processing helix chain 'K' and resid 160 through 163 Processing helix chain 'K' and resid 167 through 180 removed outlier: 3.627A pdb=" N VAL K 178 " --> pdb=" O VAL K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 197 No H-bonds generated for 'chain 'K' and resid 194 through 197' Processing helix chain 'K' and resid 212 through 221 removed outlier: 5.256A pdb=" N LYS K 217 " --> pdb=" O ASP K 214 " (cutoff:3.500A) Proline residue: K 218 - end of helix Processing helix chain 'K' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU K 241 " --> pdb=" O ARG K 237 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS K 242 " --> pdb=" O ASN K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 248 Processing helix chain 'K' and resid 262 through 277 removed outlier: 4.639A pdb=" N ASP K 272 " --> pdb=" O GLN K 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU K 273 " --> pdb=" O GLY K 269 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR K 274 " --> pdb=" O ILE K 270 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN K 275 " --> pdb=" O ARG K 271 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLN K 276 " --> pdb=" O ASP K 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS K 277 " --> pdb=" O LEU K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN K 296 " --> pdb=" O ASP K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 303 through 319 Processing helix chain 'K' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL K 330 " --> pdb=" O ASP K 326 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 371 Processing helix chain 'K' and resid 380 through 391 Processing helix chain 'K' and resid 402 through 416 removed outlier: 3.644A pdb=" N LYS K 407 " --> pdb=" O ILE K 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA K 410 " --> pdb=" O LEU K 406 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS K 411 " --> pdb=" O LYS K 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS K 416 " --> pdb=" O ARG K 412 " (cutoff:3.500A) Processing helix chain 'K' and resid 421 through 436 Processing helix chain 'K' and resid 460 through 470 removed outlier: 3.789A pdb=" N LEU K 465 " --> pdb=" O LEU K 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA K 466 " --> pdb=" O ALA K 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 481 through 484 No H-bonds generated for 'chain 'K' and resid 481 through 484' Processing helix chain 'K' and resid 497 through 506 removed outlier: 3.857A pdb=" N VAL K 501 " --> pdb=" O THR K 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY K 502 " --> pdb=" O ALA K 498 " (cutoff:3.500A) Processing helix chain 'K' and resid 511 through 516 Processing helix chain 'K' and resid 536 through 544 removed outlier: 3.905A pdb=" N GLN K 540 " --> pdb=" O THR K 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL K 541 " --> pdb=" O LEU K 537 " (cutoff:3.500A) Processing helix chain 'K' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG K 588 " --> pdb=" O GLU K 584 " (cutoff:3.500A) Proline residue: K 591 - end of helix Processing helix chain 'K' and resid 595 through 599 Processing helix chain 'K' and resid 613 through 633 removed outlier: 4.091A pdb=" N SER K 616 " --> pdb=" O GLU K 613 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS K 617 " --> pdb=" O ASP K 614 " (cutoff:3.500A) Processing helix chain 'K' and resid 641 through 651 Processing helix chain 'K' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL K 665 " --> pdb=" O LEU K 661 " (cutoff:3.500A) Processing helix chain 'K' and resid 668 through 678 removed outlier: 3.503A pdb=" N ASP K 675 " --> pdb=" O ASP K 671 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 89 Processing helix chain 'L' and resid 99 through 109 removed outlier: 4.017A pdb=" N ALA L 105 " --> pdb=" O GLU L 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER L 106 " --> pdb=" O ILE L 102 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU L 107 " --> pdb=" O GLN L 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 140 removed outlier: 4.364A pdb=" N VAL L 131 " --> pdb=" O LYS L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 147 No H-bonds generated for 'chain 'L' and resid 145 through 147' Processing helix chain 'L' and resid 160 through 163 Processing helix chain 'L' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL L 178 " --> pdb=" O VAL L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 194 through 197 No H-bonds generated for 'chain 'L' and resid 194 through 197' Processing helix chain 'L' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS L 217 " --> pdb=" O ASP L 214 " (cutoff:3.500A) Proline residue: L 218 - end of helix Processing helix chain 'L' and resid 233 through 242 removed outlier: 4.506A pdb=" N LEU L 241 " --> pdb=" O ARG L 237 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS L 242 " --> pdb=" O ASN L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 248 Processing helix chain 'L' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP L 272 " --> pdb=" O GLN L 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU L 273 " --> pdb=" O GLY L 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR L 274 " --> pdb=" O ILE L 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN L 275 " --> pdb=" O ARG L 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN L 276 " --> pdb=" O ASP L 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS L 277 " --> pdb=" O LEU L 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN L 296 " --> pdb=" O ASP L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 303 through 319 Processing helix chain 'L' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL L 330 " --> pdb=" O ASP L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 371 Processing helix chain 