Starting phenix.real_space_refine on Thu Mar 14 11:06:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t15_8342/03_2024/5t15_8342.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t15_8342/03_2024/5t15_8342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t15_8342/03_2024/5t15_8342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t15_8342/03_2024/5t15_8342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t15_8342/03_2024/5t15_8342.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t15_8342/03_2024/5t15_8342.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 76 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 S 644 5.16 5 C 76520 2.51 5 N 21392 2.21 5 O 22232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1271": "NH1" <-> "NH2" Residue "B ARG 1594": "NH1" <-> "NH2" Residue "B ARG 1607": "NH1" <-> "NH2" Residue "B ARG 1656": "NH1" <-> "NH2" Residue "B ARG 1725": "NH1" <-> "NH2" Residue "B ARG 1743": "NH1" <-> "NH2" Residue "B ARG 1797": "NH1" <-> "NH2" Residue "B ARG 1827": "NH1" <-> "NH2" Residue "B ARG 1996": "NH1" <-> "NH2" Residue "B ARG 2140": "NH1" <-> "NH2" Residue "B ARG 2355": "NH1" <-> "NH2" Residue "B ARG 2452": "NH1" <-> "NH2" Residue "B ARG 3648": "NH1" <-> "NH2" Residue "B ARG 3886": "NH1" <-> "NH2" Residue "B ARG 3904": "NH1" <-> "NH2" Residue "B ARG 3949": "NH1" <-> "NH2" Residue "B ARG 3984": "NH1" <-> "NH2" Residue "B ARG 4042": "NH1" <-> "NH2" Residue "B PHE 4125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4137": "NH1" <-> "NH2" Residue "B ARG 4159": "NH1" <-> "NH2" Residue "B ARG 4175": "NH1" <-> "NH2" Residue "B ARG 4192": "NH1" <-> "NH2" Residue "B ARG 4548": "NH1" <-> "NH2" Residue "B ARG 4557": "NH1" <-> "NH2" Residue "B ARG 4563": "NH1" <-> "NH2" Residue "B TYR 4638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4673": "NH1" <-> "NH2" Residue "B ARG 4703": "NH1" <-> "NH2" Residue "B ARG 4722": "NH1" <-> "NH2" Residue "B ARG 4734": "NH1" <-> "NH2" Residue "B ARG 4736": "NH1" <-> "NH2" Residue "B PHE 4807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4824": "NH1" <-> "NH2" Residue "B ARG 4860": "NH1" <-> "NH2" Residue "B ARG 4892": "NH1" <-> "NH2" Residue "B ARG 4913": "NH1" <-> "NH2" Residue "B TYR 4988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 5017": "NH1" <-> "NH2" Residue "B ARG 5029": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 266": "NH1" <-> "NH2" Residue "E ARG 426": "NH1" <-> "NH2" Residue "E ARG 553": "NH1" <-> "NH2" Residue "E PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1271": "NH1" <-> "NH2" Residue "E ARG 1594": "NH1" <-> "NH2" Residue "E ARG 1607": "NH1" <-> "NH2" Residue "E ARG 1656": "NH1" <-> "NH2" Residue "E ARG 1725": "NH1" <-> "NH2" Residue "E ARG 1743": "NH1" <-> "NH2" Residue "E ARG 1797": "NH1" <-> "NH2" Residue "E ARG 1827": "NH1" <-> "NH2" Residue "E ARG 1996": "NH1" <-> "NH2" Residue "E ARG 2140": "NH1" <-> "NH2" Residue "E ARG 2355": "NH1" <-> "NH2" Residue "E ARG 2452": "NH1" <-> "NH2" Residue "E ARG 3648": "NH1" <-> "NH2" Residue "E ARG 3886": "NH1" <-> "NH2" Residue "E ARG 3904": "NH1" <-> "NH2" Residue "E ARG 3949": "NH1" <-> "NH2" Residue "E ARG 3984": "NH1" <-> "NH2" Residue "E ARG 4042": "NH1" <-> "NH2" Residue "E PHE 4125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4137": "NH1" <-> "NH2" Residue "E ARG 4159": "NH1" <-> "NH2" Residue "E ARG 4175": "NH1" <-> "NH2" Residue "E ARG 4192": "NH1" <-> "NH2" Residue "E ARG 4548": "NH1" <-> "NH2" Residue "E ARG 4557": "NH1" <-> "NH2" Residue "E ARG 4563": "NH1" <-> "NH2" Residue "E TYR 4638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4673": "NH1" <-> "NH2" Residue "E ARG 4703": "NH1" <-> "NH2" Residue "E ARG 4722": "NH1" <-> "NH2" Residue "E ARG 4734": "NH1" <-> "NH2" Residue "E ARG 4736": "NH1" <-> "NH2" Residue "E PHE 4807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4824": "NH1" <-> "NH2" Residue "E ARG 4860": "NH1" <-> "NH2" Residue "E ARG 4892": "NH1" <-> "NH2" Residue "E ARG 4913": "NH1" <-> "NH2" Residue "E TYR 4988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 5017": "NH1" <-> "NH2" Residue "E ARG 5029": "NH1" <-> "NH2" Residue "I ARG 76": "NH1" <-> "NH2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I ARG 266": "NH1" <-> "NH2" Residue "I ARG 426": "NH1" <-> "NH2" Residue "I ARG 553": "NH1" <-> "NH2" Residue "I PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 1271": "NH1" <-> "NH2" Residue "I ARG 1594": "NH1" <-> "NH2" Residue "I ARG 1607": "NH1" <-> "NH2" Residue "I ARG 1656": "NH1" <-> "NH2" Residue "I ARG 1725": "NH1" <-> "NH2" Residue "I ARG 1743": "NH1" <-> "NH2" Residue "I ARG 1797": "NH1" <-> "NH2" Residue "I ARG 1827": "NH1" <-> "NH2" Residue "I ARG 1996": "NH1" <-> "NH2" Residue "I ARG 2140": "NH1" <-> "NH2" Residue "I ARG 2355": "NH1" <-> "NH2" Residue "I ARG 2452": "NH1" <-> "NH2" Residue "I ARG 3648": "NH1" <-> "NH2" Residue "I ARG 3886": "NH1" <-> "NH2" Residue "I ARG 3904": "NH1" <-> "NH2" Residue "I ARG 3949": "NH1" <-> "NH2" Residue "I ARG 3984": "NH1" <-> "NH2" Residue "I ARG 4042": "NH1" <-> "NH2" Residue "I PHE 4125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 4137": "NH1" <-> "NH2" Residue "I ARG 4159": "NH1" <-> "NH2" Residue "I ARG 4175": "NH1" <-> "NH2" Residue "I ARG 4192": "NH1" <-> "NH2" Residue "I ARG 4548": "NH1" <-> "NH2" Residue "I ARG 4557": "NH1" <-> "NH2" Residue "I ARG 4563": "NH1" <-> "NH2" Residue "I TYR 4638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 4673": "NH1" <-> "NH2" Residue "I ARG 4703": "NH1" <-> "NH2" Residue "I ARG 4722": "NH1" <-> "NH2" Residue "I ARG 4734": "NH1" <-> "NH2" Residue "I ARG 4736": "NH1" <-> "NH2" Residue "I PHE 4807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 4824": "NH1" <-> "NH2" Residue "I ARG 4860": "NH1" <-> "NH2" Residue "I ARG 4892": "NH1" <-> "NH2" Residue "I ARG 4913": "NH1" <-> "NH2" Residue "I TYR 4988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 5017": "NH1" <-> "NH2" Residue "I ARG 5029": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G ARG 178": "NH1" <-> "NH2" Residue "G ARG 266": "NH1" <-> "NH2" Residue "G ARG 426": "NH1" <-> "NH2" Residue "G ARG 553": "NH1" <-> "NH2" Residue "G PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1271": "NH1" <-> "NH2" Residue "G ARG 1594": "NH1" <-> "NH2" Residue "G ARG 1607": "NH1" <-> "NH2" Residue "G ARG 1656": "NH1" <-> "NH2" Residue "G ARG 1725": "NH1" <-> "NH2" Residue "G ARG 1743": "NH1" <-> "NH2" Residue "G ARG 1797": "NH1" <-> "NH2" Residue "G ARG 1827": "NH1" <-> "NH2" Residue "G ARG 1996": "NH1" <-> "NH2" Residue "G ARG 2140": "NH1" <-> "NH2" Residue "G ARG 2355": "NH1" <-> "NH2" Residue "G ARG 2452": "NH1" <-> "NH2" Residue "G ARG 3648": "NH1" <-> "NH2" Residue "G ARG 3886": "NH1" <-> "NH2" Residue "G ARG 3904": "NH1" <-> "NH2" Residue "G ARG 3949": "NH1" <-> "NH2" Residue "G ARG 3984": "NH1" <-> "NH2" Residue "G ARG 4042": "NH1" <-> "NH2" Residue "G PHE 4125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 4137": "NH1" <-> "NH2" Residue "G ARG 4159": "NH1" <-> "NH2" Residue "G ARG 4175": "NH1" <-> "NH2" Residue "G ARG 4192": "NH1" <-> "NH2" Residue "G ARG 4548": "NH1" <-> "NH2" Residue "G ARG 4557": "NH1" <-> "NH2" Residue "G ARG 4563": "NH1" <-> "NH2" Residue "G TYR 4638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 4673": "NH1" <-> "NH2" Residue "G ARG 4703": "NH1" <-> "NH2" Residue "G ARG 4722": "NH1" <-> "NH2" Residue "G ARG 4734": "NH1" <-> "NH2" Residue "G ARG 4736": "NH1" <-> "NH2" Residue "G PHE 4807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 4824": "NH1" <-> "NH2" Residue "G ARG 4860": "NH1" <-> "NH2" Residue "G ARG 4892": "NH1" <-> "NH2" Residue "G ARG 4913": "NH1" <-> "NH2" Residue "G TYR 4988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 5017": "NH1" <-> "NH2" Residue "G ARG 5029": "NH1" <-> "NH2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 120796 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "J" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 29379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4170, 29379 Classifications: {'peptide': 4170} Incomplete info: {'truncation_to_alanine': 1247} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4012} Chain breaks: 25 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3029 Unresolved non-hydrogen angles: 4232 Unresolved non-hydrogen dihedrals: 1880 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 46, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 83, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1760 Chain: "E" Number of atoms: 29379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4170, 29379 Classifications: {'peptide': 4170} Incomplete info: {'truncation_to_alanine': 1247} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4012} Chain breaks: 25 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3029 Unresolved non-hydrogen angles: 4232 Unresolved non-hydrogen dihedrals: 1880 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 46, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 83, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1760 Chain: "I" Number of atoms: 29379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4170, 29379 Classifications: {'peptide': 4170} Incomplete info: {'truncation_to_alanine': 1247} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4012} Chain breaks: 25 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3029 Unresolved non-hydrogen angles: 4232 Unresolved non-hydrogen dihedrals: 1880 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 46, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 83, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1760 Chain: "G" Number of atoms: 29379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4170, 29379 Classifications: {'peptide': 4170} Incomplete info: {'truncation_to_alanine': 1247} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4012} Chain breaks: 25 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3029 Unresolved non-hydrogen angles: 4232 Unresolved non-hydrogen dihedrals: 1880 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 46, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 83, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1760 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 31980 SG CYS B4958 178.379 203.921 90.555 1.00 60.20 S ATOM 32005 SG CYS B4961 180.819 204.619 93.424 1.00 55.07 S ATOM 61359 SG CYS E4958 203.925 208.166 90.559 1.00 60.60 S ATOM 61384 SG CYS E4961 204.625 205.726 93.428 1.00 55.36 S ATOM 90738 SG CYS I4958 182.613 178.374 90.557 1.00 60.37 S ATOM 90763 SG CYS I4961 181.914 180.814 93.426 1.00 55.29 S ATOM A0FIT SG CYS G4958 208.168 182.614 90.552 1.00 60.01 S ATOM A0FJI SG CYS G4961 205.728 181.916 93.421 1.00 54.66 S Time building chain proxies: 44.75, per 1000 atoms: 0.37 Number of scatterers: 120796 At special positions: 0 Unit cell: (387.795, 387.795, 210.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 644 16.00 O 22232 8.00 N 21392 7.00 C 76520 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: 31.18 Conformation dependent library (CDL) restraints added in 13.