Starting phenix.real_space_refine on Tue Dec 12 03:17:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k57_22676/12_2023/7k57_22676.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k57_22676/12_2023/7k57_22676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k57_22676/12_2023/7k57_22676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k57_22676/12_2023/7k57_22676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k57_22676/12_2023/7k57_22676.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k57_22676/12_2023/7k57_22676.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 372 5.16 5 C 44088 2.51 5 N 12360 2.21 5 O 13284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 29": "OD1" <-> "OD2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A ASP 55": "OD1" <-> "OD2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ASP 630": "OD1" <-> "OD2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "A PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B ASP 55": "OD1" <-> "OD2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B ASP 368": "OD1" <-> "OD2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B ASP 630": "OD1" <-> "OD2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B GLU 724": "OE1" <-> "OE2" Residue "B ASP 749": "OD1" <-> "OD2" Residue "B PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ASP 55": "OD1" <-> "OD2" Residue "C ASP 75": "OD1" <-> "OD2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C GLU 578": "OE1" <-> "OE2" Residue "C ARG 625": "NH1" <-> "NH2" Residue "C ASP 630": "OD1" <-> "OD2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C GLU 724": "OE1" <-> "OE2" Residue "C ASP 749": "OD1" <-> "OD2" Residue "C PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D ASP 79": "OD1" <-> "OD2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D GLU 417": "OE1" <-> "OE2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D ARG 625": "NH1" <-> "NH2" Residue "D ASP 630": "OD1" <-> "OD2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D GLU 724": "OE1" <-> "OE2" Residue "D ASP 749": "OD1" <-> "OD2" Residue "D PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 29": "OD1" <-> "OD2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E ASP 55": "OD1" <-> "OD2" Residue "E ASP 75": "OD1" <-> "OD2" Residue "E ASP 79": "OD1" <-> "OD2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E GLU 141": "OE1" <-> "OE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E GLU 379": "OE1" <-> "OE2" Residue "E GLU 417": "OE1" <-> "OE2" Residue "E ARG 453": "NH1" <-> "NH2" Residue "E GLU 578": "OE1" <-> "OE2" Residue "E ARG 625": "NH1" <-> "NH2" Residue "E ASP 630": "OD1" <-> "OD2" Residue "E GLU 650": "OE1" <-> "OE2" Residue "E GLU 724": "OE1" <-> "OE2" Residue "E ASP 749": "OD1" <-> "OD2" Residue "E PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 29": "OD1" <-> "OD2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F ASP 55": "OD1" <-> "OD2" Residue "F ASP 75": "OD1" <-> "OD2" Residue "F ASP 79": "OD1" <-> "OD2" Residue "F ASP 98": "OD1" <-> "OD2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F ASP 368": "OD1" <-> "OD2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "F ARG 453": "NH1" <-> "NH2" Residue "F GLU 578": "OE1" <-> "OE2" Residue "F ARG 625": "NH1" <-> "NH2" Residue "F ASP 630": "OD1" <-> "OD2" Residue "F GLU 650": "OE1" <-> "OE2" Residue "F GLU 724": "OE1" <-> "OE2" Residue "F ASP 749": "OD1" <-> "OD2" Residue "F PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 29": "OD1" <-> "OD2" Residue "G GLU 30": "OE1" <-> "OE2" Residue "G ASP 55": "OD1" <-> "OD2" Residue "G ASP 75": "OD1" <-> "OD2" Residue "G ASP 79": "OD1" <-> "OD2" Residue "G ASP 98": "OD1" <-> "OD2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G GLU 187": "OE1" <-> "OE2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G GLU 321": "OE1" <-> "OE2" Residue "G ASP 368": "OD1" <-> "OD2" Residue "G GLU 379": "OE1" <-> "OE2" Residue "G GLU 417": "OE1" <-> "OE2" Residue "G ARG 453": "NH1" <-> "NH2" Residue "G GLU 578": "OE1" <-> "OE2" Residue "G ARG 625": "NH1" <-> "NH2" Residue "G ASP 630": "OD1" <-> "OD2" Residue "G GLU 650": "OE1" <-> "OE2" Residue "G GLU 724": "OE1" <-> "OE2" Residue "G ASP 749": "OD1" <-> "OD2" Residue "G PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 29": "OD1" <-> "OD2" Residue "H GLU 30": "OE1" <-> "OE2" Residue "H ASP 55": "OD1" <-> "OD2" Residue "H ASP 75": "OD1" <-> "OD2" Residue "H ASP 79": "OD1" <-> "OD2" Residue "H ASP 98": "OD1" <-> "OD2" Residue "H GLU 132": "OE1" <-> "OE2" Residue "H GLU 141": "OE1" <-> "OE2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "H GLU 321": "OE1" <-> "OE2" Residue "H ASP 368": "OD1" <-> "OD2" Residue "H GLU 379": "OE1" <-> "OE2" Residue "H GLU 417": "OE1" <-> "OE2" Residue "H ARG 453": "NH1" <-> "NH2" Residue "H GLU 578": "OE1" <-> "OE2" Residue "H ARG 625": "NH1" <-> "NH2" Residue "H ASP 630": "OD1" <-> "OD2" Residue "H GLU 650": "OE1" <-> "OE2" Residue "H GLU 724": "OE1" <-> "OE2" Residue "H ASP 749": "OD1" <-> "OD2" Residue "H PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 29": "OD1" <-> "OD2" Residue "I GLU 30": "OE1" <-> "OE2" Residue "I ASP 55": "OD1" <-> "OD2" Residue "I ASP 75": "OD1" <-> "OD2" Residue "I ASP 79": "OD1" <-> "OD2" Residue "I ASP 98": "OD1" <-> "OD2" Residue "I GLU 132": "OE1" <-> "OE2" Residue "I GLU 141": "OE1" <-> "OE2" Residue "I GLU 187": "OE1" <-> "OE2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I GLU 321": "OE1" <-> "OE2" Residue "I ASP 368": "OD1" <-> "OD2" Residue "I GLU 379": "OE1" <-> "OE2" Residue "I GLU 417": "OE1" <-> "OE2" Residue "I ARG 453": "NH1" <-> "NH2" Residue "I GLU 578": "OE1" <-> "OE2" Residue "I ARG 625": "NH1" <-> "NH2" Residue "I ASP 630": "OD1" <-> "OD2" Residue "I GLU 650": "OE1" <-> "OE2" Residue "I GLU 724": "OE1" <-> "OE2" Residue "I ASP 749": "OD1" <-> "OD2" Residue "I PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 29": "OD1" <-> "OD2" Residue "J GLU 30": "OE1" <-> "OE2" Residue "J ASP 55": "OD1" <-> "OD2" Residue "J ASP 75": "OD1" <-> "OD2" Residue "J ASP 79": "OD1" <-> "OD2" Residue "J ASP 98": "OD1" <-> "OD2" Residue "J GLU 132": "OE1" <-> "OE2" Residue "J GLU 141": "OE1" <-> "OE2" Residue "J GLU 187": "OE1" <-> "OE2" Residue "J GLU 218": "OE1" <-> "OE2" Residue "J GLU 321": "OE1" <-> "OE2" Residue "J ASP 368": "OD1" <-> "OD2" Residue "J GLU 379": "OE1" <-> "OE2" Residue "J GLU 417": "OE1" <-> "OE2" Residue "J ARG 453": "NH1" <-> "NH2" Residue "J GLU 578": "OE1" <-> "OE2" Residue "J ARG 625": "NH1" <-> "NH2" Residue "J ASP 630": "OD1" <-> "OD2" Residue "J GLU 650": "OE1" <-> "OE2" Residue "J GLU 724": "OE1" <-> "OE2" Residue "J ASP 749": "OD1" <-> "OD2" Residue "J PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 29": "OD1" <-> "OD2" Residue "K GLU 30": "OE1" <-> "OE2" Residue "K ASP 55": "OD1" <-> "OD2" Residue "K ASP 75": "OD1" <-> "OD2" Residue "K ASP 79": "OD1" <-> "OD2" Residue "K ASP 98": "OD1" <-> "OD2" Residue "K GLU 132": "OE1" <-> "OE2" Residue "K GLU 141": "OE1" <-> "OE2" Residue "K GLU 187": "OE1" <-> "OE2" Residue "K GLU 218": "OE1" <-> "OE2" Residue "K GLU 321": "OE1" <-> "OE2" Residue "K ASP 368": "OD1" <-> "OD2" Residue "K GLU 379": "OE1" <-> "OE2" Residue "K GLU 417": "OE1" <-> "OE2" Residue "K ARG 453": "NH1" <-> "NH2" Residue "K GLU 578": "OE1" <-> "OE2" Residue "K ARG 625": "NH1" <-> "NH2" Residue "K ASP 630": "OD1" <-> "OD2" Residue "K GLU 650": "OE1" <-> "OE2" Residue "K GLU 724": "OE1" <-> "OE2" Residue "K ASP 749": "OD1" <-> "OD2" Residue "K PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 29": "OD1" <-> "OD2" Residue "L GLU 30": "OE1" <-> "OE2" Residue "L ASP 55": "OD1" <-> "OD2" Residue "L ASP 75": "OD1" <-> "OD2" Residue "L ASP 79": "OD1" <-> "OD2" Residue "L ASP 98": "OD1" <-> "OD2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L GLU 218": "OE1" <-> "OE2" Residue "L GLU 321": "OE1" <-> "OE2" Residue "L ASP 368": "OD1" <-> "OD2" Residue "L GLU 379": "OE1" <-> "OE2" Residue "L GLU 417": "OE1" <-> "OE2" Residue "L ARG 453": "NH1" <-> "NH2" Residue "L GLU 578": "OE1" <-> "OE2" Residue "L ARG 625": "NH1" <-> "NH2" Residue "L ASP 630": "OD1" <-> "OD2" Residue "L GLU 650": "OE1" <-> "OE2" Residue "L GLU 724": "OE1" <-> "OE2" Residue "L ASP 749": "OD1" <-> "OD2" Residue "L PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 70104 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "B" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "C" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "D" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "E" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "F" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "G" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "H" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "I" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "J" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "K" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "L" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Time building chain proxies: 27.36, per 1000 atoms: 0.39 Number of scatterers: 70104 At special positions: 0 Unit cell: (178.538, 178.538, 218.903, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 372 16.00 O 13284 8.00 N 12360 7.00 C 44088 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: 20.44 Conformation dependent library (CDL) restraints added in 10.1 seconds 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16728 Finding SS restraints... Secondary structure from input PDB file: 408 helices and 72 sheets defined 42.9% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.79 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 removed outlier: 4.136A pdb=" N ARG A 64 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 135 through 140 removed outlier: 4.449A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.656A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.552A pdb=" N ILE A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.701A pdb=" N ARG A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.584A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE A 479 " --> pdb=" O TRP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 4.183A pdb=" N ALA A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 569 removed outlier: 3.887A pdb=" N ALA A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU A 607 " --> pdb=" O GLN A 603 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.666A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 660 Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 686 through 711 removed outlier: 3.654A pdb=" N ILE A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN A 692 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 709 " --> pdb=" O SER A 705 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 removed outlier: 4.231A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 4.136A pdb=" N ARG B 64 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 135 through 140 removed outlier: 4.449A pdb=" N LEU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 196 Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.567A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.214A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.554A pdb=" N ILE B 274 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 296 Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 319 through 334 Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU B 381 " --> pdb=" O ARG B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.583A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.518A pdb=" N ILE B 479 " --> pdb=" O TRP B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 494 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 535 removed outlier: 4.182A pdb=" N ALA B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR B 549 " --> pdb=" O PRO B 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 553 " --> pdb=" O THR B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 569 removed outlier: 3.887A pdb=" N ALA B 566 " --> pdb=" O ILE B 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU B 607 " --> pdb=" O GLN B 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.665A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 660 Processing helix chain 'B' and resid 672 through 677 Processing helix chain 'B' and resid 686 through 711 removed outlier: 3.654A pdb=" N ILE B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N CYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 709 " --> pdb=" O SER B 705 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 710 " --> pdb=" O GLU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 4.232A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 751 through 762 removed outlier: 3.650A pdb=" N TYR B 755 " --> pdb=" O ASP B 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 4.138A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 135 through 140 removed outlier: 4.450A pdb=" N LEU C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.569A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.212A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE C 274 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 306 through 309 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG C 358 " --> pdb=" O PRO C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 383 removed outlier: 3.712A pdb=" N LEU C 381 " --> pdb=" O ARG C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.583A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE C 479 " --> pdb=" O TRP C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 494 Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 535 removed outlier: 4.182A pdb=" N ALA C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR C 549 " --> pdb=" O PRO C 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 553 " --> pdb=" O THR C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 569 removed outlier: 3.888A pdb=" N ALA C 566 " --> pdb=" O ILE C 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 609 removed outlier: 3.581A pdb=" N GLU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.666A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 660 Processing helix chain 'C' and resid 672 through 677 Processing helix chain 'C' and resid 686 through 711 removed outlier: 3.654A pdb=" N ILE C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN C 692 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS C 695 " --> pdb=" O CYS C 691 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 707 " --> pdb=" O ILE C 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG C 708 " --> pdb=" O GLU C 704 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 709 " --> pdb=" O SER C 705 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 removed outlier: 4.232A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 743 No H-bonds generated for 'chain 'C' and resid 741 through 743' Processing helix chain 'C' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 removed outlier: 4.137A pdb=" N ARG D 64 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 135 through 140 removed outlier: 4.450A pdb=" N LEU D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 196 Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.567A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE D 274 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 296 Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 334 Processing helix chain 'D' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG D 358 " --> pdb=" O PRO D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU D 381 " --> pdb=" O ARG D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 407 through 425 Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.584A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE D 479 " --> pdb=" O TRP D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 494 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 535 removed outlier: 4.182A pdb=" N ALA D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.606A pdb=" N THR D 549 " --> pdb=" O PRO D 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY D 553 " --> pdb=" O THR D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 569 removed outlier: 3.888A pdb=" N ALA D 566 " --> pdb=" O ILE D 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 569 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.665A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 660 Processing helix chain 'D' and resid 672 through 677 Processing helix chain 'D' and resid 686 through 711 removed outlier: 3.653A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS D 691 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN D 692 " --> pdb=" O THR D 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS D 695 " --> pdb=" O CYS D 691 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 707 " --> pdb=" O ILE D 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG D 708 " --> pdb=" O GLU D 704 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG D 709 " --> pdb=" O SER D 705 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 710 " --> pdb=" O GLU D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 removed outlier: 4.231A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 751 through 762 removed outlier: 3.648A pdb=" N TYR D 755 " --> pdb=" O ASP D 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 4.138A pdb=" N ARG E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 135 through 140 removed outlier: 4.449A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.656A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 261 Processing helix chain 'E' and resid 271 through 275 removed outlier: 3.552A pdb=" N ILE E 274 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 296 Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG E 358 " --> pdb=" O PRO E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU E 381 " --> pdb=" O ARG E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 407 through 425 Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.584A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER E 459 " --> pdb=" O ALA E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE E 479 " --> pdb=" O TRP E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 494 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 535 removed outlier: 4.183A pdb=" N ALA E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR E 549 " --> pdb=" O PRO E 545 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY E 553 " --> pdb=" O THR E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 569 removed outlier: 3.887A pdb=" N ALA E 566 " --> pdb=" O ILE E 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 569 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU E 607 " --> pdb=" O GLN E 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.666A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 660 Processing helix chain 'E' and resid 672 through 677 Processing helix chain 'E' and resid 686 through 711 removed outlier: 3.653A pdb=" N ILE E 690 " --> pdb=" O ASP E 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS E 691 " --> pdb=" O LEU E 687 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN E 692 " --> pdb=" O THR E 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS E 695 " --> pdb=" O CYS E 691 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU E 701 " --> pdb=" O LEU E 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE E 707 " --> pdb=" O ILE E 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG E 708 " --> pdb=" O GLU E 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG E 709 " --> pdb=" O SER E 705 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E 710 " --> pdb=" O GLU E 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 removed outlier: 4.231A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR E 755 " --> pdb=" O ASP E 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 65 removed outlier: 4.137A pdb=" N ARG F 64 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 130 through 135 Processing helix chain 'F' and resid 135 through 140 removed outlier: 4.449A pdb=" N LEU F 140 " --> pdb=" O LYS F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.567A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 261 Processing helix chain 'F' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE F 274 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 296 Processing helix chain 'F' and resid 306 through 309 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'F' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG F 358 " --> pdb=" O PRO F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU F 381 " --> pdb=" O ARG F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 407 through 425 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.584A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER F 459 " --> pdb=" O ALA F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 