Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 13:23:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt5_12581/05_2023/7nt5_12581.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt5_12581/05_2023/7nt5_12581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt5_12581/05_2023/7nt5_12581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt5_12581/05_2023/7nt5_12581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt5_12581/05_2023/7nt5_12581.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt5_12581/05_2023/7nt5_12581.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 77 5.49 5 S 195 5.16 5 C 25275 2.51 5 N 6795 2.21 5 O 7858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B GLU 286": "OE1" <-> "OE2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B ARG 361": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C ARG 193": "NH1" <-> "NH2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C ARG 343": "NH1" <-> "NH2" Residue "C ARG 361": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "D GLU 66": "OE1" <-> "OE2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D ARG 343": "NH1" <-> "NH2" Residue "D GLU 356": "OE1" <-> "OE2" Residue "D ARG 361": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 36": "NH1" <-> "NH2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 66": "OE1" <-> "OE2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E GLU 276": "OE1" <-> "OE2" Residue "E ARG 278": "NH1" <-> "NH2" Residue "E GLU 315": "OE1" <-> "OE2" Residue "E ARG 343": "NH1" <-> "NH2" Residue "E ARG 361": "NH1" <-> "NH2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F GLU 50": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F ARG 193": "NH1" <-> "NH2" Residue "F ARG 218": "NH1" <-> "NH2" Residue "F GLU 237": "OE1" <-> "OE2" Residue "F GLU 260": "OE1" <-> "OE2" Residue "F GLU 261": "OE1" <-> "OE2" Residue "F ARG 272": "NH1" <-> "NH2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "F GLU 303": "OE1" <-> "OE2" Residue "F ARG 343": "NH1" <-> "NH2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F GLU 356": "OE1" <-> "OE2" Residue "F ARG 361": "NH1" <-> "NH2" Residue "G ARG 12": "NH1" <-> "NH2" Residue "G ARG 36": "NH1" <-> "NH2" Residue "G GLU 50": "OE1" <-> "OE2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G ARG 193": "NH1" <-> "NH2" Residue "G ARG 272": "NH1" <-> "NH2" Residue "G ARG 278": "NH1" <-> "NH2" Residue "G ARG 343": "NH1" <-> "NH2" Residue "G PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 361": "NH1" <-> "NH2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H ARG 12": "NH1" <-> "NH2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H GLU 50": "OE1" <-> "OE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H GLU 188": "OE1" <-> "OE2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "H ARG 193": "NH1" <-> "NH2" Residue "H GLU 216": "OE1" <-> "OE2" Residue "H GLU 233": "OE1" <-> "OE2" Residue "H GLU 260": "OE1" <-> "OE2" Residue "H ARG 272": "NH1" <-> "NH2" Residue "H ARG 278": "NH1" <-> "NH2" Residue "H GLU 303": "OE1" <-> "OE2" Residue "H GLU 316": "OE1" <-> "OE2" Residue "H ARG 343": "NH1" <-> "NH2" Residue "H ARG 361": "NH1" <-> "NH2" Residue "I ARG 12": "NH1" <-> "NH2" Residue "I ARG 36": "NH1" <-> "NH2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I GLU 98": "OE1" <-> "OE2" Residue "I GLU 123": "OE1" <-> "OE2" Residue "I GLU 124": "OE1" <-> "OE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I ARG 193": "NH1" <-> "NH2" Residue "I GLU 233": "OE1" <-> "OE2" Residue "I GLU 260": "OE1" <-> "OE2" Residue "I ARG 272": "NH1" <-> "NH2" Residue "I ARG 278": "NH1" <-> "NH2" Residue "I ARG 343": "NH1" <-> "NH2" Residue "I GLU 356": "OE1" <-> "OE2" Residue "I ARG 361": "NH1" <-> "NH2" Residue "J ARG 12": "NH1" <-> "NH2" Residue "J ARG 36": "NH1" <-> "NH2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "J ARG 193": "NH1" <-> "NH2" Residue "J GLU 216": "OE1" <-> "OE2" Residue "J GLU 237": "OE1" <-> "OE2" Residue "J ARG 272": "NH1" <-> "NH2" Residue "J GLU 276": "OE1" <-> "OE2" Residue "J ARG 278": "NH1" <-> "NH2" Residue "J GLU 286": "OE1" <-> "OE2" Residue "J ARG 343": "NH1" <-> "NH2" Residue "J GLU 356": "OE1" <-> "OE2" Residue "J ARG 361": "NH1" <-> "NH2" Residue "K ARG 12": "NH1" <-> "NH2" Residue "K ARG 36": "NH1" <-> "NH2" Residue "K GLU 115": "OE1" <-> "OE2" Residue "K GLU 123": "OE1" <-> "OE2" Residue "K TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 193": "NH1" <-> "NH2" Residue "K GLU 250": "OE1" <-> "OE2" Residue "K ARG 272": "NH1" <-> "NH2" Residue "K ARG 278": "NH1" <-> "NH2" Residue "K GLU 303": "OE1" <-> "OE2" Residue "K ARG 343": "NH1" <-> "NH2" Residue "K ARG 361": "NH1" <-> "NH2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L ARG 12": "NH1" <-> "NH2" Residue "L ARG 36": "NH1" <-> "NH2" Residue "L PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 126": "OE1" <-> "OE2" Residue "L ARG 193": "NH1" <-> "NH2" Residue "L GLU 237": "OE1" <-> "OE2" Residue "L ARG 272": "NH1" <-> "NH2" Residue "L ARG 278": "NH1" <-> "NH2" Residue "L GLU 315": "OE1" <-> "OE2" Residue "L ARG 343": "NH1" <-> "NH2" Residue "L ARG 352": "NH1" <-> "NH2" Residue "L ARG 361": "NH1" <-> "NH2" Residue "M ARG 12": "NH1" <-> "NH2" Residue "M ARG 36": "NH1" <-> "NH2" Residue "M PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 187": "OE1" <-> "OE2" Residue "M GLU 188": "OE1" <-> "OE2" Residue "M ARG 193": "NH1" <-> "NH2" Residue "M ARG 272": "NH1" <-> "NH2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M ARG 343": "NH1" <-> "NH2" Residue "M ARG 361": "NH1" <-> "NH2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 40200 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2974 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 15, 'TRANS': 378} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2974 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 15, 'TRANS': 378} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 65 Chain: "E" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 65 Chain: "F" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 65 Chain: "G" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 65 Chain: "H" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 65 Chain: "I" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 65 Chain: "J" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 65 Chain: "K" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 65 Chain: "L" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2969 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 15, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "M" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2916 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 15, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "N" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1556 Classifications: {'RNA': 78} Modifications used: {'5*END': 1, 'rna2p_pyr': 14, 'rna3p_pyr': 63} Link IDs: {'rna2p': 14, 'rna3p': 63} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 20.21, per 1000 atoms: 0.50 Number of scatterers: 40200 At special positions: 0 Unit cell: (213.792, 215.888, 127.