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B5101 " pdb="ZN ZN B5101 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4958 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4961 " pdb=" ZN E5101 " pdb="ZN ZN E5101 " - pdb=" ND1 HIS E4983 " pdb="ZN ZN E5101 " - pdb=" NE2 HIS E4978 " pdb="ZN ZN E5101 " - pdb=" SG CYS E4958 " pdb="ZN ZN E5101 " - pdb=" SG CYS E4961 " pdb=" ZN G5101 " pdb="ZN ZN G5101 " - pdb=" ND1 HIS G4983 " pdb="ZN ZN G5101 " - pdb=" NE2 HIS G4978 " pdb="ZN ZN G5101 " - pdb=" SG CYS G4958 " pdb="ZN ZN G5101 " - pdb=" SG CYS G4961 " pdb=" ZN I5101 " pdb="ZN ZN I5101 " - pdb=" ND1 HIS I4983 " pdb="ZN ZN I5101 " - pdb=" NE2 HIS I4978 " pdb="ZN ZN I5101 " - pdb=" SG CYS I4958 " pdb="ZN ZN I5101 " - pdb=" SG CYS I4961 " Number of angles added : 8 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 32376 Finding SS restraints... Secondary structure from input PDB file: 742 helices and 84 sheets defined 60.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 16.43 Creating SS restraints... Processing helix chain 'F' and resid 56 through 65 removed outlier: 3.819A pdb=" N GLY F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 63 " --> pdb=" O PHE F 59 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 81 Processing helix chain 'A' and resid 56 through 65 removed outlier: 3.819A pdb=" N GLY A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'H' and resid 56 through 65 removed outlier: 3.820A pdb=" N GLY H 62 " --> pdb=" O GLY H 58 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA H 63 " --> pdb=" O PHE H 59 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 81 Processing helix chain 'J' and resid 56 through 65 removed outlier: 3.820A pdb=" N GLY J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA J 63 " --> pdb=" O PHE J 59 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA J 64 " --> pdb=" O GLU J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'B' and resid 74 through 82 Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.737A pdb=" N THR B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.700A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 420 removed outlier: 4.023A pdb=" N GLN B 399 " --> pdb=" O GLN B 395 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 452 removed outlier: 3.695A pdb=" N SER B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 481 removed outlier: 3.635A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 478 " --> pdb=" O ARG B 474 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 494 removed outlier: 3.715A pdb=" N CYS B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 529 removed outlier: 3.727A pdb=" N ILE B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 538 removed outlier: 3.797A pdb=" N CYS B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 533 through 538' Processing helix chain 'B' and resid 539 through 541 No H-bonds generated for 'chain 'B' and resid 539 through 541' Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.556A pdb=" N VAL B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.740A pdb=" N VAL B 567 " --> pdb=" O VAL B 563 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 576 removed outlier: 4.053A pdb=" N LEU B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 594 Processing helix chain 'B' and resid 597 through 608 removed outlier: 3.850A pdb=" N LEU B 603 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 624 removed outlier: 4.002A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 888 removed outlier: 3.731A pdb=" N ILE B 870 " --> pdb=" O HIS B 866 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS B 879 " --> pdb=" O ALA B 875 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG B 886 " --> pdb=" O TRP B 882 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 913 removed outlier: 3.612A pdb=" N LEU B 913 " --> pdb=" O PHE B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 934 removed outlier: 3.667A pdb=" N GLN B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 927 " --> pdb=" O GLN B 923 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.077A pdb=" N ASP B 986 " --> pdb=" O THR B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1041 removed outlier: 3.953A pdb=" N LYS B1032 " --> pdb=" O ASP B1028 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN B1041 " --> pdb=" O ASP B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1049 removed outlier: 3.540A pdb=" N LEU B1046 " --> pdb=" O ALA B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1082 Processing helix chain 'B' and resid 1575 through 1579 removed outlier: 3.735A pdb=" N MET B1579 " --> pdb=" O SER B1576 " (cutoff:3.500A) Processing helix chain 'B' and resid 1652 through 1657 removed outlier: 3.805A pdb=" N LEU B1657 " --> pdb=" O LEU B1653 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1674 removed outlier: 4.022A pdb=" N HIS B1665 " --> pdb=" O ARG B1661 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR B1670 " --> pdb=" O THR B1666 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B1671 " --> pdb=" O LEU B1667 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1683 Processing helix chain 'B' and resid 1695 through 1700 removed outlier: 4.331A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B1700 " --> pdb=" O HIS B1696 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1695 through 1700' Processing helix chain 'B' and resid 1710 through 1714 removed outlier: 3.634A pdb=" N ASP B1713 " --> pdb=" O GLY B1710 " (cutoff:3.500A) Processing helix chain 'B' and resid 1715 through 1719 removed outlier: 3.770A pdb=" N ILE B1718 " --> pdb=" O LEU B1715 " (cutoff:3.500A) Processing helix chain 'B' and resid 1720 through 1732 removed outlier: 3.977A pdb=" N ARG B1725 " --> pdb=" O GLU B1721 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER B1726 " --> pdb=" O SER B1722 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B1729 " --> pdb=" O ARG B1725 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET B1730 " --> pdb=" O SER B1726 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER B1732 " --> pdb=" O ARG B1728 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1744 removed outlier: 3.549A pdb=" N ALA B1744 " --> pdb=" O PRO B1740 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1823 removed outlier: 3.879A pdb=" N LEU B1807 " --> pdb=" O PRO B1803 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP B1809 " --> pdb=" O GLU B1805 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1838 Processing helix chain 'B' and resid 1840 through 1851 removed outlier: 3.542A pdb=" N MET B1851 " --> pdb=" O THR B1847 " (cutoff:3.500A) Processing helix chain 'B' and resid 1855 through 1863 Processing helix chain 'B' and resid 1866 through 1871 Processing helix chain 'B' and resid 1933 through 1977 removed outlier: 4.015A pdb=" N TYR B1945 " --> pdb=" O ASN B1941 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B1946 " --> pdb=" O LEU B1942 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B1951 " --> pdb=" O CYS B1947 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B1963 " --> pdb=" O ALA B1959 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B1964 " --> pdb=" O ALA B1960 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B1966 " --> pdb=" O ALA B1962 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN B1972 " --> pdb=" O LYS B1968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1977 through 1982 Processing helix chain 'B' and resid 1989 through 1994 Processing helix chain 'B' and resid 1995 through 1998 Processing helix chain 'B' and resid 2001 through 2012 removed outlier: 3.752A pdb=" N ASN B2007 " --> pdb=" O GLN B2003 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET B2008 " --> pdb=" O GLU B2004 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS B2011 " --> pdb=" O ASN B2007 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE B2012 " --> pdb=" O MET B2008 " (cutoff:3.500A) Processing helix chain 'B' and resid 2029 through 2042 removed outlier: 3.686A pdb=" N LEU B2039 " --> pdb=" O HIS B2035 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B2040 " --> pdb=" O GLN B2036 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2108 removed outlier: 3.657A pdb=" N HIS B2100 " --> pdb=" O GLU B2096 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B2103 " --> pdb=" O SER B2099 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B2106 " --> pdb=" O VAL B2102 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2129 removed outlier: 3.928A pdb=" N VAL B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B2126 " --> pdb=" O SER B2122 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN B2127 " --> pdb=" O LEU B2123 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR B2128 " --> pdb=" O LEU B2124 " (cutoff:3.500A) Processing helix chain 'B' and resid 2129 through 2136 Processing helix chain 'B' and resid 2137 through 2139 No H-bonds generated for 'chain 'B' and resid 2137 through 2139' Processing helix chain 'B' and resid 2149 through 2165 removed outlier: 3.696A pdb=" N GLY B2160 " --> pdb=" O LEU B2156 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B2161 " --> pdb=" O GLU B2157 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B2165 " --> pdb=" O GLN B2161 " (cutoff:3.500A) Processing helix chain 'B' and resid 2166 through 2168 No H-bonds generated for 'chain 'B' and resid 2166 through 2168' Processing helix chain 'B' and resid 2171 through 2186 removed outlier: 3.722A pdb=" N ASN B2176 " --> pdb=" O PRO B2172 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2194 Processing helix chain 'B' and resid 2194 through 2201 removed outlier: 4.270A pdb=" N MET B2198 " --> pdb=" O HIS B2194 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B2199 " --> pdb=" O PRO B2195 " (cutoff:3.500A) Processing helix chain 'B' and resid 2202 through 2216 removed outlier: 3.532A pdb=" N VAL B2207 " --> pdb=" O MET B2203 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B2208 " --> pdb=" O HIS B2204 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN B2213 " --> pdb=" O GLU B2209 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL B2214 " --> pdb=" O VAL B2210 " (cutoff:3.500A) Processing helix chain 'B' and resid 2228 through 2242 removed outlier: 4.042A pdb=" N TYR B2238 " --> pdb=" O ARG B2234 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2250 Processing helix chain 'B' and resid 2253 through 2261 removed outlier: 3.747A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2279 removed outlier: 3.945A pdb=" N ALA B2276 " --> pdb=" O PRO B2272 " (cutoff:3.500A) Processing helix chain 'B' and resid 2294 through 2306 removed outlier: 3.692A pdb=" N VAL B2299 " --> pdb=" O LEU B2295 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B2300 " --> pdb=" O GLU B2296 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2315 removed outlier: 4.138A pdb=" N ALA B2315 " --> pdb=" O PRO B2311 " (cutoff:3.500A) Processing helix chain 'B' and resid 2326 through 2331 Processing helix chain 'B' and resid 2332 through 2337 Processing helix chain 'B' and resid 2346 through 2358 removed outlier: 3.998A pdb=" N ALA B2350 " --> pdb=" O VAL B2346 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL B2353 " --> pdb=" O ASN B2349 " (cutoff:3.500A) Processing helix chain 'B' and resid 2360 through 2364 Processing helix chain 'B' and resid 2375 through 2388 removed outlier: 3.690A pdb=" N ARG B2385 " --> pdb=" O GLU B2381 " (cutoff:3.500A) Processing helix chain 'B' and resid 2389 through 2393 removed outlier: 3.778A pdb=" N ARG B2392 " --> pdb=" O ASP B2389 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP B2393 " --> pdb=" O PRO B2390 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2389 through 2393' Processing helix chain 'B' and resid 2418 through 2436 removed outlier: 3.680A pdb=" N PHE B2425 " --> pdb=" O ALA B2421 " (cutoff:3.500A) Processing helix chain 'B' and resid 2440 through 2445 removed outlier: 4.164A