removed outlier: 3.518A pdb=" N ILE F 479 " --> pdb=" O TRP F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 494 Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 535 removed outlier: 4.182A pdb=" N ALA F 530 " --> pdb=" O LEU F 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR F 549 " --> pdb=" O PRO F 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY F 553 " --> pdb=" O THR F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 569 removed outlier: 3.888A pdb=" N ALA F 566 " --> pdb=" O ILE F 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA F 569 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU F 607 " --> pdb=" O GLN F 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP F 609 " --> pdb=" O LEU F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.665A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 660 Processing helix chain 'F' and resid 672 through 677 Processing helix chain 'F' and resid 686 through 711 removed outlier: 3.653A pdb=" N ILE F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN F 692 " --> pdb=" O THR F 688 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N CYS F 695 " --> pdb=" O CYS F 691 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE F 707 " --> pdb=" O ILE F 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG F 708 " --> pdb=" O GLU F 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG F 709 " --> pdb=" O SER F 705 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F 710 " --> pdb=" O GLU F 706 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 740 removed outlier: 4.232A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 743 No H-bonds generated for 'chain 'F' and resid 741 through 743' Processing helix chain 'F' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR F 755 " --> pdb=" O ASP F 751 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 65 removed outlier: 4.137A pdb=" N ARG G 64 " --> pdb=" O GLY G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 92 Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'G' and resid 135 through 140 removed outlier: 4.449A pdb=" N LEU G 140 " --> pdb=" O LYS G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 Processing helix chain 'G' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE G 206 " --> pdb=" O TYR G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU G 222 " --> pdb=" O GLU G 218 " (cutoff:3.500A) Proline residue: G 223 - end of helix Processing helix chain 'G' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE G 230 " --> pdb=" O HIS G 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS G 231 " --> pdb=" O PRO G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 261 Processing helix chain 'G' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE G 274 " --> pdb=" O GLY G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 306 through 309 Processing helix chain 'G' and resid 312 through 316 Processing helix chain 'G' and resid 319 through 334 Processing helix chain 'G' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG G 358 " --> pdb=" O PRO G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU G 381 " --> pdb=" O ARG G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 402 Processing helix chain 'G' and resid 407 through 425 Processing helix chain 'G' and resid 448 through 459 removed outlier: 3.583A pdb=" N PHE G 452 " --> pdb=" O THR G 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER G 459 " --> pdb=" O ALA G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE G 479 " --> pdb=" O TRP G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 482 through 494 Processing helix chain 'G' and resid 494 through 499 Processing helix chain 'G' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE G 506 " --> pdb=" O LYS G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 535 removed outlier: 4.183A pdb=" N ALA G 530 " --> pdb=" O LEU G 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE G 531 " --> pdb=" O LEU G 527 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA G 532 " --> pdb=" O ALA G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR G 549 " --> pdb=" O PRO G 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET G 550 " --> pdb=" O GLU G 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP G 551 " --> pdb=" O LEU G 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY G 553 " --> pdb=" O THR G 549 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 569 removed outlier: 3.887A pdb=" N ALA G 566 " --> pdb=" O ILE G 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA G 569 " --> pdb=" O LYS G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU G 607 " --> pdb=" O GLN G 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP G 609 " --> pdb=" O LEU G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 630 through 635 removed outlier: 3.665A pdb=" N ARG G 635 " --> pdb=" O ALA G 632 " (cutoff:3.500A) Processing helix chain 'G' and resid 649 through 660 Processing helix chain 'G' and resid 672 through 677 Processing helix chain 'G' and resid 686 through 711 removed outlier: 3.653A pdb=" N ILE G 690 " --> pdb=" O ASP G 686 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS G 691 " --> pdb=" O LEU G 687 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN G 692 " --> pdb=" O THR G 688 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N CYS G 695 " --> pdb=" O CYS G 691 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU G 701 " --> pdb=" O LEU G 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU G 706 " --> pdb=" O SER G 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE G 707 " --> pdb=" O ILE G 703 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG G 708 " --> pdb=" O GLU G 704 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG G 709 " --> pdb=" O SER G 705 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU G 710 " --> pdb=" O GLU G 706 " (cutoff:3.500A) Processing helix chain 'G' and resid 732 through 740 removed outlier: 4.232A pdb=" N PHE G 736 " --> pdb=" O ARG G 732 " (cutoff:3.500A) Processing helix chain 'G' and resid 741 through 743 No H-bonds generated for 'chain 'G' and resid 741 through 743' Processing helix chain 'G' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR G 755 " --> pdb=" O ASP G 751 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.137A pdb=" N ARG H 64 " --> pdb=" O GLY H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 92 Processing helix chain 'H' and resid 130 through 135 Processing helix chain 'H' and resid 135 through 140 removed outlier: 4.449A pdb=" N LEU H 140 " --> pdb=" O LYS H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 196 Processing helix chain 'H' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE H 206 " --> pdb=" O TYR H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU H 222 " --> pdb=" O GLU H 218 " (cutoff:3.500A) Proline residue: H 223 - end of helix Processing helix chain 'H' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE H 230 " --> pdb=" O HIS H 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS H 231 " --> pdb=" O PRO H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 261 Processing helix chain 'H' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE H 274 " --> pdb=" O GLY H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 296 Processing helix chain 'H' and resid 306 through 309 Processing helix chain 'H' and resid 312 through 316 Processing helix chain 'H' and resid 319 through 334 Processing helix chain 'H' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG H 358 " --> pdb=" O PRO H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU H 381 " --> pdb=" O ARG H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 402 Processing helix chain 'H' and resid 407 through 425 Processing helix chain 'H' and resid 448 through 459 removed outlier: 3.584A pdb=" N PHE H 452 " --> pdb=" O THR H 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER H 459 " --> pdb=" O ALA H 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE H 479 " --> pdb=" O TRP H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 482 through 494 Processing helix chain 'H' and resid 494 through 499 Processing helix chain 'H' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE H 506 " --> pdb=" O LYS H 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 524 through 535 removed outlier: 4.183A pdb=" N ALA H 530 " --> pdb=" O LEU H 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE H 531 " --> pdb=" O LEU H 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA H 532 " --> pdb=" O ALA H 528 " (cutoff:3.500A) Processing helix chain 'H' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR H 549 " --> pdb=" O PRO H 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET H 550 " --> pdb=" O GLU H 546 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP H 551 " --> pdb=" O LEU H 547 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY H 553 " --> pdb=" O THR H 549 " (cutoff:3.500A) Processing helix chain 'H' and resid 559 through 569 removed outlier: 3.888A pdb=" N ALA H 566 " --> pdb=" O ILE H 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA H 569 " --> pdb=" O LYS H 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU H 607 " --> pdb=" O GLN H 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP H 609 " --> pdb=" O LEU H 605 " (cutoff:3.500A) Processing helix chain 'H' and resid 630 through 635 removed outlier: 3.666A pdb=" N ARG H 635 " --> pdb=" O ALA H 632 " (cutoff:3.500A) Processing helix chain 'H' and resid 649 through 660 Processing helix chain 'H' and resid 672 through 677 Processing helix chain 'H' and resid 686 through 711 removed outlier: 3.653A pdb=" N ILE H 690 " --> pdb=" O ASP H 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS H 691 " --> pdb=" O LEU H 687 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN H 692 " --> pdb=" O THR H 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS H 695 " --> pdb=" O CYS H 691 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU H 701 " --> pdb=" O LEU H 697 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU H 706 " --> pdb=" O SER H 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE H 707 " --> pdb=" O ILE H 703 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG H 708 " --> pdb=" O GLU H 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG H 709 " --> pdb=" O SER H 705 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU H 710 " --> pdb=" O GLU H 706 " (cutoff:3.500A) Processing