'L' and resid 380 through 391 Processing helix chain 'L' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS L 407 " --> pdb=" O ILE L 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA L 410 " --> pdb=" O LEU L 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS L 411 " --> pdb=" O LYS L 407 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS L 416 " --> pdb=" O ARG L 412 " (cutoff:3.500A) Processing helix chain 'L' and resid 421 through 436 Processing helix chain 'L' and resid 460 through 470 removed outlier: 3.789A pdb=" N LEU L 465 " --> pdb=" O LEU L 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA L 466 " --> pdb=" O ALA L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 481 through 484 No H-bonds generated for 'chain 'L' and resid 481 through 484' Processing helix chain 'L' and resid 497 through 506 removed outlier: 3.858A pdb=" N VAL L 501 " --> pdb=" O THR L 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY L 502 " --> pdb=" O ALA L 498 " (cutoff:3.500A) Processing helix chain 'L' and resid 511 through 516 Processing helix chain 'L' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN L 540 " --> pdb=" O THR L 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL L 541 " --> pdb=" O LEU L 537 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG L 588 " --> pdb=" O GLU L 584 " (cutoff:3.500A) Proline residue: L 591 - end of helix Processing helix chain 'L' and resid 595 through 599 Processing helix chain 'L' and resid 613 through 633 removed outlier: 4.091A pdb=" N SER L 616 " --> pdb=" O GLU L 613 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS L 617 " --> pdb=" O ASP L 614 " (cutoff:3.500A) Processing helix chain 'L' and resid 641 through 651 Processing helix chain 'L' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL L 665 " --> pdb=" O LEU L 661 " (cutoff:3.500A) Processing helix chain 'L' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP L 675 " --> pdb=" O ASP L 671 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 89 Processing helix chain 'M' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA M 105 " --> pdb=" O GLU M 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER M 106 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU M 107 " --> pdb=" O GLN M 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE M 108 " --> pdb=" O GLU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL M 131 " --> pdb=" O LYS M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 147 No H-bonds generated for 'chain 'M' and resid 145 through 147' Processing helix chain 'M' and resid 160 through 163 Processing helix chain 'M' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL M 178 " --> pdb=" O VAL M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 197 No H-bonds generated for 'chain 'M' and resid 194 through 197' Processing helix chain 'M' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS M 217 " --> pdb=" O ASP M 214 " (cutoff:3.500A) Proline residue: M 218 - end of helix Processing helix chain 'M' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU M 241 " --> pdb=" O ARG M 237 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS M 242 " --> pdb=" O ASN M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 244 through 248 Processing helix chain 'M' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP M 272 " --> pdb=" O GLN M 268 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU M 273 " --> pdb=" O GLY M 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR M 274 " --> pdb=" O ILE M 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN M 275 " --> pdb=" O ARG M 271 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLN M 276 " --> pdb=" O ASP M 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS M 277 " --> pdb=" O LEU M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN M 296 " --> pdb=" O ASP M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 303 through 319 Processing helix chain 'M' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL M 330 " --> pdb=" O ASP M 326 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 371 Processing helix chain 'M' and resid 380 through 391 Processing helix chain 'M' and resid 402 through 416 removed outlier: 3.644A pdb=" N LYS M 407 " --> pdb=" O ILE M 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA M 410 " --> pdb=" O LEU M 406 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS M 411 " --> pdb=" O LYS M 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS M 416 " --> pdb=" O ARG M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 421 through 436 Processing helix chain 'M' and resid 460 through 470 removed outlier: 3.789A pdb=" N LEU M 465 " --> pdb=" O LEU M 461 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA M 466 " --> pdb=" O ALA M 462 " (cutoff:3.500A) Processing helix chain 'M' and resid 481 through 484 No H-bonds generated for 'chain 'M' and resid 481 through 484' Processing helix chain 'M' and resid 497 through 506 removed outlier: 3.857A pdb=" N VAL M 501 " --> pdb=" O THR M 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY M 502 " --> pdb=" O ALA M 498 " (cutoff:3.500A) Processing helix chain 'M' and resid 511 through 516 Processing helix chain 'M' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN M 540 " --> pdb=" O THR M 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL M 541 " --> pdb=" O LEU M 537 " (cutoff:3.500A) Processing helix chain 'M' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG M 588 " --> pdb=" O GLU M 584 " (cutoff:3.500A) Proline residue: M 591 - end of helix Processing helix chain 'M' and resid 595 through 599 Processing helix chain 'M' and resid 613 through 633 removed outlier: 4.090A pdb=" N SER M 616 " --> pdb=" O GLU M 613 