pdb=" N ALA B2445 " --> pdb=" O HIS B2441 " (cutoff:3.500A) Processing helix chain 'B' and resid 2450 through 2461 removed outlier: 3.747A pdb=" N ARG B2454 " --> pdb=" O ALA B2450 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B2459 " --> pdb=" O ALA B2455 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B2461 " --> pdb=" O LEU B2457 " (cutoff:3.500A) Processing helix chain 'B' and resid 2466 through 2471 removed outlier: 3.512A pdb=" N SER B2471 " --> pdb=" O VAL B2467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2495 through 2499 removed outlier: 3.547A pdb=" N UNK B2498 " --> pdb=" O UNK B2495 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N UNK B2499 " --> pdb=" O UNK B2496 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2495 through 2499' Processing helix chain 'B' and resid 2502 through 2507 removed outlier: 3.757A pdb=" N UNK B2506 " --> pdb=" O UNK B2502 " (cutoff:3.500A) Processing helix chain 'B' and resid 2516 through 2521 Processing helix chain 'B' and resid 2524 through 2531 removed outlier: 3.904A pdb=" N UNK B2528 " --> pdb=" O UNK B2524 " (cutoff:3.500A) Processing helix chain 'B' and resid 2542 through 2547 removed outlier: 3.753A pdb=" N UNK B2546 " --> pdb=" O UNK B2542 " (cutoff:3.500A) Processing helix chain 'B' and resid 2551 through 2557 removed outlier: 4.021A pdb=" N UNK B2555 " --> pdb=" O UNK B2551 " (cutoff:3.500A) Processing helix chain 'B' and resid 2567 through 2581 Processing helix chain 'B' and resid 2587 through 2600 removed outlier: 3.660A pdb=" N UNK B2597 " --> pdb=" O UNK B2593 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N UNK B2598 " --> pdb=" O UNK B2594 " (cutoff:3.500A) Processing helix chain 'B' and resid 2610 through 2618 removed outlier: 3.823A pdb=" N UNK B2617 " --> pdb=" O UNK B2613 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N UNK B2618 " --> pdb=" O UNK B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2626 through 2640 removed outlier: 3.959A pdb=" N UNK B2630 " --> pdb=" O UNK B2626 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N UNK B2631 " --> pdb=" O UNK B2627 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N UNK B2635 " --> pdb=" O UNK B2631 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNK B2636 " --> pdb=" O UNK B2632 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N UNK B2639 " --> pdb=" O UNK B2635 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N UNK B2640 " --> pdb=" O UNK B2636 " (cutoff:3.500A) Processing helix chain 'B' and resid 2641 through 2643 No H-bonds generated for 'chain 'B' and resid 2641 through 2643' Processing helix chain 'B' and resid 2650 through 2666 Processing helix chain 'B' and resid 2667 through 2670 Processing helix chain 'B' and resid 2687 through 2691 removed outlier: 3.699A pdb=" N UNK B2690 " --> pdb=" O UNK B2687 " (cutoff:3.500A) Processing helix chain 'B' and resid 2748 through 2773 removed outlier: 3.831A pdb=" N SER B2753 " --> pdb=" O GLU B2749 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B2754 " --> pdb=" O LYS B2750 " (cutoff:3.500A) Processing helix chain 'B' and resid 2793 through 2797 removed outlier: 3.781A pdb=" N PHE B2797 " --> pdb=" O TYR B2794 " (cutoff:3.500A) Processing helix chain 'B' and resid 2802 through 2806 Processing helix chain 'B' and resid 2809 through 2820 removed outlier: 4.301A pdb=" N ALA B2815 " --> pdb=" O GLU B2811 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B2817 " --> pdb=" O LEU B2813 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2895 removed outlier: 4.248A pdb=" N MET B2874 " --> pdb=" O GLU B2870 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B2875 " --> pdb=" O LEU B2871 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B2876 " --> pdb=" O GLN B2872 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B2880 " --> pdb=" O GLU B2876 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TRP B2886 " --> pdb=" O TYR B2882 " (cutoff:3.500A) Processing helix chain 'B' and resid 2907 through 2911 Processing helix chain 'B' and resid 2914 through 2919 removed outlier: 4.091A pdb=" N ARG B2918 " --> pdb=" O LYS B2914 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B2919 " --> pdb=" O GLU B2915 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2914 through 2919' Processing helix chain 'B' and resid 2920 through 2932 removed outlier: 3.504A pdb=" N PHE B2929 " --> pdb=" O GLU B2925 " (cutoff:3.500A) Processing helix chain 'B' and resid 2950 through 2966 removed outlier: 4.368A pdb=" N UNK B2956 " --> pdb=" O UNK B2952 " (cutoff:3.500A) Processing helix chain 'B' and resid 2966 through 2976 Processing helix chain 'B' and resid 2999 through 3015 removed outlier: 3.801A pdb=" N UNK B3004 " --> pdb=" O UNK B3000 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N UNK B3006 " --> pdb=" O UNK B3002 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N UNK B3009 " --> pdb=" O UNK B3005 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N UNK B3010 " --> pdb=" O UNK B3006 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N UNK B3013 " --> pdb=" O UNK B3009 " (cutoff:3.500A) Processing helix chain 'B' and resid 3017 through 3022 Processing helix chain 'B' and resid 3025 through 3040 removed outlier: 3.553A pdb=" N UNK B3031 " --> pdb=" O UNK B3027 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N UNK B3032 " --> pdb=" O UNK B3028 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N UNK B3040 " --> pdb=" O UNK B3036 " (cutoff:3.500A) Processing helix chain 'B' and resid 3052 through 3063 removed outlier: 4.364A pdb=" N UNK B3056 " --> pdb=" O UNK B3052 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N UNK B3057 " --> pdb=" O UNK B3053 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N UNK B3061 " --> pdb=" O UNK B3057 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N UNK B3062 " --> pdb=" O UNK B3058 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N UNK B3063 " --> pdb=" O UNK B3059 " (cutoff:3.500A) Processing helix chain 'B' and resid 3141 through 3151 removed outlier: 3.963A pdb=" N UNK B3148 " --> pdb=" O UNK B3144 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N UNK B3149 " --> pdb=" O UNK B3145 " (cutoff:3.500A) Processing helix chain 'B' and resid 3151 through 3161 removed outlier: 3.504A pdb=" N UNK B3155 " --> pdb=" O UNK B3151 " (cutoff:3.500A) Processing helix chain 'B' and resid 3175 through 3187 removed outlier: 3.526A pdb=" N UNK B3181 " --> pdb=" O UNK B3177 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N UNK B3182 " --> pdb=" O UNK B3178 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N UNK B3183 " --> pdb=" O UNK B3179 " (cutoff:3.500A) Processing helix chain 'B' and resid 3198 through 3212 removed outlier: 3.694A pdb=" N UNK B3205 " --> pdb=" O UNK B3201 " (cutoff:3.500A) Processing helix chain 'B' and resid 3224 through 3230 removed outlier: 3.942A pdb=" N UNK B3228 " --> pdb=" O UNK B3224 " (cutoff:3.500A) Processing helix chain 'B' and resid 3248 through 3254 removed outlier: 3.530A pdb=" N UNK B3252 " --> pdb=" O UNK B3248 " (cutoff:3.500A) Processing helix chain 'B' and resid 3271 through 3285 removed outlier: 3.656A pdb=" N UNK B3281 " --> pdb=" O UNK B3277 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N UNK B3282 " --> pdb=" O UNK B3278 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N UNK B3284 " --> pdb=" O UNK B3280 " (cutoff:3.500A) Processing helix chain 'B' and resid 3305 through 3310 Processing helix chain 'B' and resid 3316 through 3321 removed outlier: 3.613A pdb=" N UNK B3321 " --> pdb=" O UNK B3317 " (cutoff:3.500A) Processing helix chain 'B' and resid 3321 through 3330 removed outlier: 3.722A pdb=" N UNK B3330 " --> pdb=" O UNK B3326 " (cutoff:3.500A) Processing helix chain 'B' and resid 3331 through 3333 No H-bonds generated for 'chain 'B' and resid 3331 through 3333' Processing helix chain 'B' and resid 3344 through 3349 removed outlier: 3.739A pdb=" N UNK B3348 " --> pdb=" O UNK B3344 " (cutoff:3.500A) Processing helix chain 'B' and resid 3361 through 3388 Processing helix chain 'B' and resid 3399 through 3409 removed outlier: 3.802A pdb=" N UNK B3403 " --> pdb=" O UNK B3399 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N UNK B3404 " --> pdb=" O UNK B3400 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N UNK B3405 " --> pdb=" O UNK B3401 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N UNK B3407 " --> pdb=" O UNK B3403 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N UNK B3409 " --> pdb=" O UNK B3405 " (cutoff:3.500A) Processing helix chain 'B' and resid 3410 through 3415 Processing helix chain 'B' and resid 3415 through 3423 removed outlier: 4.356A pdb=" N UNK B3420 " --> pdb=" O UNK B3416 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK B3421 " --> pdb=" O UNK B3417 " (cutoff:3.500A) Processing helix chain 'B' and resid 3425 through 3431 Processing helix chain 'B' and resid 3437 through 3443 Processing helix chain 'B' and resid 3445 through 3450 Processing helix chain 'B' and resid 3457 through 3460 Processing helix chain 'B' and resid 3461 through 3466 Processing helix chain 'B' and resid 3518 through 3521 removed outlier: 3.514A pdb=" N UNK B3521 " --> pdb=" O UNK B3518 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3518 through 3521' Processing helix chain 'B' and resid 3522 through 3527 removed outlier: 3.546A pdb=" N UNK B3527 " --> pdb=" O UNK B3523 " (cutoff:3.500A) Processing helix chain 'B' and resid 3551 through 3560 Processing helix chain 'B' and resid 3574 through 3582 removed outlier: 3.697A pdb=" N UNK B3579 " --> pdb=" O UNK B3575 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N UNK B3580 " --> pdb=" O UNK B3576 " (cutoff:3.500A) Processing helix chain 'B' and resid 3589 through 3611 removed outlier: 4.083A pdb=" N UNK B3595 " --> pdb=" O UNK B3591 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N UNK B3600 " --> pdb=" O UNK B3596 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N UNK B3601 " --> pdb=" O UNK B3597 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N UNK B3610 " --> pdb=" O UNK B3606 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N UNK B3611 " --> pdb=" O UNK B3607 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3657 removed outlier: 3.589A pdb=" N ASN B3651 " --> pdb=" O HIS B3647 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET B3652 " --> pdb=" O ARG B3648 " (cutoff:3.500A) Processing helix chain 'B' and resid 3658 through 3661 removed outlier: 3.798A pdb=" N TRP B3661 " --> pdb=" O LYS B3658 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3658 through 3661' Processing helix chain 'B' and resid 3670 through 3680 removed outlier: 3.635A pdb=" N ILE B3674 " --> pdb=" O GLU B3670 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B3676 " --> pdb=" O ARG B3672 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B3677 " --> pdb=" O MET B3673 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B3678 " --> pdb=" O ILE B3674 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B3680 " --> pdb=" O ASP B3676 " (cutoff:3.500A) Processing helix chain 'B' and resid 3681 through 3683 No H-bonds generated for 'chain 'B' and resid 3681 through 3683' Processing helix chain 'B' and resid 3696 through 3711 removed outlier: 3.595A pdb=" N LEU B3701 " --> pdb=" O PRO B3697 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B3710 " --> pdb=" O SER B3706 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B3711 " --> pdb=" O ARG B3707 " (cutoff:3.500A) Processing helix