helix chain 'H' and resid 732 through 740 removed outlier: 4.232A pdb=" N PHE H 736 " --> pdb=" O ARG H 732 " (cutoff:3.500A) Processing helix chain 'H' and resid 741 through 743 No H-bonds generated for 'chain 'H' and resid 741 through 743' Processing helix chain 'H' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR H 755 " --> pdb=" O ASP H 751 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 65 removed outlier: 4.137A pdb=" N ARG I 64 " --> pdb=" O GLY I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 92 Processing helix chain 'I' and resid 130 through 135 Processing helix chain 'I' and resid 135 through 140 removed outlier: 4.450A pdb=" N LEU I 140 " --> pdb=" O LYS I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 196 Processing helix chain 'I' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE I 206 " --> pdb=" O TYR I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 226 removed outlier: 4.656A pdb=" N LEU I 222 " --> pdb=" O GLU I 218 " (cutoff:3.500A) Proline residue: I 223 - end of helix Processing helix chain 'I' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE I 230 " --> pdb=" O HIS I 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS I 231 " --> pdb=" O PRO I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 261 Processing helix chain 'I' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE I 274 " --> pdb=" O GLY I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 296 Processing helix chain 'I' and resid 306 through 309 Processing helix chain 'I' and resid 312 through 316 Processing helix chain 'I' and resid 319 through 334 Processing helix chain 'I' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG I 358 " --> pdb=" O PRO I 355 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU I 381 " --> pdb=" O ARG I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 402 Processing helix chain 'I' and resid 407 through 425 Processing helix chain 'I' and resid 448 through 459 removed outlier: 3.583A pdb=" N PHE I 452 " --> pdb=" O THR I 448 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER I 459 " --> pdb=" O ALA I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 479 removed outlier: 3.518A pdb=" N ILE I 479 " --> pdb=" O TRP I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 482 through 494 Processing helix chain 'I' and resid 494 through 499 Processing helix chain 'I' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE I 506 " --> pdb=" O LYS I 502 " (cutoff:3.500A) Processing helix chain 'I' and resid 524 through 535 removed outlier: 4.182A pdb=" N ALA I 530 " --> pdb=" O LEU I 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE I 531 " --> pdb=" O LEU I 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA I 532 " --> pdb=" O ALA I 528 " (cutoff:3.500A) Processing helix chain 'I' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR I 549 " --> pdb=" O PRO I 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET I 550 " --> pdb=" O GLU I 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP I 551 " --> pdb=" O LEU I 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY I 553 " --> pdb=" O THR I 549 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 569 removed outlier: 3.887A pdb=" N ALA I 566 " --> pdb=" O ILE I 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA I 569 " --> pdb=" O LYS I 565 " (cutoff:3.500A) Processing helix chain 'I' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU I 607 " --> pdb=" O GLN I 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP I 609 " --> pdb=" O LEU I 605 " (cutoff:3.500A) Processing helix chain 'I' and resid 630 through 635 removed outlier: 3.664A pdb=" N ARG I 635 " --> pdb=" O ALA I 632 " (cutoff:3.500A) Processing helix chain 'I' and resid 649 through 660 Processing helix chain 'I' and resid 672 through 677 Processing helix chain 'I' and resid 686 through 711 removed outlier: 3.654A pdb=" N ILE I 690 " --> pdb=" O ASP I 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS I 691 " --> pdb=" O LEU I 687 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN I 692 " --> pdb=" O THR I 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS I 695 " --> pdb=" O CYS I 691 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU I 701 " --> pdb=" O LEU I 697 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU I 706 " --> pdb=" O SER I 702 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE I 707 " --> pdb=" O ILE I 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG I 708 " --> pdb=" O GLU I 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG I 709 " --> pdb=" O SER I 705 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU I 710 " --> pdb=" O GLU I 706 " (cutoff:3.500A) Processing helix chain 'I' and resid 732 through 740 removed outlier: 4.231A pdb=" N PHE I 736 " --> pdb=" O ARG I 732 " (cutoff:3.500A) Processing helix chain 'I' and resid 741 through 743 No H-bonds generated for 'chain 'I' and resid 741 through 743' Processing helix chain 'I' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR I 755 " --> pdb=" O ASP I 751 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 65 removed outlier: 4.136A pdb=" N ARG J 64 " --> pdb=" O GLY J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 92 Processing helix chain 'J' and resid 130 through 135 Processing helix chain 'J' and resid 135 through 140 removed outlier: 4.449A pdb=" N LEU J 140 " --> pdb=" O LYS J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 196 Processing helix chain 'J' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE J 206 " --> pdb=" O TYR J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU J 222 " --> pdb=" O GLU J 218 " (cutoff:3.500A) Proline residue: J 223 - end of helix Processing helix chain 'J' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE J 230 " --> pdb=" O HIS J 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS J 231 " --> pdb=" O PRO J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 261 Processing helix chain 'J' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE J 274 " --> pdb=" O GLY J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 296 Processing helix chain 'J' and resid 306 through 309 Processing helix chain 'J' and resid 312 through 316 Processing helix chain 'J' and resid 319 through 334 Processing helix chain 'J' and resid 354 through 358 removed outlier: 3.701A pdb=" N ARG J 358 " --> pdb=" O PRO J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU J 381 " --> pdb=" O ARG J 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 402 Processing helix chain 'J' and resid 407 through 425 Processing helix chain 'J' and resid 448 through 459 removed outlier: 3.583A pdb=" N PHE J 452 " --> pdb=" O THR J 448 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER J 459 " --> pdb=" O ALA J 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE J 479 " --> pdb=" O TRP J 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 482 through 494 Processing helix chain 'J' and resid 494 through 499 Processing helix chain 'J' and resid 501 through 506 removed outlier: 3.914A pdb=" N PHE J 506 " --> pdb=" O LYS J 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 524 through 535 removed outlier: 4.181A pdb=" N ALA J 530 " --> pdb=" O LEU J 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE J 531 " --> pdb=" O LEU J 527 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA J 532 " --> pdb=" O ALA J 528 " (cutoff:3.500A) Processing helix chain 'J' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR J 549 " --> pdb=" O PRO J 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET J 550 " --> pdb=" O GLU J 546 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP J 551 " --> pdb=" O LEU J 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY J 553 " --> pdb=" O THR J 549 " (cutoff:3.500A) Processing helix chain 'J' and resid 559 through 569 removed outlier: 3.888A pdb=" N ALA J 566 " --> pdb=" O ILE J 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA J 569 " --> pdb=" O LYS J 565 " (cutoff:3.500A) Processing helix chain 'J' and resid 600 through 609 removed outlier: 3.581A pdb=" N GLU J 607 " --> pdb=" O GLN J 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP J 609 " --> pdb=" O LEU J 605 " (cutoff:3.500A) Processing helix chain 'J' and resid 630 through 635 removed outlier: 3.666A pdb=" N ARG J 635 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 660 Processing helix chain 'J' and resid 672 through 677 Processing helix chain 'J' and resid 686 through 711 removed outlier: 3.653A pdb=" N ILE J 690 " --> pdb=" O ASP J 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS J 691 " --> pdb=" O LEU J 687 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN J 692 " --> pdb=" O THR J 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS J 695 " --> pdb=" O CYS J 691 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU J 701 " --> pdb=" O LEU J 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU J 706 " --> pdb=" O SER J 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE J 707 " --> pdb=" O ILE J 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG J 708 " --> pdb=" O GLU J 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG J 709 " --> pdb=" O SER J 705 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU J 710 " --> pdb=" O GLU J 706 " (cutoff:3.500A) Processing helix chain 'J' and resid 732 through 740 removed outlier: 4.232A pdb=" N PHE J 736 " --> pdb=" O ARG J 732 " (cutoff:3.500A) Processing helix chain 'J' and resid 741 through 743 No H-bonds generated for 'chain 'J' and resid 741 through 743' Processing helix chain 'J' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR J 755 " --> pdb=" O ASP J 751 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 65 removed outlier: 4.137A pdb=" N ARG K 64 " --> pdb=" O GLY K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 92 Processing helix chain 'K' and resid 130 through 135 Processing helix chain 'K' and resid 135 through 140 removed outlier: 4.451A pdb=" N LEU K 140 " --> pdb=" O LYS K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 196 Processing helix chain 'K' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE K 206 " --> pdb=" O TYR K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 226 removed outlier: 4.654A pdb=" N LEU K 222 " --> pdb=" O GLU K 218 " (cutoff:3.500A) Proline residue: K 223 - end of helix Processing helix chain 'K' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE K 230 " --> pdb=" O HIS K 226 