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 195 16.00 P 77 15.00 O 7858 8.00 N 6795 7.00 C 25275 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: 17.85 Conformation dependent library (CDL) restraints added in 6.0 seconds 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9538 Finding SS restraints... Secondary structure from input PDB file: 298 helices and 13 sheets defined 69.1% alpha, 3.0% beta 0 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 10.28 Creating SS restraints... Processing helix chain 'A' and resid 4 through 18 removed outlier: 3.804A pdb=" N ALA A 8 " --> pdb=" O ILE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 44 through 61 removed outlier: 3.777A pdb=" N ARG A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.995A pdb=" N GLY A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 105 through 108 removed outlier: 4.323A pdb=" N VAL A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 105 through 108' Processing helix chain 'A' and resid 123 through 139 Processing helix chain 'A' and resid 147 through 153 removed outlier: 4.113A pdb=" N TYR A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 180 removed outlier: 4.328A pdb=" N LEU A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA A 177 " --> pdb=" O TRP A 173 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 210 through 224 Processing helix chain 'A' and resid 224 through 240 removed outlier: 3.716A pdb=" N ARG A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.679A pdb=" N ASN A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 279 through 286 removed outlier: 5.755A pdb=" N ASN A 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU A 286 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 Processing helix chain 'A' and resid 306 through 311 Proline residue: A 309 - end of helix No H-bonds generated for 'chain 'A' and resid 306 through 311' Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.546A pdb=" N PHE A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'B' and resid 5 through 18 removed outlier: 3.898A pdb=" N SER B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 44 through 61 Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 117 through 121 removed outlier: 3.623A pdb=" N ALA B 121 " --> pdb=" O GLY B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 139 Processing helix chain 'B' and resid 147 through 153 removed outlier: 4.065A pdb=" N TYR B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 180 removed outlier: 4.764A pdb=" N THR B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU B 175 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA B 177 " --> pdb=" O TRP B 173 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LYS B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 removed outlier: 4.674A pdb=" N SER B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 210 through 224 Processing helix chain 'B' and resid 224 through 240 removed outlier: 4.040A pdb=" N ARG B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 260 removed outlier: 3.656A pdb=" N ASN B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.657A pdb=" N ALA B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 305 removed outlier: 4.272A pdb=" N SER B 289 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 Proline residue: B 309 - end of helix No H-bonds generated for 'chain 'B' and resid 306 through 311' Processing helix chain 'B' and resid 318 through 323 removed outlier: 3.589A pdb=" N PHE B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 327 through 342 Processing helix chain 'B' and resid 356 through 369 Processing helix chain 'B' and resid 385 through 397 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 44 through 61 Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 83 through 92 removed outlier: 3.525A pdb=" N LEU C 87 " --> pdb=" O ARG C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 139 Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 157 through 180 removed outlier: 4.169A pdb=" N LEU C 175 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 176 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA C 177 " --> pdb=" O TRP C 173 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LYS C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 210 through 224 Processing helix chain 'C' and resid 224 through 240 removed outlier: 3.683A pdb=" N ARG C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 260 removed outlier: 3.662A pdb=" N ASN C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR C 258 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 274 Processing helix chain 'C' and resid 279 through 286 removed outlier: 5.862A pdb=" N ASN C 285 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU C 286 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 305 Processing helix chain 'C' and resid 306 through 309 Proline residue: C 309 - end of helix No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 310 through 315 Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.556A pdb=" N PHE C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 327 through 342 removed outlier: 3.563A pdb=" N THR C 340 " --> pdb=" O GLY C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 356 through 368 Processing helix chain 'C' and resid 385 through 396 Processing helix chain 'D' and resid 5 through 18 removed outlier: 3.581A pdb=" N ALA D 9 " --> pdb=" O PHE D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 44 through 61 Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.853A pdb=" N GLY D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 122 through 139 Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 157 through 180 removed outlier: 4.163A pdb=" N LEU D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 176 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA D 177 " --> pdb=" O TRP D 173 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYS D 178 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 200 removed outlier: 4.610A pdb=" N SER D 189 " --> pdb=" O THR D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 208 Processing helix chain 'D' and resid 210 through 224 Processing helix chain 'D' and resid 224 through 240 removed outlier: 3.752A pdb=" N ARG D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 260 removed outlier: 3.660A pdb=" N ASN D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 274 Processing helix chain 'D' and resid 279 through 285 removed outlier: 5.779A pdb=" N ASN D 285 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.071A pdb=" N ASP D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 311 Proline residue: D 309 - end