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS M 617 " --> pdb=" O ASP M 614 " (cutoff:3.500A) Processing helix chain 'M' and resid 641 through 651 Processing helix chain 'M' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL M 665 " --> pdb=" O LEU M 661 " (cutoff:3.500A) Processing helix chain 'M' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP M 675 " --> pdb=" O ASP M 671 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 89 Processing helix chain 'N' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA N 105 " --> pdb=" O GLU N 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER N 106 " --> pdb=" O ILE N 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU N 107 " --> pdb=" O GLN N 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE N 108 " --> pdb=" O GLU N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL N 131 " --> pdb=" O LYS N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 147 No H-bonds generated for 'chain 'N' and resid 145 through 147' Processing helix chain 'N' and resid 160 through 163 Processing helix chain 'N' and resid 167 through 180 removed outlier: 3.627A pdb=" N VAL N 178 " --> pdb=" O VAL N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 197 No H-bonds generated for 'chain 'N' and resid 194 through 197' Processing helix chain 'N' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS N 217 " --> pdb=" O ASP N 214 " (cutoff:3.500A) Proline residue: N 218 - end of helix Processing helix chain 'N' and resid 233 through 242 removed outlier: 4.506A pdb=" N LEU N 241 " --> pdb=" O ARG N 237 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS N 242 " --> pdb=" O ASN N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 244 through 248 Processing helix chain 'N' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP N 272 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU N 273 " --> pdb=" O GLY N 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR N 274 " --> pdb=" O ILE N 270 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN N 275 " --> pdb=" O ARG N 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN N 276 " --> pdb=" O ASP N 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS N 277 " --> pdb=" O LEU N 273 " (cutoff:3.500A) Processing helix chain 'N' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN N 296 " --> pdb=" O ASP N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 303 through 319 Processing helix chain 'N' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL N 330 " --> pdb=" O ASP N 326 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 371 Processing helix chain 'N' and resid 380 through 391 Processing helix chain 'N' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS N 407 " --> pdb=" O ILE N 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA N 410 " --> pdb=" O LEU N 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS N 411 " --> pdb=" O LYS N 407 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS N 416 " --> pdb=" O ARG N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 421 through 436 Processing helix chain 'N' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU N 465 " --> pdb=" O LEU N 461 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA N 466 " --> pdb=" O ALA N 462 " (cutoff:3.500A) Processing helix chain 'N' and resid 481 through 484 No H-bonds generated for 'chain 'N' and resid 481 through 484' Processing helix chain 'N' and resid 497 through 506 removed outlier: 3.859A pdb=" N VAL N 501 " --> pdb=" O THR N 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY N 502 " --> pdb=" O ALA N 498 " (cutoff:3.500A) Processing helix chain 'N' and resid 511 through 516 Processing helix chain 'N' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN N 540 " --> pdb=" O THR N 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL N 541 " --> pdb=" O LEU N 537 " (cutoff:3.500A) Processing helix chain 'N' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG N 588 " --> pdb=" O GLU N 584 " (cutoff:3.500A) Proline residue: N 591 - end of helix Processing helix chain 'N' and resid 595 through 599 Processing helix chain 'N' and resid 613 through 633 removed outlier: 4.090A pdb=" N SER N 616 " --> pdb=" O GLU N 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS N 617 " --> pdb=" O ASP N 614 " (cutoff:3.500A) Processing helix chain 'N' and resid 641 through 651 Processing helix chain 'N' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL N 665 " --> pdb=" O LEU N 661 " (cutoff:3.500A) Processing helix chain 'N' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP N 675 " --> pdb=" O ASP N 671 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 80 through 82 Processing sheet with id= B, first strand: chain 'A' and resid 116 through 120 Processing sheet with id= C, first strand: chain 'A' and resid 603 through 607 removed outlier: 3.987A pdb=" N ALA A 603 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 546 through 548 Processing sheet with id= E, first strand: chain 'A' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU A 686 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 80 through 82 Processing sheet with id= G, first strand: chain 'B' and resid 116 through 120 Processing sheet with id= H, first strand: chain 'B' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA B 603 " --> pdb=" O ASN B 447 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 546 through 548 Processing sheet with id= J, first strand: chain 'B' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU B 686 " --> pdb=" O VAL B 638 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 80 through 82 Processing sheet with id= L, first strand: chain 'C' and resid 116 through 120 Processing sheet with id= M, first strand: chain 