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS K 231 " --> pdb=" O PRO K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 261 Processing helix chain 'K' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE K 274 " --> pdb=" O GLY K 271 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 296 Processing helix chain 'K' and resid 306 through 309 Processing helix chain 'K' and resid 312 through 316 Processing helix chain 'K' and resid 319 through 334 Processing helix chain 'K' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG K 358 " --> pdb=" O PRO K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU K 381 " --> pdb=" O ARG K 377 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 402 Processing helix chain 'K' and resid 407 through 425 Processing helix chain 'K' and resid 448 through 459 removed outlier: 3.584A pdb=" N PHE K 452 " --> pdb=" O THR K 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER K 459 " --> pdb=" O ALA K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 475 through 479 removed outlier: 3.518A pdb=" N ILE K 479 " --> pdb=" O TRP K 476 " (cutoff:3.500A) Processing helix chain 'K' and resid 482 through 494 Processing helix chain 'K' and resid 494 through 499 Processing helix chain 'K' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE K 506 " --> pdb=" O LYS K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 524 through 535 removed outlier: 4.182A pdb=" N ALA K 530 " --> pdb=" O LEU K 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE K 531 " --> pdb=" O LEU K 527 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA K 532 " --> pdb=" O ALA K 528 " (cutoff:3.500A) Processing helix chain 'K' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR K 549 " --> pdb=" O PRO K 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET K 550 " --> pdb=" O GLU K 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP K 551 " --> pdb=" O LEU K 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY K 553 " --> pdb=" O THR K 549 " (cutoff:3.500A) Processing helix chain 'K' and resid 559 through 569 removed outlier: 3.887A pdb=" N ALA K 566 " --> pdb=" O ILE K 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA K 569 " --> pdb=" O LYS K 565 " (cutoff:3.500A) Processing helix chain 'K' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU K 607 " --> pdb=" O GLN K 603 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP K 609 " --> pdb=" O LEU K 605 " (cutoff:3.500A) Processing helix chain 'K' and resid 630 through 635 removed outlier: 3.665A pdb=" N ARG K 635 " --> pdb=" O ALA K 632 " (cutoff:3.500A) Processing helix chain 'K' and resid 649 through 660 Processing helix chain 'K' and resid 672 through 677 Processing helix chain 'K' and resid 686 through 711 removed outlier: 3.653A pdb=" N ILE K 690 " --> pdb=" O ASP K 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS K 691 " --> pdb=" O LEU K 687 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN K 692 " --> pdb=" O THR K 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS K 695 " --> pdb=" O CYS K 691 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU K 701 " --> pdb=" O LEU K 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU K 706 " --> pdb=" O SER K 702 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE K 707 " --> pdb=" O ILE K 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG K 708 " --> pdb=" O GLU K 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG K 709 " --> pdb=" O SER K 705 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU K 710 " --> pdb=" O GLU K 706 " (cutoff:3.500A) Processing helix chain 'K' and resid 732 through 740 removed outlier: 4.231A pdb=" N PHE K 736 " --> pdb=" O ARG K 732 " (cutoff:3.500A) Processing helix chain 'K' and resid 741 through 743 No H-bonds generated for 'chain 'K' and resid 741 through 743' Processing helix chain 'K' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR K 755 " --> pdb=" O ASP K 751 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 removed outlier: 4.137A pdb=" N ARG L 64 " --> pdb=" O GLY L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 92 Processing helix chain 'L' and resid 130 through 135 Processing helix chain 'L' and resid 135 through 140 removed outlier: 4.450A pdb=" N LEU L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 196 Processing helix chain 'L' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE L 206 " --> pdb=" O TYR L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU L 222 " --> pdb=" O GLU L 218 " (cutoff:3.500A) Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE L 230 " --> pdb=" O HIS L 226 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS L 231 " --> pdb=" O PRO L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 261 Processing helix chain 'L' and resid 271 through 275 removed outlier: 3.552A pdb=" N ILE L 274 " --> pdb=" O GLY L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 281 through 296 Processing helix chain 'L' and resid 306 through 309 Processing helix chain 'L' and resid 312 through 316 Processing helix chain 'L' and resid 319 through 334 Processing helix chain 'L' and resid 354 through 358 removed outlier: 3.701A pdb=" N ARG L 358 " --> pdb=" O PRO L 355 " (cutoff:3.500A) Processing helix chain 'L' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU L 381 " --> pdb=" O ARG L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 395 through 402 Processing helix chain 'L' and resid 407 through 425 Processing helix chain 'L' and resid 448 through 459 removed outlier: 3.583A pdb=" N PHE L 452 " --> pdb=" O THR L 448 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER L 459 " --> pdb=" O ALA L 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE L 479 " --> pdb=" O TRP L 476 " (cutoff:3.500A) Processing helix chain 'L' and resid 482 through 494 Processing helix chain 'L' and resid 494 through 499 Processing helix chain 'L' and resid 501 through 506 removed outlier: 3.912A pdb=" N PHE L 506 " --> pdb=" O LYS L 502 " (cutoff:3.500A) Processing helix chain 'L' and resid 524 through 535 removed outlier: 4.182A pdb=" N ALA L 530 " --> pdb=" O LEU L 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE L 531 " --> pdb=" O LEU L 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA L 532 " --> pdb=" O ALA L 528 " (cutoff:3.500A) Processing helix chain 'L' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR L 549 " --> pdb=" O PRO L 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET L 550 " --> pdb=" O GLU L 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP L 551 " --> pdb=" O LEU L 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY L 553 " --> pdb=" O THR L 549 " (cutoff:3.500A) Processing helix chain 'L' and resid 559 through 569 removed outlier: 3.888A pdb=" N ALA L 566 " --> pdb=" O ILE L 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA L 569 " --> pdb=" O LYS L 565 " (cutoff:3.500A) Processing helix chain 'L' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU L 607 " --> pdb=" O GLN L 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP L 609 " --> pdb=" O LEU L 605 " (cutoff:3.500A) Processing helix chain 'L' and resid 630 through 635 removed outlier: 3.665A pdb=" N ARG L 635 " --> pdb=" O ALA L 632 " (cutoff:3.500A) Processing helix chain 'L' and resid 649 through 660 Processing helix chain 'L' and resid 672 through 677 Processing helix chain 'L' and resid 686 through 711 removed outlier: 3.654A pdb=" N ILE L 690 " --> pdb=" O ASP L 686 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS L 691 " --> pdb=" O LEU L 687 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN L 692 " --> pdb=" O THR L 688 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N CYS L 695 " --> pdb=" O CYS L 691 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU L 701 " --> pdb=" O LEU L 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU L 706 " --> pdb=" O SER L 702 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE L 707 " --> pdb=" O ILE L 703 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG L 708 " --> pdb=" O GLU L 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG L 709 " --> pdb=" O SER L 705 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU L 710 " --> pdb=" O GLU L 706 " (cutoff:3.500A) Processing helix chain 'L' and resid 732 through 740 removed outlier: 4.231A pdb=" N PHE L 736 " --> pdb=" O ARG L 732 " (cutoff:3.500A) Processing helix chain 'L' and resid 741 through 743 No H-bonds generated for 'chain 'L' and resid 741 through 743' Processing helix chain 'L' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR L 755 " --> pdb=" O ASP L 751 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 42 removed outlier: 3.608A pdb=" N ASP A 74 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 67 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE A 342 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 517 Processing sheet with id=AA6, first strand: chain 'A' and resid 573 through 575 removed outlier: 6.467A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP B 74 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 67 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA9, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AB1, first strand: chain 'B' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE B 342 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 514 through 517 Processing sheet with id=AB3, first strand: chain 'B' and resid 573 through 575 removed outlier: 6.465A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP C 74 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 67 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB6, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AB7, first strand: chain 'C' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE C 342 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 514 through 517 Processing sheet with id=AB9, first strand: chain 'C' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP D 74 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 67 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AC3, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AC4, first strand: chain 'D' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE D 342 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 514 through 517 Processing sheet with id=AC6, first strand: chain 'D' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 38 through 42 removed outlier: 3.608A pdb=" N ASP E 74 