chain 'B' and resid 3719 through 3738 removed outlier: 3.569A pdb=" N MET B3723 " --> pdb=" O ASP B3719 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B3724 " --> pdb=" O TYR B3720 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B3725 " --> pdb=" O LEU B3721 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B3728 " --> pdb=" O ALA B3724 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS B3733 " --> pdb=" O MET B3729 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B3735 " --> pdb=" O LYS B3731 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU B3736 " --> pdb=" O SER B3732 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3768 removed outlier: 3.819A pdb=" N LYS B3760 " --> pdb=" O LYS B3756 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B3762 " --> pdb=" O MET B3758 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU B3763 " --> pdb=" O GLU B3759 " (cutoff:3.500A) Processing helix chain 'B' and resid 3774 through 3778 Processing helix chain 'B' and resid 3791 through 3805 removed outlier: 4.078A pdb=" N LYS B3799 " --> pdb=" O SER B3795 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B3800 " --> pdb=" O SER B3796 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B3805 " --> pdb=" O GLY B3801 " (cutoff:3.500A) Processing helix chain 'B' and resid 3809 through 3824 removed outlier: 3.882A pdb=" N TYR B3819 " --> pdb=" O LYS B3815 " (cutoff:3.500A) Processing helix chain 'B' and resid 3828 through 3838 Processing helix chain 'B' and resid 3843 through 3854 removed outlier: 3.525A pdb=" N ARG B3849 " --> pdb=" O ASN B3845 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN B3850 " --> pdb=" O ALA B3846 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN B3851 " --> pdb=" O PHE B3847 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B3852 " --> pdb=" O GLU B3848 " (cutoff:3.500A) Processing helix chain 'B' and resid 3855 through 3857 No H-bonds generated for 'chain 'B' and resid 3855 through 3857' Processing helix chain 'B' and resid 3880 through 3891 removed outlier: 3.983A pdb=" N PHE B3885 " --> pdb=" O THR B3881 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B3886 " --> pdb=" O GLN B3882 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B3887 " --> pdb=" O ASP B3883 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3905 removed outlier: 3.711A pdb=" N ARG B3904 " --> pdb=" O GLN B3900 " (cutoff:3.500A) Processing helix chain 'B' and resid 3914 through 3938 removed outlier: 3.630A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B3920 " --> pdb=" O ILE B3916 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR B3922 " --> pdb=" O CYS B3918 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER B3929 " --> pdb=" O ARG B3925 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B3932 " --> pdb=" O GLU B3928 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR B3936 " --> pdb=" O ASP B3932 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3967 removed outlier: 3.669A pdb=" N PHE B3951 " --> pdb=" O GLY B3947 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B3953 " --> pdb=" O ARG B3949 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA B3954 " --> pdb=" O ASN B3950 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B3958 " --> pdb=" O ALA B3954 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B3967 " --> pdb=" O ASN B3963 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3982 Processing helix chain 'B' and resid 3984 through 4003 removed outlier: 3.764A pdb=" N ALA B3988 " --> pdb=" O ARG B3984 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY B3991 " --> pdb=" O ASP B3987 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B3992 " --> pdb=" O ALA B3988 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B3993 " --> pdb=" O VAL B3989 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET B4000 " --> pdb=" O PHE B3996 " (cutoff:3.500A) Processing helix chain 'B' and resid 4004 through 4008 removed outlier: 5.473A pdb=" N SER B4007 " --> pdb=" O ALA B4004 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER B4008 " --> pdb=" O GLN B4005 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4004 through 4008' Processing helix chain 'B' and resid 4009 through 4030 removed outlier: 3.808A pdb=" N ASP B4018 " --> pdb=" O LYS B4014 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS B4021 " --> pdb=" O LEU B4017 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B4024 " --> pdb=" O GLN B4020 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N MET B4026 " --> pdb=" O ASP B4022 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B4027 " --> pdb=" O MET B4023 " (cutoff:3.500A) Processing helix chain 'B' and resid 4040 through 4051 removed outlier: 3.569A pdb=" N VAL B4045 " --> pdb=" O ALA B4041 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B4046 " --> pdb=" O ARG B4042 " (cutoff:3.500A) Processing helix chain 'B' and resid 4051 through 4072 removed outlier: 3.790A pdb=" N GLU B4056 " --> pdb=" O SER B4052 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B4058 " --> pdb=" O ASN B4054 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B4065 " --> pdb=" O PHE B4061 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B4066 " --> pdb=" O PHE B4062 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B4069 " --> pdb=" O PHE B4065 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP B4070 " --> pdb=" O LEU B4066 " (cutoff:3.500A) Processing helix chain 'B' and resid 4074 through 4079 Processing helix chain 'B' and resid 4090 through 4100 removed outlier: 3.704A pdb=" N MET B4097 " --> pdb=" O PHE B4093 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP B4098 " --> pdb=" O GLN B4094 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN B4100 " --> pdb=" O ALA B4096 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4115 Processing helix chain 'B' and resid 4124 through 4129 removed outlier: 3.513A pdb=" N ALA B4129 " --> pdb=" O PHE B4125 " (cutoff:3.500A) Processing helix chain 'B' and resid 4130 through 4133 Processing helix chain 'B' and resid 4136 through 4154 removed outlier: 4.040A pdb=" N GLY B4140 " --> pdb=" O ALA B4136 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B4148 " --> pdb=" O ALA B4144 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B4152 " --> pdb=" O THR B4148 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B4153 " --> pdb=" O ASN B4149 " (cutoff:3.500A) Processing helix chain 'B' and resid 4157 through 4167 removed outlier: 3.590A pdb=" N ARG B4161 " --> pdb=" O ASP B4157 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B4162 " --> pdb=" O PRO B4158 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE B4163 " --> pdb=" O ARG B4159 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU B4165 " --> pdb=" O ARG B4161 " (cutoff:3.500A) Processing helix chain 'B' and resid 4167 through 4174 removed outlier: 3.800A pdb=" N LEU B4171 " --> pdb=" O ALA B4167 " (cutoff:3.500A) Processing helix chain 'B' and resid 4200 through 4206 Processing helix chain 'B' and resid 4207 through 4224 removed outlier: 4.022A pdb=" N SER B4213 " --> pdb=" O GLN B4209 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B4222 " --> pdb=" O ILE B4218 " (cutoff:3.500A) Processing helix chain 'B' and resid 4228 through 4239 removed outlier: 3.623A pdb=" N VAL B4235 " --> pdb=" O MET B4231 " (cutoff:3.500A) Processing helix chain 'B' and resid 4240 through 4249 Processing helix chain 'B' and resid 4543 through 4558 removed outlier: 3.902A pdb=" N VAL B4549 " --> pdb=" O GLU B4545 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR B4554 " --> pdb=" O LYS B4550 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN B4558 " --> pdb=" O TYR B4554 " (cutoff:3.500A) Processing helix chain 'B' and resid 4558 through 4576 removed outlier: 3.840A pdb=" N LEU B4562 " --> pdb=" O ASN B4558 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B4571 " --> pdb=" O LEU B4567 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B4572 " --> pdb=" O PHE B4568 " (cutoff:3.500A) Processing helix chain 'B' and resid 4643 through 4665 removed outlier: 3.955A pdb=" N LEU B4648 " --> pdb=" O TRP B4644 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU B4649 " --> pdb=" O CYS B4645 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B4651 " --> pdb=" O SER B4647 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS B4657 " --> pdb=" O VAL B4653 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B4659 " --> pdb=" O PHE B4655 " (cutoff:3.500A) Processing helix chain 'B' and resid 4667 through 4683 removed outlier: 3.732A pdb=" N GLU B4676 " --> pdb=" O LYS B4672 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B4682 " --> pdb=" O ALA B4678 " (cutoff:3.500A) Processing helix chain 'B' and resid 4696 through 4702 removed outlier: 3.536A pdb=" N GLN B4700 " --> pdb=" O ASP B4696 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP B4702 " --> pdb=" O LYS B4698 " (cutoff:3.500A) Processing helix chain 'B' and resid 4703 through 4705 No H-bonds generated for 'chain 'B' and resid 4703 through 4705' Processing helix chain 'B' and resid 4719 through 4728 removed outlier: 3.565A pdb=" N LEU B4725 " --> pdb=" O LYS B4721 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP B4726 " --> pdb=" O ARG B4722 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4741 Processing helix chain 'B' and resid 4745 through 4753 removed outlier: 4.832A pdb=" N THR B4751 " --> pdb=" O SER B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4772 through 4784 Processing helix chain 'B' and resid 4786 through 4802 removed outlier: 3.752A pdb=" N SER B4799 " --> pdb=" O TYR B4795 " (cutoff:3.500A) Processing helix chain 'B' and resid 4811 through 4816 removed outlier: 4.551A pdb=" N ASP B4815 " --> pdb=" O ALA B4811 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B4816 " --> pdb=" O HIS B4812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4811 through 4816' Processing helix chain 'B' and resid 4817 through 4819 No H-bonds generated for 'chain 'B' and resid 4817 through 4819' Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.622A pdb=" N ARG B4824 " --> pdb=" O VAL B4820 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B4825 " --> pdb=" O LYS B4821 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) Processing helix chain 'B' and resid 4836 through 4858 removed outlier: 3.975A pdb=" N GLY B4842 " --> pdb=" O VAL B4838 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B4847 " --> pdb=" O LEU B4843 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B4854 " --> pdb=" O LEU B4850 " (cutoff:3.500A) Processing helix chain 'B' and resid 4859 through 4863 removed outlier: 3.572A pdb=" N PHE B4862 " --> pdb=" O PHE B4859 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B4863 " --> pdb=" O ARG B4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4859 through 4863' Processing helix chain 'B' and resid 4879 through 4894 removed outlier: 3.643A pdb=" N MET B4887 " --> pdb=" O TYR B4883 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY B4894 " --> pdb=" O GLY B4890 " (cutoff:3.500A) Processing helix chain 'B' and resid 4909 through 4924 removed outlier: 3.615A pdb=" N VAL B4914 " --> pdb=" O GLU B4910 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL B4915 " --> pdb=" O LEU B4911 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B4924 " --> pdb=" O PHE B4920 " (cutoff:3.500A) Processing helix chain 'B' and resid 4927 through 4933 removed outlier: 