'C' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA C 603 " --> pdb=" O ASN C 447 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 546 through 548 Processing sheet with id= O, first strand: chain 'C' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU C 686 " --> pdb=" O VAL C 638 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 80 through 82 Processing sheet with id= Q, first strand: chain 'D' and resid 116 through 120 Processing sheet with id= R, first strand: chain 'D' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA D 603 " --> pdb=" O ASN D 447 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 546 through 548 Processing sheet with id= T, first strand: chain 'D' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU D 686 " --> pdb=" O VAL D 638 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 80 through 82 Processing sheet with id= V, first strand: chain 'E' and resid 116 through 120 Processing sheet with id= W, first strand: chain 'E' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA E 603 " --> pdb=" O ASN E 447 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 546 through 548 Processing sheet with id= Y, first strand: chain 'E' and resid 637 through 639 removed outlier: 6.726A pdb=" N LEU E 686 " --> pdb=" O VAL E 638 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 80 through 82 Processing sheet with id= AA, first strand: chain 'F' and resid 116 through 120 Processing sheet with id= AB, first strand: chain 'F' and resid 603 through 607 removed outlier: 3.987A pdb=" N ALA F 603 " --> pdb=" O ASN F 447 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 546 through 548 Processing sheet with id= AD, first strand: chain 'F' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU F 686 " --> pdb=" O VAL F 638 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 80 through 82 Processing sheet with id= AF, first strand: chain 'G' and resid 116 through 120 Processing sheet with id= AG, first strand: chain 'G' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA G 603 " --> pdb=" O ASN G 447 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 546 through 548 Processing sheet with id= AI, first strand: chain 'G' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU G 686 " --> pdb=" O VAL G 638 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 80 through 82 Processing sheet with id= AK, first strand: chain 'H' and resid 116 through 120 Processing sheet with id= AL, first strand: chain 'H' and resid 603 through 607 removed outlier: 3.987A pdb=" N ALA H 603 " --> pdb=" O ASN H 447 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 546 through 548 Processing sheet with id= AN, first strand: chain 'H' and resid 637 through 639 removed outlier: 6.726A pdb=" N LEU H 686 " --> pdb=" O VAL H 638 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 80 through 82 Processing sheet with id= AP, first strand: chain 'I' and resid 116 through 120 Processing sheet with id= AQ, first strand: chain 'I' and resid 603 through 607 removed outlier: 3.985A pdb=" N ALA I 603 " --> pdb=" O ASN I 447 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'I' and resid 546 through 548 Processing sheet with id= AS, first strand: chain 'I' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU I 686 " --> pdb=" O VAL I 638 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'J' and resid 80 through 82 Processing sheet with id= AU, first strand: chain 'J' and resid 116 through 120 Processing sheet with id= AV, first strand: chain 'J' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA J 603 " --> pdb=" O ASN J 447 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'J' and resid 546 through 548 Processing sheet with id= AX, first strand: chain 'J' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU J 686 " --> pdb=" O VAL J 638 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'K' and resid 80 through 82 Processing sheet with id= AZ, first strand: chain 'K' and resid 116 through 120 Processing sheet with id= BA, first strand: chain 'K' and resid 603 through 607 removed outlier: 3.987A pdb=" N ALA K 603 " --> pdb=" O ASN K 447 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'K' and resid 546 through 548 Processing sheet with id= BC, first strand: chain 'K' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU K 686 " --> pdb=" O VAL K 638 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'L' and resid 80 through 82 Processing sheet with id= BE, first strand: chain 'L' and resid 116 through 120 Processing sheet with id= BF, first strand: chain 'L' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA L 603 " --> pdb=" O ASN L 447 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'L' and resid 546 through 548 Processing sheet with id= BH, first strand: chain 'L' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU L 686 " --> pdb=" O VAL L 638 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'M' and resid 80 through 82 Processing sheet with id= BJ, first strand: chain 'M' and resid 116 through 120 Processing sheet with id= BK, first strand: chain 'M' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA M 603 " --> pdb=" O ASN M 447 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'M' and resid 546 through 548 Processing sheet with id= BM, first strand: chain 'M' and resid 637 through 639 removed outlier: 6.726A pdb=" N LEU M 686 " --> pdb=" O VAL M 638 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'N' and resid 80 through 82 Processing sheet with id= BO, first strand: chain 'N' and resid 116 through 120 Processing sheet with id= BP, first strand: chain 'N' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA N 603 " --> pdb=" O ASN N 447 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'N' and resid 546 through 548 Processing sheet with id= BR, first strand: chain 'N' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU N 686 " --> pdb=" O VAL N 638 " (cutoff:3.500A) 2898 hydrogen bonds defined for protein. 