of helix No H-bonds generated for 'chain 'D' and resid 306 through 311' Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.561A pdb=" N PHE D 322 " --> pdb=" O ILE D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 327 through 342 removed outlier: 3.546A pdb=" N THR D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 368 removed outlier: 3.773A pdb=" N PHE D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 396 Processing helix chain 'E' and resid 5 through 18 Processing helix chain 'E' and resid 25 through 29 Processing helix chain 'E' and resid 44 through 61 removed outlier: 3.552A pdb=" N GLU E 50 " --> pdb=" O GLU E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 78 Processing helix chain 'E' and resid 79 through 81 No H-bonds generated for 'chain 'E' and resid 79 through 81' Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 123 through 139 removed outlier: 3.732A pdb=" N SER E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 157 through 177 removed outlier: 3.963A pdb=" N LEU E 175 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA E 177 " --> pdb=" O TRP E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'E' and resid 194 through 199 removed outlier: 3.560A pdb=" N VAL E 198 " --> pdb=" O TRP E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 208 Processing helix chain 'E' and resid 210 through 223 removed outlier: 3.622A pdb=" N GLU E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 240 removed outlier: 4.036A pdb=" N ARG E 228 " --> pdb=" O SER E 224 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS E 240 " --> pdb=" O ILE E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 260 removed outlier: 4.086A pdb=" N TYR E 258 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'E' and resid 279 through 286 removed outlier: 6.016A pdb=" N ASN E 285 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLU E 286 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 305 Processing helix chain 'E' and resid 306 through 311 Proline residue: E 309 - end of helix No H-bonds generated for 'chain 'E' and resid 306 through 311' Processing helix chain 'E' and resid 318 through 323 removed outlier: 3.557A pdb=" N PHE E 322 " --> pdb=" O ILE E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 326 No H-bonds generated for 'chain 'E' and resid 324 through 326' Processing helix chain 'E' and resid 327 through 342 removed outlier: 3.532A pdb=" N THR E 340 " --> pdb=" O GLY E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 368 Processing helix chain 'E' and resid 385 through 397 removed outlier: 3.779A pdb=" N VAL E 389 " --> pdb=" O SER E 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 18 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 44 through 61 Processing helix chain 'F' and resid 65 through 77 removed outlier: 3.515A pdb=" N GLY F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'F' and resid 123 through 139 Processing helix chain 'F' and resid 148 through 153 Processing helix chain 'F' and resid 157 through 180 removed outlier: 3.643A pdb=" N LEU F 175 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE F 176 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA F 177 " --> pdb=" O TRP F 173 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS F 178 " --> pdb=" O ILE F 174 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL F 180 " --> pdb=" O ILE F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 200 removed outlier: 3.959A pdb=" N ARG F 192 " --> pdb=" O GLU F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 208 Processing helix chain 'F' and resid 210 through 224 removed outlier: 3.817A pdb=" N GLU F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 238 removed outlier: 3.500A pdb=" N ARG F 228 " --> pdb=" O SER F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 260 removed outlier: 3.643A pdb=" N ASN F 257 " --> pdb=" O SER F 253 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR F 258 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 273 Processing helix chain 'F' and resid 284 through 286 No H-bonds generated for 'chain 'F' and resid 284 through 286' Processing helix chain 'F' and resid 287 through 305 Processing helix chain 'F' and resid 306 through 311 Proline residue: F 309 - end of helix No H-bonds generated for 'chain 'F' and resid 306 through 311' Processing helix chain 'F' and resid 318 through 323 removed outlier: 3.578A pdb=" N PHE F 322 " --> pdb=" O ILE F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 342 Processing helix chain 'F' and resid 356 through 369 removed outlier: 3.515A pdb=" N ALA F 367 " --> pdb=" O GLY F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 396 Processing helix chain 'G' and resid 5 through 18 Processing helix chain 'G' and resid 25 through 29 Processing helix chain 'G' and resid 44 through 61 removed outlier: 4.009A pdb=" N GLU G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 78 removed outlier: 3.534A pdb=" N SER G 78 " --> pdb=" O PHE G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 81 No H-bonds generated for 'chain 'G' and resid 79 through 81' Processing helix chain 'G' and resid 83 through 92 Processing helix chain 'G' and resid 122 through 139 removed outlier: 3.680A pdb=" N GLU G 126 " --> pdb=" O GLN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 153 Processing helix chain 'G' and resid 157 through 180 removed outlier: 3.562A pdb=" N THR G 167 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU G 175 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE G 176 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA G 177 " --> pdb=" O TRP G 173 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LYS G 178 " --> pdb=" O ILE G 174 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL G 180 " --> pdb=" O ILE G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 200 removed outlier: 4.737A pdb=" N SER G 189 " --> pdb=" O THR G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 208 Processing helix chain 'G' and resid 210 through 224 Processing helix chain 'G' and resid 224 through 240 removed outlier: 3.655A pdb=" N ARG G 228 " --> pdb=" O SER G 224 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS G 240 " --> pdb=" O ILE G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 260 removed outlier: 3.569A pdb=" N ASN G 257 " --> pdb=" O SER G 253 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR G 258 " --> pdb=" O ASP G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'G' and resid 279 through 285 removed outlier: 5.959A pdb=" N ASN G 285 " --> pdb=" O LEU G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 305 removed outlier: 4.550A pdb=" N ASP G 290 " --> pdb=" O GLU G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 311 Proline residue: G 309 - end of helix No H-bonds generated for 'chain 'G' and resid 306 through 311' Processing helix chain 'G' and resid 318 