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA E 67 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AC9, first strand: chain 'E' and resid 153 through 155 Processing sheet with id=AD1, first strand: chain 'E' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE E 342 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 514 through 517 Processing sheet with id=AD3, first strand: chain 'E' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP F 74 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA F 67 " --> pdb=" O LEU F 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD6, first strand: chain 'F' and resid 153 through 155 Processing sheet with id=AD7, first strand: chain 'F' and resid 266 through 269 removed outlier: 3.586A pdb=" N ILE F 342 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 514 through 517 Processing sheet with id=AD9, first strand: chain 'F' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'G' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP G 74 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA G 67 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER G 101 " --> pdb=" O LYS G 60 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 145 through 147 Processing sheet with id=AE3, first strand: chain 'G' and resid 153 through 155 Processing sheet with id=AE4, first strand: chain 'G' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE G 342 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG G 365 " --> pdb=" O GLY G 240 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 514 through 517 Processing sheet with id=AE6, first strand: chain 'G' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU G 574 " --> pdb=" O ILE G 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'H' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP H 74 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA H 67 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER H 101 " --> pdb=" O LYS H 60 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 145 through 147 Processing sheet with id=AE9, first strand: chain 'H' and resid 153 through 155 Processing sheet with id=AF1, first strand: chain 'H' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE H 342 " --> pdb=" O ALA H 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG H 365 " --> pdb=" O GLY H 240 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 514 through 517 Processing sheet with id=AF3, first strand: chain 'H' and resid 573 through 575 removed outlier: 6.467A pdb=" N LEU H 574 " --> pdb=" O ILE H 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'I' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP I 74 " --> pdb=" O LEU I 41 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA I 67 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER I 101 " --> pdb=" O LYS I 60 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 145 through 147 Processing sheet with id=AF6, first strand: chain 'I' and resid 153 through 155 Processing sheet with id=AF7, first strand: chain 'I' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE I 342 " --> pdb=" O ALA I 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG I 365 " --> pdb=" O GLY I 240 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 514 through 517 Processing sheet with id=AF9, first strand: chain 'I' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU I 574 " --> pdb=" O ILE I 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'J' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP J 74 " --> pdb=" O LEU J 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA J 67 " --> pdb=" O LEU J 59 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER J 101 " --> pdb=" O LYS J 60 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 145 through 147 Processing sheet with id=AG3, first strand: chain 'J' and resid 153 through 155 Processing sheet with id=AG4, first strand: chain 'J' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE J 342 " --> pdb=" O ALA J 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG J 365 " --> pdb=" O GLY J 240 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 514 through 517 Processing sheet with id=AG6, first strand: chain 'J' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU J 574 " --> pdb=" O ILE J 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'K' and resid 38 through 42 removed outlier: 3.608A pdb=" N ASP K 74 " --> pdb=" O LEU K 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA K 67 " --> pdb=" O LEU K 59 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER K 101 " --> pdb=" O LYS K 60 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 145 through 147 Processing sheet with id=AG9, first strand: chain 'K' and resid 153 through 155 Processing sheet with id=AH1, first strand: chain 'K' and resid 266 through 269 removed outlier: 3.588A pdb=" N ILE K 342 " --> pdb=" O ALA K 299 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG K 365 " --> pdb=" O GLY K 240 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 514 through 517 Processing sheet with id=AH3, first strand: chain 'K' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU K 574 " --> pdb=" O ILE K 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'L' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP L 74 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA L 67 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER L 101 " --> pdb=" O LYS L 60 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 145 through 147 Processing sheet with id=AH6, first strand: chain 'L' and resid 153 through 155 Processing sheet with id=AH7, first strand: chain 'L' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE L 342 " --> pdb=" O ALA L 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG L 365 " --> pdb=" O GLY L 240 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 514 through 517 Processing sheet with id=AH9, first strand: chain 'L' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU L 574 " --> pdb=" O ILE L 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 2220 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 0 stacking parallelities Total time for adding SS restraints: 26.78 Time building geometry restraints manager: 22.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23934 1.34 - 1.46: 11990 1.46 - 1.58: 34756 1.58 - 1.69: 0 1.69 - 1.81: 600 Bond restraints: 71280 Sorted by residual: bond pdb=" CB VAL B 600 " pdb=" CG2 VAL B 600 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.42e+00 bond pdb=" CB VAL I 600 " pdb=" CG2 VAL I 600 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.41e+00 bond pdb=" CB VAL G 600 " pdb=" CG2 VAL G 600 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 bond pdb=" CB VAL L 600 " pdb=" CG2 VAL L 600 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 bond pdb=" CB VAL C 600 " pdb=" CG2 VAL C 600 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.35e+00 ... (remaining 71275 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.57: 2558 106.57 - 113.80: 40059 113.80 - 121.03: 33602 121.03 - 128.26: 19546 128.26 - 135.49: 487 Bond angle restraints: 96252 Sorted by residual: angle pdb=" C LEU J 140 " pdb=" N GLU J 141 " pdb=" CA GLU J 141 " ideal model delta sigma weight residual 121.54 130.29 -8.75 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C LEU B 140 " pdb=" N GLU B 141 " pdb=" CA GLU B 141 " ideal model delta sigma weight residual 121.54 130.29 -8.75 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C LEU F 140 " pdb=" N GLU F 141 " pdb=" CA GLU F 141 " ideal model delta sigma weight residual 121.54 130.26 -8.72 1.91e+00 2.74e-01 2.09e+01 angle pdb=" C LEU E 140 " pdb=" N GLU E 141 " pdb=" CA GLU E 141 " ideal model delta sigma weight residual 121.54 130.26 -8.72 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C LEU L 140 " pdb=" N GLU L 141 " pdb=" CA GLU L 141 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 ... (remaining 96247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 38733 17.31 - 34.62: 4514 34.62 - 51.93: 865 51.93 - 69.24: 228 69.24 - 86.55: 108 Dihedral angle restraints: 44448 sinusoidal: 18720 harmonic: 25728 Sorted by residual: dihedral pdb=" CA PHE K 506 " pdb=" C PHE K 506 " pdb=" N GLY K 507 " pdb=" CA GLY K 507 " ideal model delta harmonic sigma weight residual 180.00 153.13 26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA PHE J 506 " pdb=" C PHE J 506 " pdb=" N GLY J 507 " pdb=" CA GLY J 507 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA PHE L 506 " pdb=" C PHE L 506 " pdb=" N GLY L 507 " pdb=" CA GLY L 507 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 44445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 7365 0.054 - 0.107: 2613 0.107 - 0.161: 678 0.161 - 0.215: 107 0.215 - 0.269: 49 Chirality restraints: 10812 Sorted by residual: chirality pdb=" CA GLN A 50 " pdb=" N GLN A 50 " pdb=" C GLN A 50 " pdb=" CB GLN A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA GLN G 50 " pdb=" N GLN G 50 " pdb=" C GLN G 50 " pdb=" CB GLN G 50 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA GLN B 50 " pdb=" N GLN B 50 " pdb=" C GLN B 50 " pdb=" CB GLN B 50 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 10809 not shown) Planarity restraints: 12780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 552 " 0.022 2.00e-02 2.50e+03 2.40e-02 1.01e+01 pdb=" CG PHE B 552 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE B 552 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE B 552 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 552 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 552 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 552 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 552 " -0.022 2.00e-02 2.50e+03 2.40e-02 1.01e+01 pdb=" CG PHE F 552 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE F 552 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE F 552 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 552 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 552 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE F 552 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 552 " -0.022 2.00e-02 2.50e+03 2.39e-02 1.00e+01 pdb=" CG PHE I 552 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE I 552 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE I 552 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE I 552 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE I 552 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE I 552 " 0.001 2.00e-02 2.50e+03 ... (remaining 12777 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1315 2.67 - 3.22: 63528 3.22 - 3.78: 107010 3.78 - 4.34: 132074 4.34 - 4.90: 214713 Nonbonded interactions: 518640 Sorted by model distance: nonbonded pdb=" OG SER B 276 " pdb=" OG SER C 326 " model vdw 2.107 2.440 nonbonded pdb=" OG SER H 276 " pdb=" OG SER I 326 " model vdw 2.222 2.440 nonbonded pdb=" O GLU E 712 " pdb=" OG1 THR E 715 " model vdw 2.239 2.440 nonbonded pdb=" O GLU A 712 " pdb=" OG1 THR A 715 " model vdw 2.239 2.440 nonbonded pdb=" O GLU B 712 " pdb=" OG1 THR B 715 " model vdw 2.239 2.440 ... (remaining 518635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 6.790 Check model and map are aligned: 0.790 Set scattering table: 0.510 Process input model: 141.600 Find NCS groups from input model: 3.730 Set up NCS constraints: 0.400 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: 0.010 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 71280 Z= 0.473 Angle : 1.026 12.704 96252 Z= 0.538 Chirality : 0.060 0.269 10812 Planarity : 0.007 0.067 12780 Dihedral : 15.808 86.547 27720 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.94 % Allowed : 9.38 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.07), residues: 8844 helix: -3.24 (0.06), residues: 3228 sheet: -2.98 (0.13), residues: 1140 loop : -2.68 (0.08), residues: 4476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP I 551 HIS 0.006 0.001 HIS J 317 PHE 0.055 0.003 PHE B 552 TYR 0.013 0.002 TYR B 244 ARG 0.012 0.001 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 672 time to evaluate : 6.264 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: 72 outliers final: 48 residues processed: 744 average time/residue: 0.6354 time to fit residues: 819.6894 Evaluate side-chains 489 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 441 time to evaluate : 6.231 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.4774 time to fit residues: 53.1967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 749 optimal weight: 50.0000 chunk 673 optimal weight: 50.0000 chunk 373 optimal weight: 8.9990 chunk 229 optimal weight: 40.0000 chunk 454 optimal weight: 9.9990 chunk 359 optimal weight: 6.9990 chunk 696 optimal weight: 0.9990 chunk 269 optimal weight: 0.7980 chunk 423 optimal weight: 4.9990 chunk 518 optimal weight: 8.9990 chunk 806 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 91 ASN A 199 ASN A 285 ASN A 384 HIS ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 91 ASN B 199 ASN B 285 ASN B 384 HIS ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN B 760 GLN B 764 GLN C 90 ASN C 91 ASN C 199 ASN C 285 ASN C 384 HIS ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** C 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN D 91 ASN D 199 ASN D 285 ASN D 384 HIS ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** D 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** D 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 91 ASN E 199 ASN E 285 ASN E 384 HIS ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN F 90 ASN F 91 ASN F 199 ASN F 285 ASN F 384 HIS ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN ** F 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN ** F 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN G 91 ASN G 199 ASN G 285 ASN G 384 HIS ** G 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 ASN ** G 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 602 ASN ** G 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 760 GLN G 764 GLN H 90 ASN H 91 ASN H 115 HIS H 199 ASN H 285 ASN H 384 HIS H 460 ASN ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 ASN ** H 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 602 ASN H 760 GLN H 764 GLN I 90 ASN I 91 ASN I 199 ASN I 285 ASN I 317 HIS I 384 HIS ** I 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 533 ASN ** I 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 ASN ** I 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN J 91 ASN J 199 ASN J 285 ASN J 384 HIS ** J 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 ASN ** J 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 602 ASN K 90 ASN K 91 ASN K 199 ASN K 285 ASN K 384 HIS ** K 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 533 ASN ** K 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 602 ASN K 760 GLN K 764 GLN L 90 ASN L 91 ASN L 199 ASN L 285 ASN L 384 HIS ** L 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 ASN ** L 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 602 ASN ** L 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 95 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 71280 Z= 0.371 Angle : 0.710 8.807 96252 Z= 0.358 Chirality : 0.046 0.153 10812 Planarity : 0.005 0.044 12780 Dihedral : 5.330 29.182 9684 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.31 % Allowed : 15.35 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.08), residues: 8844 helix: -1.40 (0.09), residues: 3276 sheet: -2.65 (0.14), residues: 1152 loop : -1.91 (0.09), residues: 4416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 454 HIS 0.004 0.001 HIS E 499 PHE 0.025 0.002 PHE E 506 TYR 0.022 0.001 TYR L 244 ARG 0.007 0.001 ARG H 772 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 459 time to evaluate : 6.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 177 outliers final: 96 residues processed: 620 average time/residue: 0.5871 time to fit residues: 661.5342 Evaluate side-chains 494 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 398 time to evaluate : 6.315 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 0 residues processed: 96 average time/residue: 0.5103 time to fit residues: 103.3550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 448 optimal weight: 30.0000 chunk 250 optimal weight: 0.0870 chunk 671 optimal weight: 0.0030 chunk 549 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 807 optimal weight: 10.0000 chunk 872 optimal weight: 2.9990 chunk 719 optimal weight: 0.8980 chunk 801 optimal weight: 0.9980 chunk 275 optimal weight: 0.6980 chunk 648 optimal weight: 4.9990 overall best weight: 0.5368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN A 764 GLN B 460 ASN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 GLN C 760 GLN C 764 GLN ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 760 GLN F 764 GLN ** G 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 460 ASN ** G 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 538 ASN I 317 HIS ** I 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 GLN I 764 GLN ** J 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 460 ASN ** J 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 538 ASN ** J 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 760 GLN L 764 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 71280 Z= 0.152 Angle : 0.582 9.106 96252 Z= 0.286 Chirality : 0.043 0.161 10812 Planarity : 0.004 0.044 12780 Dihedral : 4.793 21.741 9684 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.74 % Allowed : 16.98 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.09), residues: 8844 helix: -0.63 (0.09), residues: 3180 sheet: -2.07 (0.15), residues: 1116 loop : -1.68 (0.09), residues: 4548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 454 HIS 0.001 0.000 HIS B 404 PHE 0.019 0.001 PHE E 363 TYR 0.030 0.001 TYR K 244 ARG 0.015 0.000 ARG G 772 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 486 time to evaluate : 6.183 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: 133 outliers final: 63 residues processed: 609 average time/residue: 0.5869 time to fit residues: 650.3069 Evaluate side-chains 480 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 417 time to evaluate : 6.294 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.4929 time to fit residues: 68.5088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 798 optimal weight: 0.9980 chunk 607 optimal weight: 6.9990 chunk 419 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 385 optimal weight: 0.9980 chunk 542 optimal weight: 1.9990 chunk 810 optimal weight: 5.9990 chunk 858 optimal weight: 6.9990 chunk 423 optimal weight: 10.0000 chunk 768 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN B 387 ASN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 GLN ** G 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 568 GLN H 115 HIS H 387 ASN ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 317 HIS ** I 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 568 GLN ** K 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 568 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 71280 Z= 0.214 Angle : 0.588 8.716 96252 Z= 0.289 Chirality : 0.044 0.159 10812 Planarity : 0.003 0.043 12780 Dihedral : 4.608 22.001 9684 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.16 % Allowed : 18.10 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.09), residues: 8844 helix: -0.24 (0.09), residues: 3264 sheet: -2.03 (0.15), residues: 1152 loop : -1.46 (0.09), residues: 4428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 551 HIS 0.006 0.000 HIS E 115 PHE 0.017 0.001 PHE I 618 TYR 0.029 0.001 TYR H 244 ARG 0.004 0.000 ARG B 772 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 414 time to evaluate : 6.205 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 outliers start: 165 outliers final: 75 residues processed: 556 average time/residue: 0.5831 time to fit residues: 594.8456 Evaluate side-chains 478 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 403 time to evaluate : 6.253 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 0 residues processed: 75 average time/residue: 0.5142 time to fit residues: 83.0417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 714 optimal weight: 4.9990 chunk 487 optimal weight: 7.9990 chunk 12 optimal weight: 50.0000 chunk 639 optimal weight: 5.9990 chunk 354 optimal weight: 2.9990 chunk 732 optimal weight: 5.9990 chunk 593 optimal weight: 50.0000 chunk 1 optimal weight: 8.9990 chunk 438 optimal weight: 7.9990 chunk 770 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 ASN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 387 ASN ** G 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 387 ASN ** I 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 GLN ** I 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 387 ASN ** J 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 387 ASN ** K 