4.028A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B4933 " --> pdb=" O LEU B4929 " (cutoff:3.500A) Processing helix chain 'B' and resid 4933 through 4944 removed outlier: 3.536A pdb=" N ILE B4937 " --> pdb=" O GLN B4933 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B4940 " --> pdb=" O ILE B4936 " (cutoff:3.500A) Processing helix chain 'B' and resid 4947 through 4952 Processing helix chain 'B' and resid 4964 through 4969 removed outlier: 3.876A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B4969 " --> pdb=" O SER B4965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4964 through 4969' Processing helix chain 'B' and resid 4973 through 4979 Processing helix chain 'B' and resid 4986 through 4997 removed outlier: 3.665A pdb=" N LEU B4992 " --> pdb=" O TYR B4988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B4996 " --> pdb=" O LEU B4992 " (cutoff:3.500A) Processing helix chain 'B' and resid 4999 through 5003 removed outlier: 3.903A pdb=" N HIS B5003 " --> pdb=" O GLU B5000 " (cutoff:3.500A) Processing helix chain 'B' and resid 5006 through 5017 removed outlier: 3.602A pdb=" N MET B5013 " --> pdb=" O TYR B5009 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 82 Processing helix chain 'E' and resid 251 through 255 removed outlier: 3.737A pdb=" N THR E 254 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 369 removed outlier: 3.701A pdb=" N LEU E 369 " --> pdb=" O LYS E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 420 removed outlier: 4.023A pdb=" N GLN E 399 " --> pdb=" O GLN E 395 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE E 404 " --> pdb=" O ALA E 400 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS E 405 " --> pdb=" O ALA E 401 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN E 413 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE E 414 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS E 416 " --> pdb=" O ASN E 412 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY E 417 " --> pdb=" O GLN E 413 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER E 420 " --> pdb=" O LYS E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 452 removed outlier: 3.695A pdb=" N SER E 444 " --> pdb=" O ALA E 440 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY E 450 " --> pdb=" O GLN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 481 removed outlier: 3.633A pdb=" N SER E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER E 470 " --> pdb=" O SER E 466 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG E 474 " --> pdb=" O SER E 470 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE E 478 " --> pdb=" O ARG E 474 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN E 479 " --> pdb=" O GLN E 475 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU E 480 " --> pdb=" O SER E 476 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU E 481 " --> pdb=" O LEU E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 494 removed outlier: 3.715A pdb=" N CYS E 490 " --> pdb=" O LEU E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 529 removed outlier: 3.727A pdb=" N ILE E 518 " --> pdb=" O SER E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 538 removed outlier: 3.798A pdb=" N CYS E 537 " --> pdb=" O ASN E 533 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 538 " --> pdb=" O ARG E 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 533 through 538' Processing helix chain 'E' and resid 539 through 541 No H-bonds generated for 'chain 'E' and resid 539 through 541' Processing helix chain 'E' and resid 543 through 551 removed outlier: 3.555A pdb=" N VAL E 548 " --> pdb=" O LEU E 544 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS E 550 " --> pdb=" O TRP E 546 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU E 551 " --> pdb=" O VAL E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 571 removed outlier: 3.740A pdb=" N VAL E 567 " --> pdb=" O VAL E 563 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 568 " --> pdb=" O LEU E 564 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE E 569 " --> pdb=" O TYR E 565 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU E 570 " --> pdb=" O CYS E 566 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER E 571 " --> pdb=" O VAL E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 576 removed outlier: 4.053A pdb=" N LEU E 575 " --> pdb=" O SER E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 594 Processing helix chain 'E' and resid 597 through 608 removed outlier: 3.850A pdb=" N LEU E 603 " --> pdb=" O VAL E 599 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS E 607 " --> pdb=" O LEU E 603 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL E 608 " --> pdb=" O CYS E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 624 removed outlier: 4.002A pdb=" N GLN E 618 " --> pdb=" O VAL E 614 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP E 619 " --> pdb=" O ARG E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 888 removed outlier: 3.731A pdb=" N ILE E 870 " --> pdb=" O HIS E 866 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU E 872 " --> pdb=" O GLU E 868 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS E 873 " --> pdb=" O ARG E 869 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS E 879 " --> pdb=" O ALA E 875 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG E 886 " --> pdb=" O TRP E 882 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE E 887 " --> pdb=" O ALA E 883 " (cutoff:3.500A) Processing helix chain 'E' and resid 909 through 913 removed outlier: 3.611A pdb=" N LEU E 913 " --> pdb=" O PHE E 910 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 934 removed outlier: 3.667A pdb=" N GLN E 923 " --> pdb=" O ASN E 919 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU E 927 " --> pdb=" O GLN E 923 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA E 934 " --> pdb=" O LYS E 930 " (cutoff:3.500A) Processing helix chain 'E' and resid 980 through 1001 removed outlier: 4.076A pdb=" N ASP E 986 " --> pdb=" O THR E 982 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1041 removed outlier: 3.953A pdb=" N LYS E1032 " --> pdb=" O ASP E1028 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E1039 " --> pdb=" O ASN E1035 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN E1041 " --> pdb=" O ASP E1037 " (cutoff:3.500A) Processing helix chain 'E' and resid 1042 through 1049 removed outlier: 3.540A pdb=" N LEU E1046 " --> pdb=" O ALA E1042 " (cutoff:3.500A) Processing helix chain 'E' and resid 1078 through 1082 Processing helix chain 'E' and resid 1575 through 1579 removed outlier: 3.735A pdb=" N MET E1579 " --> pdb=" O SER E1576 " (cutoff:3.500A) Processing helix chain 'E' and resid 1652 through 1657 removed outlier: 3.805A pdb=" N LEU E1657 " --> pdb=" O LEU E1653 " (cutoff:3.500A) Processing helix chain 'E' and resid 1658 through 1674 removed outlier: 4.023A pdb=" N HIS E1665 " --> pdb=" O ARG E1661 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR E1670 " --> pdb=" O THR E1666 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG E1671 " --> pdb=" O LEU E1667 " (cutoff:3.500A) Processing helix chain 'E' and resid 1678 through 1683 Processing helix chain 'E' and resid 1695 through 1700 removed outlier: 4.332A pdb=" N GLU E1699 " --> pdb=" O LEU E1695 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP E1700 " --> pdb=" O HIS E1696 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1695 through 1700' Processing helix chain 'E' and resid 1710 through 1714 removed outlier: 3.633A pdb=" N ASP E1713 " --> pdb=" O GLY E1710 " (cutoff:3.500A) Processing helix chain 'E' and resid 1715 through 1719 removed outlier: 3.770A pdb=" N ILE E1718 " --> pdb=" O LEU E1715 " (cutoff:3.500A) Processing helix chain 'E' and resid 1720 through 1732 removed outlier: 3.977A pdb=" N ARG E1725 " --> pdb=" O GLU E1721 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER E1726 " --> pdb=" O SER E1722 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER E1729 " --> pdb=" O ARG E1725 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET E1730 " --> pdb=" O SER E1726 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER E1732 " --> pdb=" O ARG E1728 " (cutoff:3.500A) Processing helix chain 'E' and resid 1739 through 1744 removed outlier: 3.550A pdb=" N ALA E1744 " --> pdb=" O PRO E1740 " (cutoff:3.500A) Processing helix chain 'E' and resid 1803 through 1823 removed outlier: 3.880A pdb=" N LEU E1807 " --> pdb=" O PRO E1803 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP E1809 " --> pdb=" O GLU E1805 " (cutoff:3.500A) Processing helix chain 'E' and resid 1833 through 1838 Processing helix chain 'E' and resid 1840 through 1851 removed outlier: 3.542A pdb=" N MET E1851 " --> pdb=" O THR E1847 " (cutoff:3.500A) Processing helix chain 'E' and resid 1855 through 1863 Processing helix chain 'E' and resid 1866 through 1871 Processing helix chain 'E' and resid 1933 through 1977 removed outlier: 4.015A pdb=" N TYR E1945 " --> pdb=" O ASN E1941 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE E1946 " --> pdb=" O LEU E1942 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E1951 " --> pdb=" O CYS E1947 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU E1963 " --> pdb=" O ALA E1959 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG E1964 " --> pdb=" O ALA E1960 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL E1966 " --> pdb=" O ALA E1962 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN E1972 " --> pdb=" O LYS E1968 " (cutoff:3.500A) Processing helix chain 'E' and resid 1977 through 1982 Processing helix chain 'E' and resid 1989 through 1994 Processing helix chain 'E' and resid 1995 through 1998 Processing helix chain 'E' and resid 2001 through 2012 removed outlier: 3.752A pdb=" N ASN E2007 " --> pdb=" O GLN E2003 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET E2008 " --> pdb=" O GLU E2004 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS E2011 " --> pdb=" O ASN E2007 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE E2012 " --> pdb=" O MET E2008 " (cutoff:3.500A) Processing helix chain 'E' and resid 2029 through 2042 removed outlier: 3.686A pdb=" N LEU E2039 " --> pdb=" O HIS E2035 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E2040 " --> pdb=" O GLN E2036 " (cutoff:3.500A) Processing helix chain 'E' and resid 2094 through 2108 removed outlier: 3.657A pdb=" N HIS E2100 " --> pdb=" O GLU E2096 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL E2103 " --> pdb=" O SER E2099 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E2106 " --> pdb=" O VAL E2102 " (cutoff:3.500A) Processing helix chain 'E' and resid 2113 through 2129 removed outlier: 3.928A pdb=" N VAL E2117 " --> pdb=" O SER E2113 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG E2126 " --> pdb=" O SER E2122 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN E2127 " --> pdb=" O LEU E2123 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR E2128 " --> pdb=" O LEU E2124 " (cutoff:3.500A) Processing helix chain 'E' and resid 2129 through 2136 Processing helix chain 'E' and resid 2137 through 2139 No H-bonds generated for 'chain 'E' and resid 2137 through 2139' Processing helix chain 'E' and resid 2149 through 2165 removed outlier: 3.696A pdb=" N GLY E2160 " --> pdb=" O LEU E2156 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN E2161 " --> pdb=" O GLU E2157 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU E2165 " --> pdb=" O GLN E2161 " (cutoff:3.500A) Processing helix chain 