through 323 removed outlier: 3.559A pdb=" N PHE G 322 " --> pdb=" O ILE G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 326 No H-bonds generated for 'chain 'G' and resid 324 through 326' Processing helix chain 'G' and resid 327 through 342 removed outlier: 3.551A pdb=" N THR G 340 " --> pdb=" O GLY G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 368 Processing helix chain 'G' and resid 385 through 396 Processing helix chain 'H' and resid 5 through 18 Processing helix chain 'H' and resid 25 through 29 Processing helix chain 'H' and resid 44 through 61 Processing helix chain 'H' and resid 65 through 79 removed outlier: 3.570A pdb=" N MET H 79 " --> pdb=" O THR H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 92 Processing helix chain 'H' and resid 122 through 139 removed outlier: 3.691A pdb=" N GLU H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 153 Processing helix chain 'H' and resid 157 through 180 removed outlier: 4.107A pdb=" N LEU H 175 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA H 177 " --> pdb=" O TRP H 173 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYS H 178 " --> pdb=" O ILE H 174 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL H 180 " --> pdb=" O ILE H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 200 removed outlier: 3.708A pdb=" N ARG H 192 " --> pdb=" O GLU H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 210 through 224 Processing helix chain 'H' and resid 224 through 240 removed outlier: 3.698A pdb=" N ARG H 228 " --> pdb=" O SER H 224 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS H 240 " --> pdb=" O ILE H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 260 removed outlier: 3.612A pdb=" N ASN H 257 " --> pdb=" O SER H 253 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR H 258 " --> pdb=" O ASP H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 273 Processing helix chain 'H' and resid 279 through 286 removed outlier: 5.413A pdb=" N ASN H 285 " --> pdb=" O LEU H 282 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLU H 286 " --> pdb=" O ALA H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 305 Processing helix chain 'H' and resid 306 through 311 Proline residue: H 309 - end of helix No H-bonds generated for 'chain 'H' and resid 306 through 311' Processing helix chain 'H' and resid 318 through 323 removed outlier: 3.542A pdb=" N PHE H 322 " --> pdb=" O ILE H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 326 No H-bonds generated for 'chain 'H' and resid 324 through 326' Processing helix chain 'H' and resid 327 through 342 removed outlier: 3.652A pdb=" N THR H 340 " --> pdb=" O GLY H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 370 removed outlier: 4.180A pdb=" N HIS H 370 " --> pdb=" O SER H 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 397 Processing helix chain 'I' and resid 5 through 16 removed outlier: 3.616A pdb=" N ALA I 9 " --> pdb=" O PHE I 5 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR I 14 " --> pdb=" O SER I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 29 Processing helix chain 'I' and resid 44 through 61 Processing helix chain 'I' and resid 65 through 77 Processing helix chain 'I' and resid 83 through 92 Processing helix chain 'I' and resid 122 through 139 Processing helix chain 'I' and resid 147 through 153 removed outlier: 4.102A pdb=" N TYR I 151 " --> pdb=" O ASP I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 180 removed outlier: 4.171A pdb=" N LEU I 175 " --> pdb=" O GLN I 171 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE I 176 " --> pdb=" O ILE I 172 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA I 177 " --> pdb=" O TRP I 173 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LYS I 178 " --> pdb=" O ILE I 174 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL I 180 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 200 removed outlier: 3.905A pdb=" N ARG I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 208 Processing helix chain 'I' and resid 210 through 224 Processing helix chain 'I' and resid 224 through 240 removed outlier: 3.729A pdb=" N ARG I 228 " --> pdb=" O SER I 224 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS I 240 " --> pdb=" O ILE I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 260 removed outlier: 3.663A pdb=" N ASN I 257 " --> pdb=" O SER I 253 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR I 258 " --> pdb=" O ASP I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 273 Processing helix chain 'I' and resid 279 through 286 removed outlier: 5.679A pdb=" N ASN I 285 " --> pdb=" O LEU I 282 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU I 286 " --> pdb=" O ALA I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 305 Processing helix chain 'I' and resid 306 through 311 Proline residue: I 309 - end of helix No H-bonds generated for 'chain 'I' and resid 306 through 311' Processing helix chain 'I' and resid 318 through 323 removed outlier: 3.616A pdb=" N PHE I 322 " --> pdb=" O ILE I 318 " (cutoff:3.500A) Processing helix chain 'I' and resid 324 through 326 No H-bonds generated for 'chain 'I' and resid 324 through 326' Processing helix chain 'I' and resid 327 through 342 removed outlier: 3.520A pdb=" N THR I 340 " --> pdb=" O GLY I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 356 through 368 Processing helix chain 'I' and resid 370 through 374 Processing helix chain 'I' and resid 387 through 396 removed outlier: 3.746A pdb=" N VAL I 396 " --> pdb=" O LEU I 392 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 18 Processing helix chain 'J' and resid 25 through 29 Processing helix chain 'J' and resid 44 through 61 Processing helix chain 'J' and resid 65 through 79 Processing helix chain 'J' and resid 83 through 92 Processing helix chain 'J' and resid 123 through 139 Processing helix chain 'J' and resid 147 through 153 removed outlier: 4.097A pdb=" N TYR J 151 " --> pdb=" O ASP J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 177 removed outlier: 4.115A pdb=" N LEU J 175 " --> pdb=" O GLN J 171 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE J 176 " --> pdb=" O ILE J 172 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA J 177 " --> pdb=" O TRP J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 200 removed outlier: 4.616A pdb=" N SER J 189 " --> pdb=" O THR J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 208 Processing helix chain 'J' and resid 210 through 224 Processing helix chain 'J' and resid 224 through 240 removed outlier: 3.687A pdb=" N ARG J 228 " --> pdb=" O SER J 224 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS J 240 " --> pdb=" O ILE J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 260 removed outlier: 3.590A pdb=" N ASN J 257 " --> pdb=" O SER J 253 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR J 258 " --> pdb=" O ASP