7812 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: 25.57 Time building geometry restraints manager: 24.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 24125 1.37 - 1.51: 20691 1.51 - 1.66: 24148 1.66 - 1.80: 256 1.80 - 1.95: 66 Bond restraints: 69286 Sorted by residual: bond pdb=" C ASP E 679 " pdb=" N HIS E 680 " ideal model delta sigma weight residual 1.329 1.347 -0.018 1.40e-02 5.10e+03 1.71e+00 bond pdb=" CG ARG I 222 " pdb=" CD ARG I 222 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CG ARG D 222 " pdb=" CD ARG D 222 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CG ARG B 222 " pdb=" CD ARG B 222 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CG ARG L 222 " pdb=" CD ARG L 222 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.65e+00 ... (remaining 69281 not shown) Histogram of bond angle deviations from ideal: 96.57 - 103.76: 700 103.76 - 110.94: 25261 110.94 - 118.13: 28273 118.13 - 125.31: 38992 125.31 - 132.50: 672 Bond angle restraints: 93898 Sorted by residual: angle pdb=" N LYS B 529 " pdb=" CA LYS B 529 " pdb=" C LYS B 529 " ideal model delta sigma weight residual 114.75 103.57 11.18 1.26e+00 6.30e-01 7.88e+01 angle pdb=" N LYS N 529 " pdb=" CA LYS N 529 " pdb=" C LYS N 529 " ideal model delta sigma weight residual 114.75 103.57 11.18 1.26e+00 6.30e-01 7.87e+01 angle pdb=" N LYS E 529 " pdb=" CA LYS E 529 " pdb=" C LYS E 529 " ideal model delta sigma weight residual 114.75 103.58 11.17 1.26e+00 6.30e-01 7.87e+01 angle pdb=" N LYS M 529 " pdb=" CA LYS M 529 " pdb=" C LYS M 529 " ideal model delta sigma weight residual 114.75 103.58 11.17 1.26e+00 6.30e-01 7.86e+01 angle pdb=" N LYS D 529 " pdb=" CA LYS D 529 " pdb=" C LYS D 529 " ideal model delta sigma weight residual 114.75 103.58 11.17 1.26e+00 6.30e-01 7.85e+01 ... (remaining 93893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.87: 41393 32.87 - 65.74: 1125 65.74 - 98.61: 98 98.61 - 131.48: 14 131.48 - 164.35: 28 Dihedral angle restraints: 42658 sinusoidal: 17500 harmonic: 25158 Sorted by residual: dihedral pdb=" CA GLU D 528 " pdb=" C GLU D 528 " pdb=" N LYS D 529 " pdb=" CA LYS D 529 " ideal model delta harmonic sigma weight residual -180.00 -46.70 -133.30 0 5.00e+00 4.00e-02 7.11e+02 dihedral pdb=" CA GLU G 528 " pdb=" C GLU G 528 " pdb=" N LYS G 529 " pdb=" CA LYS G 529 " ideal model delta harmonic sigma weight residual -180.00 -46.71 -133.29 0 5.00e+00 4.00e-02 7.11e+02 dihedral pdb=" CA GLU E 528 " pdb=" C GLU E 528 " pdb=" N LYS E 529 " pdb=" CA LYS E 529 " ideal model delta harmonic sigma weight residual -180.00 -46.71 -133.29 0 5.00e+00 4.00e-02 7.11e+02 ... (remaining 42655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 6303 0.034 - 0.068: 2956 0.068 - 0.103: 1226 0.103 - 0.137: 398 0.137 - 0.171: 79 Chirality restraints: 10962 Sorted by residual: chirality pdb=" CG LEU J 225 " pdb=" CB LEU J 225 " pdb=" CD1 LEU J 225 " pdb=" CD2 LEU J 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CG LEU N 225 " pdb=" CB LEU N 225 " pdb=" CD1 LEU N 225 " pdb=" CD2 LEU N 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CG LEU A 225 " pdb=" CB LEU A 225 " pdb=" CD1 LEU A 225 " pdb=" CD2 LEU A 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 10959 not shown) Planarity restraints: 12306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 100 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C LYS D 100 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS D 100 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU D 101 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 100 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C LYS F 100 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS F 100 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU F 101 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 100 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C LYS A 100 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS A 100 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU A 101 " 0.012 2.00e-02 2.50e+03 ... (remaining 12303 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 708 2.47 - 3.08: 53887 3.08 - 3.69: 107629 3.69 - 4.29: 154992 4.29 - 4.90: 235434 Nonbonded interactions: 552650 Sorted by model distance: nonbonded pdb="MG MG I 801 " pdb=" O3A AGS I 802 " model vdw 1.863 2.170 nonbonded pdb="MG MG H 801 " pdb=" O3A AGS H 802 " model vdw 1.863 2.170 nonbonded pdb="MG MG C 801 " pdb=" O3A AGS C 802 " model vdw 1.863 2.170 nonbonded pdb="MG MG K 801 " pdb=" O3A AGS K 802 " model vdw 1.863 2.170 nonbonded pdb="MG MG F 801 " pdb=" O3A AGS F 802 " model vdw 1.864 2.170 ... (remaining 552645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.070 Extract box with map and model: 4.890 Check model and map are aligned: 0.790 Set scattering table: 0.530 Process input model: 141.480 Find NCS groups from input model: 3.800 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 69286 Z= 0.371 Angle : 0.925 11.184 93898 Z= 0.550 Chirality : 0.048 0.171 10962 Planarity : 0.004 0.036 12306 Dihedral : 15.706 164.351 26390 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 25.