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 568 GLN L 387 ASN ** L 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 71280 Z= 0.448 Angle : 0.731 9.609 96252 Z= 0.362 Chirality : 0.047 0.162 10812 Planarity : 0.004 0.040 12780 Dihedral : 4.963 27.414 9684 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.38 % Allowed : 19.95 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.09), residues: 8844 helix: -0.25 (0.09), residues: 3288 sheet: -2.00 (0.15), residues: 1152 loop : -1.41 (0.10), residues: 4404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 551 HIS 0.004 0.001 HIS J 115 PHE 0.026 0.002 PHE A 552 TYR 0.024 0.001 TYR K 244 ARG 0.005 0.001 ARG L 638 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 399 time to evaluate : 6.222 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 outliers start: 182 outliers final: 95 residues processed: 562 average time/residue: 0.5889 time to fit residues: 605.8565 Evaluate side-chains 482 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 387 time to evaluate : 6.296 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 0 residues processed: 95 average time/residue: 0.5081 time to fit residues: 102.0139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 288 optimal weight: 3.9990 chunk 772 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 503 optimal weight: 0.0010 chunk 211 optimal weight: 0.0570 chunk 859 optimal weight: 2.9990 chunk 713 optimal weight: 0.9980 chunk 397 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 284 optimal weight: 0.5980 chunk 451 optimal weight: 7.9990 overall best weight: 0.5306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 GLN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 568 GLN ** H 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 317 HIS ** I 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 568 GLN ** K 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 568 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 71280 Z= 0.149 Angle : 0.582 10.771 96252 Z= 0.283 Chirality : 0.043 0.156 10812 Planarity : 0.003 0.043 12780 Dihedral : 4.507 23.523 9684 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.06 % Allowed : 20.74 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.09), residues: 8844 helix: 0.07 (0.10), residues: 3348 sheet: -1.77 (0.15), residues: 1140 loop : -1.22 (0.10), residues: 4356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 551 HIS 0.004 0.000 HIS J 115 PHE 0.014 0.001 PHE E 363 TYR 0.044 0.001 TYR F 244 ARG 0.007 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 473 time to evaluate : 6.314 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 outliers start: 81 outliers final: 33 residues processed: 535 average time/residue: 0.6048 time to fit residues: 584.7929 Evaluate side-chains 434 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 401 time to evaluate : 6.403 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.5611 time to fit residues: 43.1785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 828 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 489 optimal weight: 0.0470 chunk 627 optimal weight: 8.9990 chunk 486 optimal weight: 6.9990 chunk 723 optimal weight: 0.0270 chunk 479 optimal weight: 8.9990 chunk 855 optimal weight: 20.0000 chunk 535 optimal weight: 7.9990 chunk 521 optimal weight: 20.0000 chunk 395 optimal weight: 10.0000 overall best weight: 3.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 HIS ** H 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 317 HIS ** I 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 71280 Z= 0.285 Angle : 0.637 10.965 96252 Z= 0.312 Chirality : 0.044 0.149 10812 Planarity : 0.004 0.042 12780 Dihedral : 4.562 24.046 9684 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.16 % Allowed : 21.89 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.09), residues: 8844 helix: 0.17 (0.10), residues: 3348 sheet: -1.80 (0.15), residues: 1152 loop : -1.17 (0.10), residues: 4344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 551 HIS 0.003 0.001 HIS J 115 PHE 0.023 0.002 PHE I 363 TYR 0.027 0.001 TYR K 244 ARG 0.004 0.000 ARG L 638 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 401 time to evaluate : 6.324 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: 89 outliers final: 49 residues processed: 472 average time/residue: 0.6067 time to fit residues: 522.7711 Evaluate side-chains 427 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 378 time to evaluate : 6.211 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.5152 time to fit residues: 56.6116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 529 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 chunk 511 optimal weight: 1.9990 chunk 257 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 544 optimal weight: 4.9990 chunk 583 optimal weight: 4.9990 chunk 423 optimal weight: 7.9990 chunk 79 optimal weight: 50.0000 chunk 672 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN B 401 ASN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 71280 Z= 0.344 Angle : 0.680 10.255 96252 Z= 0.333 Chirality : 0.045 0.154 10812 Planarity : 0.004 0.041 12780 Dihedral : 4.702 27.325 9684 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.90 % Allowed : 22.54 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.09), residues: 8844 helix: 0.20 (0.10), residues: 3348 sheet: -1.93 (0.15), residues: 1152 loop : -1.10 (0.10), residues: 4344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 551 HIS 0.002 0.001 HIS J 115 PHE 0.023 0.002 PHE B 506 TYR 0.042 0.001 TYR K 244 ARG 0.004 0.000 ARG L 638 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 395 time to evaluate : 6.193 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: 69 outliers final: 33 residues processed: 453 average time/residue: 0.6072 time to fit residues: 498.6973 Evaluate side-chains 416 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 383 time to evaluate : 6.227 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.5341 time to fit residues: 41.7745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 778 optimal weight: 2.9990 chunk 819 optimal weight: 6.9990 chunk 748 optimal weight: 20.0000 chunk 797 optimal weight: 5.9990 chunk 480 optimal weight: 2.9990 chunk 347 optimal weight: 2.9990 chunk 626 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 720 optimal weight: 0.9980 chunk 754 optimal weight: 40.0000 chunk 794 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 GLN ** G 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 71280 Z= 0.179 Angle : 0.606 9.222 96252 Z= 0.296 Chirality : 0.044 0.169 10812 Planarity : 0.003 0.042 12780 Dihedral : 4.494 25.837 9684 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.35 % Allowed : 23.00 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.98 (0.09), residues: 8844 helix: 0.38 (0.10), residues: 3336 sheet: -1.87 (0.15), residues: 1152 loop : -1.05 (0.10), residues: 4356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 551 HIS 0.003 0.000 HIS J 115 PHE 0.016 0.001 PHE K 363 TYR 0.044 0.001 TYR K 244 ARG 0.005 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 421 time to evaluate : 6.398 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: 27 outliers final: 11 residues processed: 440 average time/residue: 0.6123 time to fit residues: 490.4885 Evaluate side-chains 399 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 388 time to evaluate : 6.365 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5311 time to fit residues: 19.7592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 523 optimal weight: 1.9990 chunk 843 optimal weight: 3.9990 chunk 514 optimal weight: 5.9990 chunk 400 optimal weight: 7.9990 chunk 586 optimal weight: 1.9990 chunk 884 optimal weight: 3.9990 chunk 814 optimal weight: 0.0030 chunk 704 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 544 optimal weight: 0.9990 chunk 431 optimal weight: 0.4980 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 HIS ** H 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 568 GLN ** L 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 71280 Z= 0.158 Angle : 0.601 10.976 96252 Z= 0.294 Chirality : 0.043 0.159 10812 Planarity : 0.003 0.042 12780 Dihedral : 4.363 28.775 9684 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.27 % Allowed : 23.11 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.88 (0.09), residues: 8844 helix: 0.45 (0.10), residues: 3348 sheet: -1.99 (0.14), residues: 1248 loop : -0.89 (0.10), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 551 HIS 0.003 0.000 HIS J 115 PHE 0.016 0.001 PHE G 618 TYR 0.038 0.001 TYR B 244 ARG 0.004 0.000 ARG B 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 420 time to evaluate : 6.313 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: 21 outliers final: 12 residues processed: 435 average time/residue: 0.6149 time to fit residues: 484.4244 Evaluate side-chains 405 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 393 time to evaluate : 6.255 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5297 time to fit residues: 20.8421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 559 optimal weight: 9.9990 chunk 750 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 649 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 195 optimal weight: 0.0070 chunk 705 optimal weight: 6.9990 chunk 295 optimal weight: 1.9990 chunk 724 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.141654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.100461 restraints weight = 158337.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.097446 restraints weight = 97486.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.098424 restraints weight = 106128.483| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 71280 Z= 0.319 Angle : 0.671 10.159 96252 Z= 0.330 Chirality : 0.045 0.168 10812 Planarity : 0.004 0.041 12780 Dihedral : 4.557 28.144 9684 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.37 % Allowed : 23.15 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.88 (0.09), residues: 8844 helix: 0.46 (0.10), residues: 3324 sheet: -2.07 (0.14), residues: 1260 loop : -0.85 (0.10), residues: 4260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 551 HIS 0.002 0.001 HIS J 115 PHE 0.020 0.002 PHE H 506 TYR 0.025 0.001 TYR E 244 ARG 0.005 0.000 ARG F 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11231.46 seconds wall clock time: 200 minutes 39.66 seconds (12039.66 seconds total)