J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 274 Processing helix chain 'J' and resid 279 through 286 removed outlier: 6.141A pdb=" N ASN J 285 " --> pdb=" O LEU J 282 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU J 286 " --> pdb=" O ALA J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 305 Processing helix chain 'J' and resid 306 through 311 Proline residue: J 309 - end of helix No H-bonds generated for 'chain 'J' and resid 306 through 311' Processing helix chain 'J' and resid 318 through 323 removed outlier: 3.541A pdb=" N PHE J 322 " --> pdb=" O ILE J 318 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 326 No H-bonds generated for 'chain 'J' and resid 324 through 326' Processing helix chain 'J' and resid 327 through 342 removed outlier: 3.556A pdb=" N THR J 340 " --> pdb=" O GLY J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 356 through 367 removed outlier: 3.644A pdb=" N ALA J 367 " --> pdb=" O GLY J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 removed outlier: 6.354A pdb=" N ASP J 375 " --> pdb=" O GLY J 372 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN J 377 " --> pdb=" O ILE J 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 396 Processing helix chain 'K' and resid 5 through 18 Processing helix chain 'K' and resid 25 through 29 Processing helix chain 'K' and resid 44 through 61 Processing helix chain 'K' and resid 65 through 77 Processing helix chain 'K' and resid 83 through 91 Processing helix chain 'K' and resid 117 through 121 Processing helix chain 'K' and resid 123 through 139 Processing helix chain 'K' and resid 148 through 153 Processing helix chain 'K' and resid 157 through 177 removed outlier: 4.178A pdb=" N LEU K 175 " --> pdb=" O GLN K 171 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE K 176 " --> pdb=" O ILE K 172 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA K 177 " --> pdb=" O TRP K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 200 removed outlier: 4.495A pdb=" N ARG K 192 " --> pdb=" O GLU K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 208 Processing helix chain 'K' and resid 210 through 224 Processing helix chain 'K' and resid 224 through 240 removed outlier: 3.767A pdb=" N ARG K 228 " --> pdb=" O SER K 224 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS K 240 " --> pdb=" O ILE K 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 260 removed outlier: 3.595A pdb=" N ASN K 257 " --> pdb=" O SER K 253 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR K 258 " --> pdb=" O ASP K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 273 Processing helix chain 'K' and resid 279 through 286 removed outlier: 5.955A pdb=" N ASN K 285 " --> pdb=" O LEU K 282 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLU K 286 " --> pdb=" O ALA K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 305 Processing helix chain 'K' and resid 306 through 311 Proline residue: K 309 - end of helix No H-bonds generated for 'chain 'K' and resid 306 through 311' Processing helix chain 'K' and resid 318 through 323 removed outlier: 3.571A pdb=" N PHE K 322 " --> pdb=" O ILE K 318 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 326 No H-bonds generated for 'chain 'K' and resid 324 through 326' Processing helix chain 'K' and resid 327 through 342 removed outlier: 3.547A pdb=" N THR K 340 " --> pdb=" O GLY K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 356 through 368 Processing helix chain 'K' and resid 373 through 377 Processing helix chain 'K' and resid 385 through 397 Processing helix chain 'L' and resid 5 through 18 Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 44 through 61 Processing helix chain 'L' and resid 65 through 77 removed outlier: 3.839A pdb=" N GLY L 71 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 91 Processing helix chain 'L' and resid 122 through 139 removed outlier: 3.621A pdb=" N LEU L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 153 removed outlier: 4.117A pdb=" N TYR L 151 " --> pdb=" O ASP L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 180 removed outlier: 4.314A pdb=" N LEU L 175 " --> pdb=" O GLN L 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE L 176 " --> pdb=" O ILE L 172 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA L 177 " --> pdb=" O TRP L 173 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS L 178 " --> pdb=" O ILE L 174 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL L 180 " --> pdb=" O ILE L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 200 removed outlier: 3.671A pdb=" N TYR L 197 " --> pdb=" O ARG L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 208 Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 224 through 240 removed outlier: 3.728A pdb=" N ARG L 228 " --> pdb=" O SER L 224 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS L 240 " --> pdb=" O ILE L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 260 removed outlier: 3.619A pdb=" N ASN L 257 " --> pdb=" O SER L 253 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR L 258 " --> pdb=" O ASP L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 273 Processing helix chain 'L' and resid 279 through 286 removed outlier: 5.641A pdb=" N ASN L 285 " --> pdb=" O LEU L 282 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU L 286 " --> pdb=" O ALA L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 305 Processing helix chain 'L' and resid 306 through 311 Proline residue: L 309 - end of helix No H-bonds generated for 'chain 'L' and resid 306 through 311' Processing helix chain 'L' and resid 318 through 323 removed outlier: 3.537A pdb=" N PHE L 322 " --> pdb=" O ILE L 318 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 342 removed outlier: 3.552A pdb=" N THR L 340 " --> pdb=" O GLY L 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 368 Processing helix chain 'L' and resid 370 through 374 Processing helix chain 'L' and resid 385 through 397 Processing helix chain 'M' and resid 5 through 18 Processing helix chain 'M' and resid 25 through 29 Processing helix chain 'M' and resid 44 through 61 Processing helix chain 'M' and resid 65 through 79 removed outlier: 3.566A pdb=" N MET M 79 " --> pdb=" O THR M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 92 Processing helix chain 'M' and resid 122 through 139 Processing helix chain 'M' and resid 148 through 153 Processing helix chain 'M' and resid 157 through 180 removed outlier: 4.213A pdb=" N LEU M 175 " --> pdb=" O GLN M 171 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE M 176 " --> pdb=" O ILE M 172 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA M 177 " --> pdb=" O TRP M 173 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS M 178 " --> pdb=" O ILE M 174 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL M 180 " --> pdb=" O ILE M 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 200 removed outlier: 3.704A