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.54 % Allowed : 1.73 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -0.98 (0.09), residues: 8694 helix: -0.23 (0.08), residues: 3990 sheet: -1.02 (0.16), residues: 1050 loop : -0.85 (0.10), residues: 3654 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 195 PHE 0.023 0.002 PHE H 607 TYR 0.018 0.002 TYR L 500 ARG 0.019 0.001 ARG I 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 178 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8339 (mp0) cc_final: 0.8090 (mp0) REVERT: A 192 ASP cc_start: 0.8282 (p0) cc_final: 0.7572 (p0) REVERT: A 318 LEU cc_start: 0.8779 (mt) cc_final: 0.8436 (tt) REVERT: A 335 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8391 (tm-30) REVERT: A 447 ASN cc_start: 0.8077 (m-40) cc_final: 0.7617 (p0) REVERT: A 535 ILE cc_start: 0.7374 (mp) cc_final: 0.7085 (mm) REVERT: A 555 VAL cc_start: 0.8725 (t) cc_final: 0.8516 (m) REVERT: A 588 ARG cc_start: 0.8616 (mmt180) cc_final: 0.8310 (ttt-90) REVERT: A 592 PHE cc_start: 0.7592 (m-10) cc_final: 0.6745 (m-80) REVERT: A 626 VAL cc_start: 0.9108 (t) cc_final: 0.8777 (t) outliers start: 8 outliers final: 1 residues processed: 181 average time/residue: 0.1864 time to fit residues: 40.0791 Evaluate side-chains 78 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 732 optimal weight: 0.9990 chunk 657 optimal weight: 0.1980 chunk 365 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 443 optimal weight: 2.9990 chunk 351 optimal weight: 4.9990 chunk 680 optimal weight: 0.0370 chunk 263 optimal weight: 0.0060 chunk 413 optimal weight: 0.0980 chunk 506 optimal weight: 9.9990 chunk 788 optimal weight: 0.0980 overall best weight: 0.0874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 179 ASN A 195 HIS A 196 GLN ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 69286 Z= 0.229 Angle : 0.710 9.797 93898 Z= 0.385 Chirality : 0.046 0.279 10962 Planarity : 0.006 0.092 12306 Dihedral : 12.978 170.112 9954 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.19 % Allowed : 3.46 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.88 (0.09), residues: 8694 helix: -0.11 (0.08), residues: 4298 sheet: -0.45 (0.17), residues: 1050 loop : -1.11 (0.11), residues: 3346 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 328 PHE 0.011 0.002 PHE K 607 TYR 0.020 0.002 TYR E 500 ARG 0.006 0.001 ARG K 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.8301 (p0) cc_final: 0.7408 (p0) REVERT: A 240 ILE cc_start: 0.8530 (mm) cc_final: 0.8311 (mt) REVERT: A 318 LEU cc_start: 0.8565 (mt) cc_final: 0.8222 (tt) REVERT: A 433 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.7285 (mtt180) REVERT: A 447 ASN cc_start: 0.7926 (m-40) cc_final: 0.7656 (p0) REVERT: A 481 MET cc_start: 0.6473 (ppp) cc_final: 0.6213 (ppp) REVERT: A 529 LYS cc_start: 0.6837 (tptt) cc_final: 0.6401 (mmtt) REVERT: A 588 ARG cc_start: 0.8550 (mmt180) cc_final: 0.8316 (ptm-80) REVERT: A 622 MET cc_start: 0.8399 (mpp) cc_final: 0.8114 (mpp) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1554 time to fit residues: 21.4326 Evaluate side-chains 84 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 438 optimal weight: 9.9990 chunk 244 optimal weight: 0.9990 chunk 656 optimal weight: 0.3980 chunk 536 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 789 optimal weight: 0.0040 chunk 853 optimal weight: 8.9990 chunk 703 optimal weight: 6.9990 chunk 783 optimal weight: 7.9990 chunk 269 optimal weight: 7.9990 chunk 633 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 196 GLN A 370 HIS A 533 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 69286 Z= 0.179 Angle : 0.637 10.166 93898 Z= 0.339 Chirality : 0.044 0.256 10962 Planarity : 0.004 0.036 12306 Dihedral : 12.670 174.116 9954 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.19 % Allowed : 3.65 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.77 (0.09), residues: 8694 helix: -0.10 (0.08), residues: 4256 sheet: -0.51 (0.16), residues: 1050 loop : -0.86 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS L 370 PHE 0.014 0.002 PHE L 592 TYR 0.012 0.001 TYR H 500 ARG 0.007 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8059 (tm-30) REVERT: A 183 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7202 (mp0) REVERT: A 192 ASP cc_start: 0.8266 (p0) cc_final: 0.7464 (p0) REVERT: A 314 THR cc_start: 0.9167 (m) cc_final: 0.8918 (p) REVERT: A 318 LEU cc_start: 0.8532 (mt) cc_final: 0.8325 (tt) REVERT: A 447 ASN cc_start: 0.7779 (m-40) cc_final: 0.7557 (p0) REVERT: A 481 MET cc_start: 0.6604 (ppp) cc_final: 0.6341 (ppp) REVERT: A 529 LYS cc_start: 0.7400 (tptt) cc_final: 0.7120 (mmtt) REVERT: A 588 ARG cc_start: 0.8573 (mmt180) cc_final: 0.8005 (ptm-80) REVERT: A 620 ASP cc_start: 0.9041 (m-30) cc_final: 0.8709 (p0) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.1673 time to fit residues: 22.1593 Evaluate side-chains 74 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 780 optimal weight: 10.0000 chunk 593 optimal weight: 20.0000 chunk 409 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 376 optimal weight: 2.9990 chunk 530 optimal weight: 1.9990 chunk 792 optimal weight: 0.8980 chunk 839 optimal weight: 0.9990 chunk 414 optimal weight: 10.0000 chunk 751 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 69286 Z= 0.180 Angle : 0.618 9.951 93898 Z= 0.331 Chirality : 0.043 0.245 10962 Planarity : 0.004 0.069 12306 Dihedral : 12.557 178.871 9954 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.89 (0.09), residues: 8694 helix: -0.16 (0.08), residues: 4340 sheet: -0.61 (0.16), residues: 1064 loop : -0.99 (0.11), residues: 3290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 370 PHE 0.012 0.002 PHE E 607 TYR 0.012 0.001 TYR J 500 ARG 0.009 0.001 ARG N 670 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7301 (mp0) REVERT: A 192 ASP cc_start: 0.8344 (p0) cc_final: 0.7453 (p0) REVERT: A 314 THR cc_start: 0.9346 (m) cc_final: 0.9113 (p) REVERT: A 318 LEU cc_start: 0.8631 (mt) cc_final: 0.8361 (tt) REVERT: A 445 ILE cc_start: 0.7752 (mm) cc_final: 0.7452 (mt) REVERT: A 481 MET cc_start: 0.6903 (ppp) cc_final: 0.6643 (ppp) REVERT: A 535 ILE cc_start: 0.6614 (mp) cc_final: 0.6259 (mm) REVERT: A 622 MET cc_start: 0.8466 (mpp) cc_final: 0.8017 (mpp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1322 time to fit residues: 16.5959 Evaluate side-chains 69 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 698 optimal weight: 6.9990 chunk 476 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 624 optimal weight: 0.7980 chunk 346 optimal weight: 7.9990 chunk 715 optimal weight: 0.0020 chunk 579 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 428 optimal weight: 5.9990 chunk 753 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 370 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 69286 Z= 0.189 Angle : 0.626 10.133 93898 Z= 0.332 Chirality : 0.045 0.320 10962 Planarity : 0.004 0.054 12306 Dihedral : 12.361 175.792 9954 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -0.87 (0.09), residues: 8694 helix: -0.20 (0.08), residues: 4396 sheet: -0.30 (0.16), residues: 1022 loop : -1.01 (0.11), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 370 PHE 0.023 0.002 PHE B 592 TYR 0.008 0.001 TYR M 500 ARG 0.006 0.001 ARG I 433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7518 (mp0) REVERT: A 192 ASP cc_start: 0.8206 (p0) cc_final: 0.7221 (p0) REVERT: A 314 THR cc_start: 0.9264 (m) cc_final: 0.9042 (p) REVERT: A 318 LEU cc_start: 0.8588 (mt) cc_final: 0.8273 (tt) REVERT: A 326 ASP cc_start: 0.8275 (m-30) cc_final: 0.8041 (t70) REVERT: A 374 MET cc_start: 0.6226 (tmm) cc_final: 0.5837 (tmm) REVERT: A 398 MET cc_start: 0.5317 (mmt) cc_final: 0.4970 (mmm) REVERT: A 555 VAL cc_start: 0.8874 (t) cc_final: 0.8653 (m) REVERT: A 622 MET cc_start: 0.8527 (mpp) cc_final: 0.7991 (mpp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1153 time to fit residues: 14.4079 Evaluate side-chains 68 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 282 optimal weight: 0.4980 chunk 755 optimal weight: 9.9990 chunk 165 optimal weight: 0.2980 chunk 492 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 839 optimal weight: 1.9990 chunk 697 optimal weight: 4.9990 chunk 388 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 277 optimal weight: 20.0000 chunk 440 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS A 370 HIS ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 69286 Z= 0.176 Angle : 0.617 10.178 93898 Z= 0.327 Chirality : 0.044 0.310 10962 Planarity : 0.004 0.052 12306 Dihedral : 12.118 171.127 9954 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -0.95 (0.09), residues: 8694 helix: -0.26 (0.08), residues: 4480 sheet: -0.59 (0.18), residues: 840 loop : -0.96 (0.11), residues: 3374 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 370 PHE 0.012 0.001 PHE G 607 TYR 0.008 0.001 TYR J 500 ARG 0.005 0.001 ARG E 433 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7677 (mp0) REVERT: A 192 ASP cc_start: 0.8142 (p0) cc_final: 0.7208 (p0) REVERT: A 287 LEU cc_start: 0.9031 (mp) cc_final: 0.8723 (mt) REVERT: A 314 THR cc_start: 0.9235 (m) cc_final: 0.9011 (p) REVERT: A 318 LEU cc_start: 0.8583 (mt) cc_final: 0.8321 (tt) REVERT: A 326 ASP cc_start: 0.8220 (m-30) cc_final: 0.8007 (t70) REVERT: A 387 VAL cc_start: 0.8002 (t) cc_final: 0.7686 (p) REVERT: A 398 MET cc_start: 0.5049 (mmt) cc_final: 0.4780 (mmm) REVERT: A 525 ASP cc_start: 0.7406 (m-30) cc_final: 0.7103 (m-30) REVERT: A 562 ILE cc_start: 0.7407 (mm) cc_final: 0.7099 (pt) REVERT: A 622 MET cc_start: 0.8559 (mpp) cc_final: 0.8334 (mpp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1083 time to fit residues: 13.9868 Evaluate side-chains 71 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 809 optimal weight: 1.9990 chunk 94 optimal weight: 30.0000 chunk 478 optimal weight: 0.9980 chunk 613 optimal weight: 6.9990 chunk 475 optimal weight: 0.3980 chunk 706 optimal weight: 0.0020 chunk 468 optimal weight: 6.9990 chunk 836 optimal weight: 9.9990 chunk 523 optimal weight: 10.0000 chunk 510 optimal weight: 6.9990 chunk 386 optimal weight: 6.9990 overall best weight: 2.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 370 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 69286 Z= 0.171 Angle : 0.583 10.273 93898 Z= 0.310 Chirality : 0.042 0.148 10962 Planarity : 0.004 0.063 12306 Dihedral : 11.917 166.088 9954 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -0.77 (0.09), residues: 8694 helix: -0.09 (0.08), residues: 4382 sheet: -0.38 (0.15), residues: 1022 loop : -0.95 (0.11), residues: 3290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 370 PHE 0.013 0.001 PHE I 607 TYR 0.013 0.001 TYR N 297 ARG 0.008 0.001 ARG N 433 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7718 (mp0) REVERT: A 192 ASP cc_start: 0.8171 (p0) cc_final: 0.7199 (p0) REVERT: A 195 HIS cc_start: 0.7667 (p-80) cc_final: 0.7445 (p-80) REVERT: A 314 THR cc_start: 0.9230 (m) cc_final: 0.9021 (p) REVERT: A 318 LEU cc_start: 0.8585 (mt) cc_final: 0.8267 (tt) REVERT: A 326 ASP cc_start: 0.8427 (m-30) cc_final: 0.7958 (t70) REVERT: A 374 MET cc_start: 0.5988 (tmm) cc_final: 0.5558 (tmm) REVERT: A 387 VAL cc_start: 0.8033 (t) cc_final: 0.7674 (p) REVERT: A 481 MET cc_start: 0.6949 (ppp) cc_final: 0.6743 (ppp) REVERT: A 622 MET cc_start: 0.8546 (mpp) cc_final: 0.8322 (mpp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1142 time to fit residues: 13.5986 Evaluate side-chains 66 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 517 optimal weight: 0.7980 chunk 334 optimal weight: 10.0000 chunk 499 optimal weight: 0.0980 chunk 252 optimal weight: 0.9990 chunk 164 optimal weight: 0.0670 chunk 162 optimal weight: 6.9990 chunk 531 optimal weight: 20.0000 chunk 569 optimal weight: 8.9990 chunk 413 optimal weight: 0.0470 chunk 77 optimal weight: 5.9990 chunk 657 optimal weight: 0.