pdb=" N LYS M 196 " --> pdb=" O ARG M 192 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR M 197 " --> pdb=" O ARG M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 208 Processing helix chain 'M' and resid 210 through 224 removed outlier: 3.606A pdb=" N GLU M 216 " --> pdb=" O GLN M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 240 removed outlier: 3.832A pdb=" N ARG M 228 " --> pdb=" O SER M 224 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS M 240 " --> pdb=" O ILE M 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 260 removed outlier: 3.591A pdb=" N ASN M 257 " --> pdb=" O SER M 253 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR M 258 " --> pdb=" O ASP M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 274 Processing helix chain 'M' and resid 279 through 286 removed outlier: 5.585A pdb=" N ASN M 285 " --> pdb=" O LEU M 282 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLU M 286 " --> pdb=" O ALA M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 287 through 305 Processing helix chain 'M' and resid 306 through 311 Proline residue: M 309 - end of helix No H-bonds generated for 'chain 'M' and resid 306 through 311' Processing helix chain 'M' and resid 318 through 323 removed outlier: 3.619A pdb=" N PHE M 322 " --> pdb=" O ILE M 318 " (cutoff:3.500A) Processing helix chain 'M' and resid 324 through 326 No H-bonds generated for 'chain 'M' and resid 324 through 326' Processing helix chain 'M' and resid 327 through 342 Processing helix chain 'M' and resid 356 through 368 Processing helix chain 'M' and resid 384 through 386 No H-bonds generated for 'chain 'M' and resid 384 through 386' Processing helix chain 'M' and resid 387 through 397 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 39 removed outlier: 5.848A pdb=" N THR A 33 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL A 100 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE A 35 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE A 102 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE A 37 " --> pdb=" O ILE A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 33 through 39 Processing sheet with id=AA3, first strand: chain 'C' and resid 33 through 39 removed outlier: 5.824A pdb=" N THR C 33 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL C 100 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE C 35 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE C 102 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE C 37 " --> pdb=" O ILE C 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 33 through 40 removed outlier: 5.938A pdb=" N THR D 33 " --> pdb=" O GLU D 98 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL D 100 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE D 35 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE D 102 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE D 37 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL D 104 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL D 39 " --> pdb=" O VAL D 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 33 through 39 removed outlier: 6.219A pdb=" N THR E 33 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL E 100 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E 35 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE E 102 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE E 37 " --> pdb=" O ILE E 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 33 through 39 Processing sheet with id=AA7, first strand: chain 'G' and resid 33 through 39 removed outlier: 6.131A pdb=" N THR G 33 " --> pdb=" O GLU G 98 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL G 100 " --> pdb=" O THR G 33 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE G 35 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE G 102 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE G 37 " --> pdb=" O ILE G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 36 through 39 Processing sheet with id=AA9, first strand: chain 'I' and resid 33 through 39 removed outlier: 6.447A pdb=" N THR I 33 " --> pdb=" O GLU I 98 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL I 100 " --> pdb=" O THR I 33 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE I 35 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE I 102 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE I 37 " --> pdb=" O ILE I 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 33 through 39 Processing sheet with id=AB2, first strand: chain 'K' and resid 33 through 39 removed outlier: 5.923A pdb=" N THR K 33 " --> pdb=" O GLU K 98 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL K 100 " --> pdb=" O THR K 33 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE K 35 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE K 102 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE K 37 " --> pdb=" O ILE K 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 33 through 39 removed outlier: 5.388A pdb=" N THR L 33 " --> pdb=" O GLU L 98 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL L 100 " --> pdb=" O THR L 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE L 35 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE L 102 " --> pdb=" O ILE L 35 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE L 37 " --> pdb=" O ILE L 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'M' and resid 33 through 39 2201 hydrogen bonds defined for protein. 6300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 13.30 Time building geometry restraints manager: 18.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.32: 7127 1.32 - 1.48: 16108 1.48 - 1.64: 17381 1.64 - 1.80: 217 1.80 - 1.96: 183 Bond restraints: 41016 Sorted by residual: bond pdb=" NE ARG M 343 " pdb=" CZ ARG M 343 " ideal model delta sigma weight residual 1.326 1.475 -0.149 1.10e-02 8.26e+03 1.83e+02 bond pdb=" NE ARG M 302 " pdb=" CZ ARG M 302 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.38e+01 bond pdb=" CA ALA F 323 " pdb=" CB ALA F 323 " ideal model delta sigma weight residual 1.530 1.438 0.092 1.46e-02 4.69e+03 3.93e+01 bond pdb=" CG MET E 345 " pdb=" SD MET E 345 " ideal model delta sigma weight residual 1.803 1.958 -0.155 2.50e-02 1.60e+03 3.87e+01 bond pdb=" CG MET H 345 " pdb=" SD MET H 345 " ideal model delta sigma weight residual 1.803 1.957 -0.154 2.50e-02 1.60e+03 3.78e+01 ... (remaining 41011 not shown) Histogram of bond angle deviations from ideal: 92.11 - 101.36: 347 101.36 - 110.62: 9487 110.62 - 119.88: 28404 119.88 - 129.13: 17444 129.13 - 138.39: 179 Bond angle restraints: 55861 Sorted by residual: angle pdb=" NE ARG M 343 " pdb=" CZ ARG M 343 " pdb=" NH2 ARG M 343 " ideal model delta sigma weight residual 119.20 107.85 11.35 9.00e-01 1.23e+00 1.59e+02 angle pdb=" CD ARG M 302 " pdb=" NE ARG M 302 " pdb=" CZ ARG M 302 " ideal model delta sigma weight residual 124.40 138.39 -13.99 1.40e+00 5.10e-01 9.98e+01 angle pdb=" CD ARG M 343 " pdb=" NE ARG M 343 " pdb=" CZ ARG M 343 " ideal model delta sigma weight residual 124.40 137.99 -13.59 1.40e+00 5.10e-01 9.43e+01 angle pdb=" C4' U N 44 " pdb=" C3' U N 44 " pdb=" O3' U N 44 " ideal model delta sigma weight residual 113.00 99.71 13.29 1.50e+00 4.44e-01 7.86e+01 angle pdb=" C4' U N 68 " pdb=" C3' U N 68 " pdb=" O3' U N 68 " ideal model delta sigma weight residual 113.00 100.14 12.86 1.50e+00 4.44e-01 7.35e+01 ... (remaining 55856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.79: 22711 20.79 - 41.58: 1762 41.58 - 62.36: 265 62.36 - 83.15: 59 83.15 - 103.94: 18 Dihedral angle restraints: 24815 sinusoidal: 10031 harmonic: 14784 Sorted by residual: dihedral pdb=" N ILE I 350 " pdb=" C ILE I 350 " pdb=" CA ILE I 350 " pdb=" CB ILE I 350 " ideal model delta harmonic sigma weight residual 123.40 144.98 -21.58 0 2.50e+00 1.60e-01 7.45e+01 dihedral pdb=" CA ALA F 283 " pdb=" C ALA F 283 " pdb=" N LEU F 284 " pdb=" CA LEU F 284 " ideal model delta harmonic sigma weight residual 180.00 137.21 42.79 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" C ILE I 350 " pdb=" N ILE I 350 " pdb=" CA ILE I 350 " pdb=" CB ILE I 350 " ideal model delta harmonic sigma weight residual -122.00 -140.94 18.94 0 2.50e+00 1.60e-01 5.74e+01 ... (remaining 24812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 4998 0.180 - 0.360: 1321 0.360 - 0.541: 192 0.541 - 0.721: 30 0.721 - 0.901: 8 Chirality restraints: 6549 Sorted by residual: chirality pdb=" CB VAL E 180 " pdb=" CA VAL E 180 " pdb=" CG1 VAL E 180 " pdb=" CG2 VAL E 180 " both_signs ideal model delta sigma weight residual False -2.63 -1.73 -0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" CB THR G 293 " pdb=" CA THR G 293 " pdb=" OG1 THR G 293 " pdb=" CG2 THR G 293 " both_signs ideal model delta sigma weight residual False 2.55 1.66 0.90 2.00e-01 2.50e+01 2.01e+01 chirality pdb=" CB VAL I 165 " pdb=" CA VAL I 165 " pdb=" CG1 VAL I 165 " pdb=" CG2 VAL I 165 " both_signs ideal model delta sigma weight residual False -2.63 -1.76 -0.86 2.00e-01 2.50e+01 1.87e+01 ... (remaining 6546 not shown) Planarity restraints: 6897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U N 24 " 0.175 2.00e-02 2.50e+03 8.53e-02 1.64e+02 pdb=" N1 U N 24 " -0.050 2.00e-02 2.50e+03 pdb=" C2 U N 24 " -0.055 2.00e-02 2.50e+03 pdb=" O2 U N 24 " -0.029 2.00e-02 2.50e+03 pdb=" N3 U N 24 " -0.044 2.00e-02 2.50e+03 pdb=" C4 U N 24 " 0.023 2.00e-02 2.50e+03 pdb=" O4 U N 24 " 0.123 2.00e-02 2.50e+03 pdb=" C5 U N 24 " -0.056 2.00e-02 2.50e+03 pdb=" C6 U N 24 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U N 70 " -0.172 2.00e-02 2.50e+03 7.86e-02 1.39e+02 pdb=" N1 U N 70 " 0.102 2.00e-02 2.50e+03 pdb=" C2 U N 70 " 0.050 2.00e-02 2.50e+03 pdb=" O2 U N 70 " 0.035 2.00e-02 2.50e+03 pdb=" N3 U N 70 " -0.018 2.00e-02 2.50e+03 pdb=" C4 U N 70 " -0.025 2.00e-02 2.50e+03 pdb=" O4 U N 70 " -0.067 2.00e-02 2.50e+03 pdb=" C5 U N 70 " 0.015 2.00e-02 2.50e+03 pdb=" C6 U N 70 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U N 68 " 0.123 2.00e-02 2.50e+03 6.70e-02 1.01e+02 pdb=" N1 U N 68 " 0.007 2.00e-02 2.50e+03 pdb=" C2 U N 68 " -0.012 2.00e-02 2.50e+03 pdb=" O2 U N 68 " -0.091 2.00e-02 2.50e+03 pdb=" N3 U N 68 " 0.036 2.00e-02 2.50e+03 pdb=" C4 U N 68 " 0.011 2.00e-02 2.50e+03 pdb=" O4 U N 68 " 0.070 2.00e-02 2.50e+03 pdb=" C5 U N 68 " -0.064 2.00e-02 2.50e+03 pdb=" C6 U N 68 " -0.080 2.00e-02 2.50e+03 ... (remaining 6894 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 56 2.49 - 3.09: 29881 3.09 - 3.70: 65346 3.70 - 4.30: 96614 4.30 - 4.90: 151303 Nonbonded interactions: 343200 Sorted by model distance: nonbonded pdb=" NZ LYS F 295 " pdb=" O ILE G 4 " model vdw 1.889 2.520 nonbonded pdb=" O GLN E 376 " pdb=" OD1 ASN F 285 " model vdw 2.010 3.040 nonbonded pdb=" NE2 GLN C 199 " pdb=" O2 U N 20 " model vdw 2.092 2.520 nonbonded pdb=" NH2 ARG C 343 " pdb=" O GLY D 353 " model vdw 2.205 2.520 nonbonded pdb=" NH1 ARG J 352 " pdb=" OP2 U N 56 " model vdw 2.224 2.520 ... (remaining 343195 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' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'B' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'C' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'D' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'E' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'F' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'G' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'H' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'I' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'J' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'K' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'L' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'M' and resid 4 through 397) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.930 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 107.200 Find NCS groups from input model: 3.180 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 0.013 0.158 41016 Z= 0.849 Angle : 2.204 18.592 55861 Z= 1.409 Chirality : 0.164 0.901 6549 Planarity : 0.014 0.102 6897 Dihedral : 15.268 103.941 15277 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.32 % Favored : 96.50 % Rotamer Outliers : 1.47 % Cbeta Deviations : 4.40 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.10), residues: 5088 helix: -1.47 (0.08), residues: 3117 sheet: -1.50 (0.32), residues: 184 loop : -1.45 (0.14), residues: 1787 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1374 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1317 time to evaluate : 4.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 9 residues processed: 1357 average time/residue: 0.5925 time to fit residues: 1240.7898 Evaluate side-chains 807 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 798 time to evaluate : 4.517 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4169 time to fit residues: 12.5904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 433 optimal weight: 7.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 402 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 299 optimal weight: 0.9980 chunk 465 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 319 GLN B 15 GLN B 109 ASN B 200 GLN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN C 171 GLN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN C 364 GLN ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN D 364 GLN E 171 GLN E 223 GLN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 212 GLN F 219 ASN F 257 ASN G 15 GLN G 200 GLN H 288 GLN I 43 ASN I 109 ASN I 211 GLN K 15 GLN K 109 ASN L 15 GLN L 43 ASN ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 223 GLN ** L 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN M 93 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 41016 Z= 0.307 Angle : 0.749 8.838 55861 Z= 0.399 Chirality : 0.046 0.267 6549 Planarity : 0.005 0.052 6897 Dihedral : 7.758 94.821 6502 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.11), residues: 5088 helix: -0.03 (0.09), residues: 3053 sheet: -0.86 (0.32), residues: 186 loop : -1.00 (0.14), residues: 1849 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 873 time to evaluate : 4.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 63 residues processed: 949 average time/residue: 0.5823 time to fit residues: 893.8842 Evaluate side-chains 770 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 707 time to evaluate : 4.593 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.3776 time to fit residues: 51.7490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 258 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 387 optimal weight: 30.0000 chunk 317 optimal weight: 7.9990 chunk 128 optimal weight: 0.6980 chunk 466 optimal weight: 20.0000 chunk 504 optimal weight: 40.0000 chunk 415 optimal weight: 1.9990 chunk 462 optimal weight: 9.9990 chunk 159 optimal weight: 0.4980 chunk 374 optimal weight: 8.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN B 43 ASN B 109 ASN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN C 212 GLN C 292 ASN D 212 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 285 ASN F 285 ASN G 93 ASN ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 ASN I 257 ASN I 288 GLN J 211 GLN K 171 GLN ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 211 GLN L 257 ASN ** L 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 ASN ** M 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 41016 Z= 0.225 Angle : 0.646 9.449 55861 Z= 0.342 Chirality : 0.042 0.286 6549 Planarity : 0.004 0.054 6897 Dihedral : 7.316 91.448 6502 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.11), residues: 5088 helix: 0.32 (0.09), residues: 3060 sheet: -0.61 (0.34), residues: 184 loop : -0.80 (0.14), residues: 1844 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 789 time to evaluate : 5.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 36 residues processed: 839 average time/residue: 0.5445 time to fit residues: 738.9169 Evaluate side-chains 705 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 669 time to evaluate : 4.716 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3879 time to fit residues: 32.0483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 461 optimal weight: 8.9990 chunk 350 optimal weight: 40.0000 chunk 242 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 222 optimal weight: 1.9990 chunk 313 optimal weight: 0.9980 chunk 468 optimal weight: 10.0000 chunk 495 optimal weight: 7.9990 chunk 244 optimal weight: 0.6980 chunk 443 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN B 292 ASN C 212 GLN E 292 ASN G 93 ASN ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 ASN I 211 GLN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 257 ASN ** L 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 41016 Z= 0.189 Angle : 0.602 10.558 55861 Z= 0.317 Chirality : 0.041 0.222 6549 Planarity : 0.004 0.053 6897 Dihedral : 7.135 91.292 6502 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.12), residues: 5088 helix: 0.56 (0.09), residues: 3013 sheet: -0.50 (0.35), residues: 184 loop : -0.51 (0.14), residues: 1891 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 759 time to evaluate : 4.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 25 residues processed: 804 average time/residue: 0.5462 time to fit residues: 714.1531 Evaluate side-chains 700 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 675 time to evaluate : 4.331 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3688 time to fit residues: 23.3960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 412 optimal weight: 1.9990 chunk 281 optimal weight: 0.0570 chunk 7 optimal weight: 20.0000 chunk 369 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 423 optimal weight: 10.0000 chunk 342 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 253 optimal weight: 2.9990 chunk 445 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN C 319 GLN ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 GLN K 93 ASN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 ASN M 364 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 41016 Z= 0.250 Angle : 0.633 11.388 55861 Z= 0.331 Chirality : 0.042 0.320 6549 Planarity : 0.004 0.055 6897 Dihedral : 7.105 92.008 6502 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.12), residues: 5088 helix: 0.58 (0.09), residues: 3032 sheet: -0.49 (0.35), residues: 184 loop : -0.68 (0.14), residues: 1872 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 716 time to evaluate : 4.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 31 residues processed: 769 average time/residue: 0.5334 time to fit residues: 669.5187 Evaluate side-chains 700 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 669 time to evaluate : 4.624 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3915 time to fit residues: 28.3943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.296 > 50: distance: 46 - 51: 7.393 distance: 51 - 52: 10.330 distance: 52 - 53: 7.575 distance: 52 - 55: 11.347 distance: 53 - 54: 30.471 distance: 53 - 59: 24.565 distance: 55 - 56: 14.885 distance: 56 - 57: 11.216 distance: 56 - 58: 10.873 distance: 59 - 60: 13.616 distance: 60 - 61: 11.882 distance: 60 - 63: 22.172 distance: 61 - 62: 29.753 distance: 61 - 66: 19.656 distance: 63 - 64: 3.147 distance: 63 - 65: 14.630 distance: 66 - 67: 22.532 distance: 67 - 68: 4.819 distance: 68 - 69: 14.366 distance: 68 - 70: 11.639 distance: 70 - 71: 10.931 distance: 71 - 72: 12.212 distance: 71 - 74: 7.235 distance: 72 - 73: 42.002 distance: 72 - 76: 39.550 distance: 74 - 75: 12.660 distance: 76 - 77: 22.080 distance: 77 - 78: 10.246 distance: 77 - 80: 16.648 distance: 78 - 79: 19.694 distance: 78 - 84: 30.537 distance: 80 - 81: 25.574 distance: 81 - 82: 7.723 distance: 82 - 83: 11.949 distance: 84 - 85: 20.090 distance: 85 - 86: 6.330 distance: 85 - 88: 31.099 distance: 86 - 87: 16.612 distance: 86 - 91: 12.408 distance: 88 - 89: 9.196 distance: 88 - 90: 6.570 distance: 91 - 92: 5.835 distance: 92 - 93: 19.944 distance: 93 - 94: 53.707 distance: 93 - 99: 3.123 distance: 95 - 96: 22.481 distance: 96 - 97: 25.194 distance: 96 - 98: 6.618 distance: 99 - 100: 7.948 distance: 100 - 101: 46.237 distance: 101 - 102: 14.252 distance: 101 - 103: 34.173 distance: 103 - 104: 14.786 distance: 104 - 105: 18.037 distance: 104 - 107: 37.579 distance: 105 - 106: 17.961 distance: 105 - 111: 31.362 distance: 107 - 108: 29.884 distance: 107 - 109: 23.423 distance: 108 - 110: 31.946 distance: 111 - 112: 25.671 distance: 111 - 117: 22.325 distance: 112 - 113: 27.243 distance: 112 - 115: 33.376 distance: 113 - 114: 24.182 distance: 113 - 118: 21.205 distance: 115 - 116: 24.734 distance: 116 - 117: 16.060