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 69286 Z= 0.162 Angle : 0.602 10.296 93898 Z= 0.316 Chirality : 0.042 0.142 10962 Planarity : 0.004 0.054 12306 Dihedral : 11.691 160.705 9954 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -0.88 (0.09), residues: 8694 helix: -0.18 (0.08), residues: 4466 sheet: -0.77 (0.17), residues: 840 loop : -0.89 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS N 370 PHE 0.012 0.001 PHE I 607 TYR 0.024 0.001 TYR K 503 ARG 0.006 0.000 ARG J 433 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7716 (mp0) REVERT: A 192 ASP cc_start: 0.8130 (p0) cc_final: 0.7166 (p0) REVERT: A 195 HIS cc_start: 0.7607 (p-80) cc_final: 0.7373 (p-80) REVERT: A 314 THR cc_start: 0.9207 (m) cc_final: 0.8986 (p) REVERT: A 318 LEU cc_start: 0.8554 (mt) cc_final: 0.8277 (tt) REVERT: A 326 ASP cc_start: 0.8341 (m-30) cc_final: 0.7894 (t70) REVERT: A 339 ASP cc_start: 0.8726 (t0) cc_final: 0.8286 (t0) REVERT: A 387 VAL cc_start: 0.7951 (t) cc_final: 0.7735 (p) REVERT: A 398 MET cc_start: 0.5348 (mmt) cc_final: 0.4828 (mpp) REVERT: A 622 MET cc_start: 0.8488 (mpp) cc_final: 0.8278 (mpp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1208 time to fit residues: 14.3653 Evaluate side-chains 71 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 761 optimal weight: 0.0980 chunk 801 optimal weight: 0.0980 chunk 731 optimal weight: 3.9990 chunk 779 optimal weight: 9.9990 chunk 469 optimal weight: 6.9990 chunk 339 optimal weight: 7.9990 chunk 612 optimal weight: 4.9990 chunk 239 optimal weight: 0.5980 chunk 704 optimal weight: 0.0770 chunk 737 optimal weight: 0.0030 chunk 776 optimal weight: 20.0000 overall best weight: 0.1748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 HIS A 370 HIS A 434 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 69286 Z= 0.156 Angle : 0.596 10.333 93898 Z= 0.312 Chirality : 0.042 0.149 10962 Planarity : 0.004 0.035 12306 Dihedral : 11.494 156.003 9954 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -0.82 (0.09), residues: 8694 helix: -0.15 (0.08), residues: 4466 sheet: -0.72 (0.17), residues: 840 loop : -0.85 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 370 PHE 0.011 0.001 PHE I 607 TYR 0.018 0.001 TYR D 503 ARG 0.004 0.000 ARG G 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7717 (mp0) REVERT: A 228 ILE cc_start: 0.7251 (pt) cc_final: 0.7025 (pt) REVERT: A 314 THR cc_start: 0.9197 (m) cc_final: 0.8964 (p) REVERT: A 318 LEU cc_start: 0.8537 (mt) cc_final: 0.8271 (tt) REVERT: A 326 ASP cc_start: 0.8315 (m-30) cc_final: 0.7896 (t70) REVERT: A 339 ASP cc_start: 0.8664 (t0) cc_final: 0.8219 (t0) REVERT: A 387 VAL cc_start: 0.8118 (t) cc_final: 0.7801 (p) REVERT: A 398 MET cc_start: 0.5478 (mmt) cc_final: 0.4922 (mpp) REVERT: A 622 MET cc_start: 0.8516 (mpp) cc_final: 0.8214 (mpp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1325 time to fit residues: 16.1863 Evaluate side-chains 69 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 511 optimal weight: 5.9990 chunk 824 optimal weight: 10.0000 chunk 503 optimal weight: 2.9990 chunk 391 optimal weight: 10.0000 chunk 573 optimal weight: 4.9990 chunk 864 optimal weight: 4.9990 chunk 795 optimal weight: 0.6980 chunk 688 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 531 optimal weight: 8.9990 chunk 422 optimal weight: 0.7980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 HIS ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 69286 Z= 0.171 Angle : 0.601 10.299 93898 Z= 0.318 Chirality : 0.042 0.154 10962 Planarity : 0.004 0.073 12306 Dihedral : 11.357 151.203 9954 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -0.73 (0.09), residues: 8694 helix: -0.04 (0.08), residues: 4466 sheet: -0.72 (0.17), residues: 840 loop : -0.83 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 370 PHE 0.013 0.001 PHE I 607 TYR 0.017 0.001 TYR N 503 ARG 0.017 0.001 ARG H 670 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7675 (mp0) REVERT: A 314 THR cc_start: 0.9231 (m) cc_final: 0.8982 (p) REVERT: A 318 LEU cc_start: 0.8533 (mt) cc_final: 0.8234 (tt) REVERT: A 326 ASP cc_start: 0.8418 (m-30) cc_final: 0.8001 (t70) REVERT: A 398 MET cc_start: 0.5666 (mmt) cc_final: 0.5246 (mmm) REVERT: A 622 MET cc_start: 0.8570 (mpp) cc_final: 0.8275 (mpp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1094 time to fit residues: 13.7365 Evaluate side-chains 66 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 546 optimal weight: 1.9990 chunk 733 optimal weight: 7.9990 chunk 210 optimal weight: 20.0000 chunk 634 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 191 optimal weight: 20.0000 chunk 689 optimal weight: 0.0070 chunk 288 optimal weight: 6.9990 chunk 708 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 HIS A 322 HIS A 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.130579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.104258 restraints weight = 15684.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.106995 restraints weight = 9777.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.108852 restraints weight = 7008.667| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.6212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 69286 Z= 0.198 Angle : 0.634 10.274 93898 Z= 0.332 Chirality : 0.043 0.152 10962 Planarity : 0.004 0.069 12306 Dihedral : 11.300 147.219 9954 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -0.79 (0.09), residues: 8694 helix: -0.04 (0.08), residues: 4564 sheet: -0.73 (0.17), residues: 840 loop : -0.99 (0.11), residues: 3290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 370 PHE 0.012 0.001 PHE I 607 TYR 0.013 0.001 TYR I 503 ARG 0.027 0.001 ARG E 433 =============================================================================== Job complete usr+sys time: 5943.06 seconds wall clock time: 109 minutes 49.73 seconds (6589.73 seconds total)