'E' and resid 2166 through 2168 No H-bonds generated for 'chain 'E' and resid 2166 through 2168' Processing helix chain 'E' and resid 2171 through 2186 removed outlier: 3.722A pdb=" N ASN E2176 " --> pdb=" O PRO E2172 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU E2177 " --> pdb=" O GLN E2173 " (cutoff:3.500A) Processing helix chain 'E' and resid 2189 through 2194 Processing helix chain 'E' and resid 2194 through 2201 removed outlier: 4.270A pdb=" N MET E2198 " --> pdb=" O HIS E2194 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG E2199 " --> pdb=" O PRO E2195 " (cutoff:3.500A) Processing helix chain 'E' and resid 2202 through 2216 removed outlier: 3.532A pdb=" N VAL E2207 " --> pdb=" O MET E2203 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET E2208 " --> pdb=" O HIS E2204 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN E2213 " --> pdb=" O GLU E2209 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL E2214 " --> pdb=" O VAL E2210 " (cutoff:3.500A) Processing helix chain 'E' and resid 2228 through 2242 removed outlier: 4.041A pdb=" N TYR E2238 " --> pdb=" O ARG E2234 " (cutoff:3.500A) Processing helix chain 'E' and resid 2245 through 2250 Processing helix chain 'E' and resid 2253 through 2261 removed outlier: 3.748A pdb=" N ASN E2260 " --> pdb=" O TYR E2256 " (cutoff:3.500A) Processing helix chain 'E' and resid 2271 through 2279 removed outlier: 3.945A pdb=" N ALA E2276 " --> pdb=" O PRO E2272 " (cutoff:3.500A) Processing helix chain 'E' and resid 2294 through 2306 removed outlier: 3.692A pdb=" N VAL E2299 " --> pdb=" O LEU E2295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER E2300 " --> pdb=" O GLU E2296 " (cutoff:3.500A) Processing helix chain 'E' and resid 2310 through 2315 removed outlier: 4.138A pdb=" N ALA E2315 " --> pdb=" O PRO E2311 " (cutoff:3.500A) Processing helix chain 'E' and resid 2326 through 2331 Processing helix chain 'E' and resid 2332 through 2337 Processing helix chain 'E' and resid 2346 through 2358 removed outlier: 3.998A pdb=" N ALA E2350 " --> pdb=" O VAL E2346 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL E2352 " --> pdb=" O GLU E2348 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL E2353 " --> pdb=" O ASN E2349 " (cutoff:3.500A) Processing helix chain 'E' and resid 2360 through 2364 Processing helix chain 'E' and resid 2375 through 2388 removed outlier: 3.689A pdb=" N ARG E2385 " --> pdb=" O GLU E2381 " (cutoff:3.500A) Processing helix chain 'E' and resid 2389 through 2393 removed outlier: 3.777A pdb=" N ARG E2392 " --> pdb=" O ASP E2389 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP E2393 " --> pdb=" O PRO E2390 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2389 through 2393' Processing helix chain 'E' and resid 2418 through 2436 removed outlier: 3.680A pdb=" N PHE E2425 " --> pdb=" O ALA E2421 " (cutoff:3.500A) Processing helix chain 'E' and resid 2440 through 2445 removed outlier: 4.165A pdb=" N ALA E2445 " --> pdb=" O HIS E2441 " (cutoff:3.500A) Processing helix chain 'E' and resid 2450 through 2461 removed outlier: 3.747A pdb=" N ARG E2454 " --> pdb=" O ALA E2450 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER E2459 " --> pdb=" O ALA E2455 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E2461 " --> pdb=" O LEU E2457 " (cutoff:3.500A) Processing helix chain 'E' and resid 2466 through 2471 removed outlier: 3.513A pdb=" N SER E2471 " --> pdb=" O VAL E2467 " (cutoff:3.500A) Processing helix chain 'E' and resid 2495 through 2499 removed outlier: 3.508A pdb=" N UNK E2498 " --> pdb=" O UNK E2495 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N UNK E2499 " --> pdb=" O UNK E2496 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2495 through 2499' Processing helix chain 'E' and resid 2502 through 2507 removed outlier: 3.725A pdb=" N UNK E2506 " --> pdb=" O UNK E2502 " (cutoff:3.500A) Processing helix chain 'E' and resid 2516 through 2521 Processing helix chain 'E' and resid 2524 through 2532 removed outlier: 3.920A pdb=" N UNK E2528 " --> pdb=" O UNK E2524 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N UNK E2532 " --> pdb=" O UNK E2528 " (cutoff:3.500A) Processing helix chain 'E' and resid 2542 through 2547 removed outlier: 3.760A pdb=" N UNK E2546 " --> pdb=" O UNK E2542 " (cutoff:3.500A) Processing helix chain 'E' and resid 2551 through 2557 removed outlier: 4.015A pdb=" N UNK E2555 " --> pdb=" O UNK E2551 " (cutoff:3.500A) Processing helix chain 'E' and resid 2567 through 2581 Processing helix chain 'E' and resid 2587 through 2600 removed outlier: 3.664A pdb=" N UNK E2597 " --> pdb=" O UNK E2593 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N UNK E2598 " --> pdb=" O UNK E2594 " (cutoff:3.500A) Processing helix chain 'E' and resid 2610 through 2618 removed outlier: 3.820A pdb=" N UNK E2617 " --> pdb=" O UNK E2613 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N UNK E2618 " --> pdb=" O UNK E2614 " (cutoff:3.500A) Processing helix chain 'E' and resid 2626 through 2640 removed outlier: 3.946A pdb=" N UNK E2630 " --> pdb=" O UNK E2626 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N UNK E2631 " --> pdb=" O UNK E2627 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N UNK E2635 " --> pdb=" O UNK E2631 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N UNK E2636 " --> pdb=" O UNK E2632 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N UNK E2639 " --> pdb=" O UNK E2635 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N UNK E2640 " --> pdb=" O UNK E2636 " (cutoff:3.500A) Processing helix chain 'E' and resid 2641 through 2643 No H-bonds generated for 'chain 'E' and resid 2641 through 2643' Processing helix chain 'E' and resid 2650 through 2666 Processing helix chain 'E' and resid 2667 through 2669 No H-bonds generated for 'chain 'E' and resid 2667 through 2669' Processing helix chain 'E' and resid 2687 through 2691 removed outlier: 3.718A pdb=" N UNK E2690 " --> pdb=" O UNK E2687 " (cutoff:3.500A) Processing helix chain 'E' and resid 2748 through 2773 removed outlier: 3.832A pdb=" N SER E2753 " --> pdb=" O GLU E2749 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE E2754 " --> pdb=" O LYS E2750 " (cutoff:3.500A) Processing helix chain 'E' and resid 2793 through 2797 removed outlier: 3.780A pdb=" N PHE E2797 " --> pdb=" O TYR E2794 " (cutoff:3.500A) Processing helix chain 'E' and resid 2809 through 2820 removed outlier: 4.301A pdb=" N ALA E2815 " --> pdb=" O GLU E2811 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE E2817 " --> pdb=" O LEU E2813 " (cutoff:3.500A) Processing helix chain 'E' and resid 2868 through 2895 removed outlier: 4.247A pdb=" N MET E2874 " --> pdb=" O GLU E2870 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA E2875 " --> pdb=" O LEU E2871 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU E2876 " --> pdb=" O GLN E2872 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E2880 " --> pdb=" O GLU E2876 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TRP E2886 " --> pdb=" O TYR E2882 " (cutoff:3.500A) Processing helix chain 'E' and resid 2907 through 2911 Processing helix chain 'E' and resid 2914 through 2919 removed outlier: 4.092A pdb=" N ARG E2918 " --> pdb=" O LYS E2914 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP E2919 " --> pdb=" O GLU E2915 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2914 through 2919' Processing helix chain 'E' and resid 2920 through 2932 removed outlier: 3.504A pdb=" N PHE E2929 " --> pdb=" O GLU E2925 " (cutoff:3.500A) Processing helix chain 'E' and resid 2950 through 2966 removed outlier: 4.403A pdb=" N UNK E2956 " --> pdb=" O UNK E2952 " (cutoff:3.500A) Processing helix chain 'E' and resid 2966 through 2976 Processing helix chain 'E' and resid 2999 through 3016 removed outlier: 3.771A pdb=" N UNK E3004 " --> pdb=" O UNK E3000 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N UNK E3006 " --> pdb=" O UNK E3002 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N UNK E3009 " --> pdb=" O UNK E3005 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N UNK E3010 " --> pdb=" O UNK E3006 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N UNK E3013 " --> pdb=" O UNK E3009 " (cutoff:3.500A) Processing helix chain 'E' and resid 3017 through 3022 Processing helix chain 'E' and resid 3025 through 3040 removed outlier: 3.537A pdb=" N UNK E3031 " --> pdb=" O UNK E3027 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N UNK E3032 " --> pdb=" O UNK E3028 " (cutoff:3.500A) Processing helix chain 'E' and resid 3052 through 3063 removed outlier: 4.367A pdb=" N UNK E3056 " --> pdb=" O UNK E3052 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N UNK E3057 " --> pdb=" O UNK E3053 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N UNK E3061 " --> pdb=" O UNK E3057 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N UNK E3062 " --> pdb=" O UNK E3058 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N UNK E3063 " --> pdb=" O UNK E3059 " (cutoff:3.500A) Processing helix chain 'E' and resid 3141 through 3151 removed outlier: 3.981A pdb=" N UNK E3148 " --> pdb=" O UNK E3144 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N UNK E3149 " --> pdb=" O UNK E3145 " (cutoff:3.500A) Processing helix chain 'E' and resid 3151 through 3161 removed outlier: 3.507A pdb=" N UNK E3155 " --> pdb=" O UNK E3151 " (cutoff:3.500A) Processing helix chain 'E' and resid 3175 through 3187 removed outlier: 3.537A pdb=" N UNK E3181 " --> pdb=" O UNK E3177 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N UNK E3182 " --> pdb=" O UNK E3178 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N UNK E3183 " --> pdb=" O UNK E3179 " (cutoff:3.500A) Processing helix chain 'E' and resid 3198 through 3212 removed outlier: 3.694A pdb=" N UNK E3205 " --> pdb=" O UNK E3201 " (cutoff:3.500A) Processing helix chain 'E' and resid 3224 through 3230 removed outlier: 3.966A pdb=" N UNK E3228 " --> pdb=" O UNK E3224 " (cutoff:3.500A) Processing helix chain 'E' and resid 3248 through 3254 removed outlier: 3.547A pdb=" N UNK E3252 " --> pdb=" O UNK E3248 " (cutoff:3.500A) Processing helix chain 'E' and resid 3271 through 3285 removed outlier: 3.725A pdb=" N UNK E3281 " --> pdb=" O UNK E3277 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N UNK E3282 " --> pdb=" O UNK E3278 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N UNK E3284 " --> pdb=" O UNK E3280 " (cutoff:3.500A) Processing helix chain 'E' and resid 3305 through 3310 Processing helix chain 'E' and resid 3316 through 3321 removed outlier: 3.618A pdb=" N UNK E3321 " --> pdb=" O UNK E3317 " (cutoff:3.500A) Processing helix chain 'E' and resid 3321 through 3330 removed outlier: 3.704A pdb=" N UNK E3330 " --> pdb=" O UNK E3326 " (cutoff:3.500A) Processing helix chain 'E' and resid 3331 through 3333 No H-bonds generated for 'chain 'E' and resid 3331 through 3333' Processing helix chain 'E' and resid 3344 through 3349 removed outlier: 3.772A pdb=" N UNK E3348 " --> pdb=" O UNK E3344 " (cutoff:3.500A) Processing helix chain 'E' and resid 3361 through 3388 Processing helix chain 'E' and resid 3399 through 3409 removed outlier: 3.829A pdb=" N UNK E3403 " --> pdb=" O UNK E3399 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N UNK E3404 " --> pdb=" O UNK E3400 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N UNK E3405 " --> pdb=" O UNK E3401 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N UNK E3407 " --> pdb=" O UNK E3403 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N UNK E3409 " --> pdb=" O UNK E3405 " (cutoff:3.500A) Processing helix chain 'E' and resid 3410 through 3415 Processing helix chain 'E' and resid 3415 through 3423 removed outlier: 4.373A pdb=" N UNK E3420 " --> pdb=" O UNK E3416 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N UNK E3421 " --> pdb=" O UNK E3417 " (cutoff:3.500A) Processing helix chain 'E' and resid 3425 through 3431 Processing helix chain 'E' and resid 3434 through 3443 removed outlier: 4.013A pdb=" N UNK E3439 " --> pdb=" O UNK E3435 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N UNK E3440 " --> pdb=" O UNK E3436 " (cutoff:3.500A) Processing helix chain 'E' and resid 3445 through 3450 Processing helix chain 'E' and resid 3457 through 3460 Processing helix chain 'E' and resid 3461 through 3466 Processing helix chain 'E' and resid 3518 through 3521 removed outlier: 3.559A pdb=" N UNK E3521 " --> pdb=" O UNK E3518 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3518 through 3521' Processing helix chain 'E' and resid 3522 through 3527 removed outlier: 3.503A pdb=" N UNK E3527 " --> pdb=" O UNK E3523 " (cutoff:3.500A) Processing helix chain 'E' and resid 3551 through 3560 Processing helix chain 'E' and resid 3577 through 3582 Processing helix chain 'E' and resid 3589 through 3611 removed outlier: 4.047A pdb=" N UNK E3595 " --> pdb=" O UNK E3591 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N UNK E3597 " --> pdb=" O UNK E3593 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N UNK E3600 " --> pdb=" O UNK E3596 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N UNK E3601 " --> pdb=" O UNK E3597 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N UNK E3610 " --> pdb=" O UNK E3606 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N UNK E3611 " --> pdb=" O UNK E3607 " (cutoff:3.500A) Processing helix chain 'E' and resid 3645 through 3657 removed outlier: 3.589A pdb=" N ASN E3651 " --> pdb=" O HIS E3647 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET E3652 " --> pdb=" O ARG E3648 " (cutoff:3.500A) Processing helix chain 'E' and resid 3658 through 3661 removed outlier: 3.798A pdb=" N TRP E3661 " --> pdb=" O LYS E3658 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3658 through 3661' Processing helix chain 'E' and resid 3670 through 3680 removed outlier: 3.634A pdb=" N ILE E3674 " --> pdb=" O GLU E3670 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP E3676 " --> pdb=" O ARG E3672 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E3677 " --> pdb=" O MET E3673 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER E3678 " --> pdb=" O ILE E3674 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA E3680 " --> pdb=" O ASP E3676 " (cutoff:3.500A) Processing helix chain 'E' and resid 3681 through 3683 No H-bonds generated for 'chain 'E' and resid 3681 through 3683' Processing helix chain 'E' and resid 3696 through 3711 removed outlier: 3.595A pdb=" N LEU E3701 " --> pdb=" O PRO E3697 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E3710 " --> pdb=" O SER E3706 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR E3711 " --> pdb=" O ARG E3707 " (cutoff:3.500A) Processing helix chain 'E' and resid 3719 through 3738 removed outlier: 3.569A pdb=" N MET E3723 " --> pdb=" O ASP E3719 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E3724 " --> pdb=" O TYR E3720 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR E3725 " --> pdb=" O LEU E3721 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E3728 " --> pdb=" O ALA E3724 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS E3733 " --> pdb=" O MET E3729 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E3735 " --> pdb=" O LYS E3731 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU E3736 " --> pdb=" O SER E3732 " (cutoff:3.500A) Processing helix chain 'E' and resid 3752 through 3768 removed outlier: 3.819A pdb=" N LYS E3760 " --> pdb=" O LYS E3756 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG E3762 " --> pdb=" O MET E3758 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU E3763 " --> pdb=" O GLU E3759 " (cutoff:3.500A) Processing helix chain 'E' and resid 3774 through 3778 Processing helix chain 'E' and resid 3791 through 3805 removed outlier: 4.078A pdb=" N LYS E3799 " --> pdb=" O SER E3795 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E3800 " --> pdb=" O SER E3796 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU E3805 " --> pdb=" O GLY E3801 " (cutoff:3.500A) Processing helix chain 'E' and resid 3809 through 3824 removed outlier: 3.882A pdb=" N TYR E3819 " --> pdb=" O LYS E3815 " (cutoff:3.500A) Processing helix chain 'E' and resid 3828 through 3838 Processing helix chain 'E' and resid 3843 through 3854 removed outlier: 3.526A pdb=" N ARG E3849 " --> pdb=" O ASN E3845 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN E3850 " --> pdb=" O ALA E3846 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN E3851 " --> pdb=" O PHE E3847 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS E3852 " --> pdb=" O GLU E3848 " (cutoff:3.500A) Processing helix chain 'E' and resid 3855 through 3857 No H-bonds generated for 'chain 'E' and resid 3855 through 3857' Processing helix chain 'E' and resid 3880 through 3891 removed outlier: 3.982A pdb=" N PHE E3885 " --> pdb=" O THR E3881 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG E3886 " --> pdb=" O GLN E3882 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE E3887 " --> pdb=" O ASP E3883 " (cutoff:3.500A) Processing helix chain 'E' and resid 3899 through 3905 removed outlier: 3.712A pdb=" N ARG E3904 " --> pdb=" O GLN E3900 " (cutoff:3.500A) Processing helix chain 'E' and resid 3914 through 3938 removed outlier: 3.630A pdb=" N CYS E3918 " --> pdb=" O ASN E3914 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL E3920 " --> pdb=" O ILE E3916 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR E3922 " --> pdb=" O CYS E3918 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER E3929 " --> pdb=" O ARG E3925 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP E3932 " --> pdb=" O GLU E3928 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR E3936 " --> pdb=" O ASP E3932 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR E3937 " --> pdb=" O PHE E3933 " (cutoff:3.500A) Processing helix chain 'E' and resid 3944 through 3967 removed outlier: 3.669A pdb=" N PHE E3951 " --> pdb=" O GLY E3947 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS E3953 " --> pdb=" O ARG E3949 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA E3954 " --> pdb=" O ASN E3950 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA E3958 " --> pdb=" O ALA E3954 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU E3967 " --> pdb=" O ASN E3963 " (cutoff:3.500A) Processing helix chain 'E' and resid 3973 through 3982 Processing helix chain 'E' and resid 3984 through 4003 removed outlier: 3.764A pdb=" N ALA E3988 " --> pdb=" O ARG E3984 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY E3991 " --> pdb=" O ASP E3987 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE E3992 " --> pdb=" O ALA E3988 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E3993 " --> pdb=" O VAL E3989 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N MET E4000 " --> pdb=" O PHE E3996 " (cutoff:3.500A) Processing helix chain 'E' and resid 4004 through 4008 removed outlier: 5.474A pdb=" N SER E4007 " --> pdb=" O ALA E4004 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER E4008 " --> pdb=" O GLN E4005 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4004 through 4008' Processing helix chain 'E' and resid 4009 through 4030 removed outlier: 3.809A pdb=" N ASP E4018 " --> pdb=" O LYS E4014 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS E4021 " --> pdb=" O LEU E4017 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E4024 " --> pdb=" O GLN E4020 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N MET E4026 " --> pdb=" O ASP E4022 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU E4027 " --> pdb=" O MET E4023 " (cutoff:3.500A) Processing helix chain 'E' and resid 4040 through 4051 removed outlier: 3.570A pdb=" N VAL E4045 " --> pdb=" O ALA E4041 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP E4046 " --> pdb=" O ARG E4042 " (cutoff:3.500A) Processing helix chain 'E' and resid 4051 through 4072 removed outlier: 3.790A pdb=" N GLU E4056 " --> pdb=" O SER E4052 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE E4058 " --> pdb=" O ASN E4054 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE E4065 " --> pdb=" O PHE E4061 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU E4066 " --> pdb=" O PHE E4062 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS E4069 " --> pdb=" O PHE E4065 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP E4070 " --> pdb=" O LEU E4066 " (cutoff:3.500A) Processing helix chain 'E' and resid 4074 through 4079 Processing helix chain 'E' and resid 4090 through 4100 removed outlier: 3.704A pdb=" N MET E4097 " --> pdb=" O PHE E4093 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP E4098 " --> pdb=" O GLN E4094 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN E4100 " --> pdb=" O ALA E4096 " (cutoff:3.500A) Processing helix chain 'E' and resid 4104 through 4115 Processing helix chain 'E' and resid 4124 through 4129 removed outlier: 3.514A pdb=" N ALA E4129 " --> pdb=" O PHE E4125 " (cutoff:3.500A) Processing helix chain 'E' and resid 4130 through 4133 Processing helix chain 'E' and resid 4136 through 4154 removed outlier: 4.040A pdb=" N GLY E4140 " --> pdb=" O ALA E4136 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR E4148 " --> pdb=" O ALA E4144 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU E4152 " --> pdb=" O THR E4148 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS E4153 " --> pdb=" O ASN E4149 " (cutoff:3.500A) Processing helix chain 'E' and resid 4157 through 4167 removed outlier: 3.591A pdb=" N ARG E4161 " --> pdb=" O ASP E4157 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN E4162 " --> pdb=" O PRO E4158 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE E4163 " --> pdb=" O ARG E4159 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU E4165 " --> pdb=" O ARG E4161 " (cutoff:3.500A) Processing helix chain 'E' and resid 4167 through 4174 removed outlier: 3.799A pdb=" N LEU E4171 " --> pdb=" O ALA E4167 " (cutoff:3.500A) Processing helix chain 'E' and resid 4200 through 4206 Processing helix chain 'E' and resid 4207 through 4224 removed outlier: 4.022A pdb=" N SER E4213 " --> pdb=" O GLN E4209 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL E4222 " --> pdb=" O ILE E4218 " (cutoff:3.500A) Processing helix chain 'E' and resid 4228 through 4239 removed outlier: 3.624A pdb=" N VAL E4235 " --> pdb=" O MET E4231 " (cutoff:3.500A) Processing helix chain 'E' and resid 4240 through 4249 Processing helix chain 'E' and resid 4543 through 4558 removed outlier: 3.902A pdb=" N VAL E4549 " --> pdb=" O GLU E4545 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR E4554 " --> pdb=" O LYS E4550 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN E4558 " --> pdb=" O TYR E4554 " (cutoff:3.500A) Processing helix chain 'E' and resid 4558 through 4576 removed outlier: 3.840A pdb=" N LEU E4562 " --> pdb=" O ASN E4558 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE E4571 " --> pdb=" O LEU E4567 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA E4572 " --> pdb=" O PHE E4568 " (cutoff:3.500A) Processing helix chain 'E' and resid 4643 through 4665 removed outlier: 3.955A pdb=" N LEU E4648 " --> pdb=" O TRP E4644 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU E4649 " --> pdb=" O CYS E4645 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR E4651 " --> pdb=" O SER E4647 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS E4657 " --> pdb=" O VAL E4653 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE E4659 " --> pdb=" O PHE E4655 " (cutoff:3.500A) Processing helix chain 'E' and resid 4667 through 4683 removed outlier: 3.734A pdb=" N GLU E4676 " --> pdb=" O LYS E4672 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU E4682 " --> pdb=" O ALA E4678 " (cutoff:3.500A) Processing helix chain 'E' and resid 4696 through 4702 removed outlier: 3.537A pdb=" N GLN E4700 " --> pdb=" O ASP E4696 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP E4702 " --> pdb=" O LYS E4698 " (cutoff:3.500A) Processing helix chain 'E' and resid 4703 through 4705 No H-bonds generated for 'chain 'E' and resid 4703 through 4705' Processing helix chain 'E' and resid 4719 through 4728 removed outlier: 3.565A pdb=" N LEU E4725 " --> pdb=" O LYS E4721 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP E4726 " --> pdb=" O ARG E4722 " (cutoff:3.500A) Processing helix chain 'E' and resid 4733 through 4741 Processing helix chain 'E' and resid 4745 through 4753 removed outlier: 4.833A pdb=" N THR E4751 " --> pdb=" O SER E4747 " (cutoff:3.500A) Processing helix chain 'E' and resid 4772 through 4784 Processing helix chain 'E' and resid 4786 through 4802 removed outlier: 3.752A pdb=" N SER E4799 " --> pdb=" O TYR E4795 " (cutoff:3.500A) Processing helix chain 'E' and resid 4811 through 4816 removed outlier: 4.551A pdb=" N ASP E4815 " --> pdb=" O ALA E4811 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE E4816 " --> pdb=" O HIS E4812 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4811 through 4816' Processing helix chain 'E' and resid 4817 through 4819 No H-bonds generated for 'chain 'E' and resid 4817 through 4819' Processing helix chain 'E' and resid 4820 through 4833 removed outlier: 3.622A pdb=" N ARG E4824 " --> pdb=" O VAL E4820 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR E4825 " --> pdb=" O LYS E4821 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER E4829 " --> pdb=" O THR E4825 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL E4830 " --> pdb=" O ILE E4826 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN E4833 " --> pdb=" O SER E4829 " (cutoff:3.500A) Processing helix chain 'E' and resid 4836 through 4858 removed outlier: 3.975A pdb=" N GLY E4842 " --> pdb=" O VAL E4838 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E4847 " --> pdb=" O LEU E4843 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL E4854 " --> pdb=" O LEU E4850 " (cutoff:3.500A) Processing helix chain 'E' and resid 4859 through 4863 removed outlier: 3.572A pdb=" N PHE E4862 " --> pdb=" O PHE E4859 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR E4863 " --> pdb=" O ARG E4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4859 through 4863' Processing helix chain 'E' and resid 4879 through 4894 removed outlier: 3.642A pdb=" N MET E4887 " --> pdb=" O TYR E4883 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL E4891 " --> pdb=" O MET E4887 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ARG E4892 " --> pdb=" O TYR E4888 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY E4894 " --> pdb=" O GLY E4890 " (cutoff:3.500A) Processing helix chain 'E' and resid 4909 through 4924 removed outlier: 3.615A pdb=" N VAL E4914 " --> pdb=" O GLU E4910 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL E4915 " --> pdb=" O LEU E4911 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL E4924 " --> pdb=" O PHE E4920 " (cutoff:3.500A) Processing helix chain 'E' and resid 4927 through 4933 removed outlier: 4.029A pdb=" N ILE E4932 " --> pdb=" O LEU E4928 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E4933 " --> pdb=" O LEU E4929 " (cutoff:3.500A) Processing helix chain 'E' and resid 4933 through 4944 removed outlier: 3.535A pdb=" N ILE E4937 " --> pdb=" O GLN E4933 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE E4940 " --> pdb=" O ILE E4936 " (cutoff:3.500A) Processing helix chain 'E' and resid 4947 through 4952 Processing helix chain 'E' and resid 4964 through 4969 removed outlier: 3.876A pdb=" N PHE E4968 " --> pdb=" O GLY E4964 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP E4969 " --> pdb=" O SER E4965 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4964 through 4969' Processing helix chain 'E' and resid 4973 through 4979 Processing helix chain 'E' and resid 4986 through 4997 removed outlier: 3.665A pdb=" N LEU E4992 " --> pdb=" O TYR E4988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE E4996 " --> pdb=" O LEU E4992 " (cutoff:3.500A) Processing helix chain 'E' and resid 4999 through 5003 removed outlier: 3.903A pdb=" N HIS E5003 " --> pdb=" O GLU E5000 " (cutoff:3.500A) Processing helix chain 'E' and resid 5006 through 5017 removed outlier: 3.602A pdb=" N MET E5013 " --> pdb=" O TYR E5009 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 82 Processing helix chain 'I' and resid 251 through 255 removed outlier: 3.737A pdb=" N THR I 254 " --> pdb=" O ALA I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 369 removed outlier: 3.700A pdb=" N LEU I 369 " --> pdb=" O LYS I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 420 removed outlier: 4.023A pdb=" N GLN I 399 " --> pdb=" O GLN I 395 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG I 402 " --> pdb=" O SER I 398 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE I 404 " --> pdb=" O ALA I 400 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS I 405 " --> pdb=" O ALA I 401 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN I 413 " --> pdb=" O GLY I 409 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE I 414 " --> pdb=" O LEU I 410 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS I 416 " --> pdb=" O ASN I 412 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY I 417 " --> pdb=" O GLN I 413 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER I 420 " --> pdb=" O LYS I 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 452 removed outlier: 3.695A pdb=" N SER I 444 " --> pdb=" O ALA I 440 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY I 450 " --> pdb=" O GLN I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 460 through 481 removed outlier: 3.634A pdb=" N SER I 466 " --> pdb=" O GLU I 462 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER I 470 " --> pdb=" O SER I 466 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG I 474 " --> pdb=" O SER I 470 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE I 478 " --> pdb=" O ARG I 474 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN I 479 " --> pdb=" O GLN I 475 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU I 480 " --> pdb=" O SER I 476 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU I 481 " --> pdb=" O LEU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 494 removed outlier: 3.715A pdb=" N CYS I 490 " --> pdb=" O LEU I 486 " (cutoff:3.500A) Processing helix chain 'I' and resid 514 through 529 removed outlier: 3.727A pdb=" N ILE I 518 " --> pdb=" O SER I 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 533 through 538 removed outlier: 3.798A pdb=" N CYS I 537 " --> pdb=" O ASN I 533 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA I 538 " --> pdb=" O ARG I 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 533 through 538' Processing helix chain 'I' and resid 539 through 541 No H-bonds generated for 'chain 'I' and resid 539 through 541' Processing helix chain 'I' and resid 543 through 551 removed outlier: 3.556A pdb=" N VAL I 548 " --> pdb=" O LEU I 544 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER I 549 " --> pdb=" O ASP I 545 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS I 550 " --> pdb=" O TRP I 546 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU I 551 " --> pdb=" O VAL I 547 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 571 removed outlier: 3.740A pdb=" N VAL I 567 " --> pdb=" O VAL I 563 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU I 568 " --> pdb=" O LEU I 564 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE I 569 " --> pdb=" O TYR I 565 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU I 570 " --> pdb=" O CYS I 566 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER I 571 " --> pdb=" O VAL I 567 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 576 removed outlier: 4.053A pdb=" N LEU I 575 " --> pdb=" O SER I 571 " (cutoff:3.500A) Processing helix chain 'I' and resid 582 through 594 Processing helix chain 'I' and resid 597 through 608 removed outlier: 3.850A pdb=" N LEU I 603 " --> pdb=" O VAL I 599 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS I 607 " --> pdb=" O LEU I 603 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL I 608 " --> pdb=" O CYS I 604 " (cutoff:3.500A) Processing helix chain 'I' and resid 614 through 624 removed outlier: 4.002A pdb=" N GLN I 618 " --> pdb=" O VAL I 614 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP I 619 " --> pdb=" O ARG I 615 " (cutoff:3.500A) Processing helix chain 'I' and resid 864 through 888 removed outlier: 3.731A pdb=" N ILE I 870 " --> pdb=" O HIS I 866 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU I 872 " --> pdb=" O GLU I 868 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS I 873 " --> pdb=" O ARG I 869 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS I 879 " --> pdb=" O ALA I 875 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG I 886 " --> pdb=" O TRP I 882 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE I 887 " --> pdb=" O ALA I 883 " (cutoff:3.500A) Processing helix chain 'I' and resid 909 through 913 removed outlier: 3.611A pdb=" N LEU I 913 " --> pdb=" O PHE I 910 " (cutoff:3.500A) Processing helix chain 'I' and resid 914 through 934 removed outlier: 3.667A pdb=" N GLN I 923 " --> pdb=" O ASN I 919 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU I 927 " --> pdb=" O GLN I 923 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA I 934 " --> pdb=" O LYS I 930 " (cutoff:3.500A) Processing helix chain 'I' and resid 980 through 1001 removed outlier: 4.077A pdb=" N ASP I 986 " --> pdb=" O THR I 982 " (cutoff:3.500A) Processing helix chain 'I' and resid 1028 through 1041 removed outlier: 3.953A pdb=" N LYS I1032 " --> pdb=" O ASP I1028 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU I1039 " --> pdb=" O ASN I1035 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN I1041 " --> pdb=" O ASP I1037 " (cutoff:3.500A) Processing helix chain 'I' and resid 1042 through 1049 removed outlier: 3.540A pdb=" N LEU I1046 " --> pdb=" O ALA I1042 " (cutoff:3.500A) Processing helix chain 'I' and resid 1078 through 1082 Processing helix chain 'I' and resid 1575 through 1579 removed outlier: 3.734A pdb=" N MET I1579 " --> pdb=" O SER I1576 " (cutoff:3.500A) Processing helix chain 'I' and resid 1652 through 1657 removed outlier: 3.805A pdb=" N LEU I1657 " --> pdb=" O LEU I1653 " (cutoff:3.500A) Processing helix chain 'I' and resid 1658 through 1674 removed outlier: 4.022A pdb=" N HIS I1665 " --> pdb=" O ARG I1661 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR I1670 " --> pdb=" O THR I1666 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG I1671 " --> pdb=" O LEU I1667 " (cutoff:3.500A) Processing helix chain 'I' and resid 1678 through 1683 Processing helix chain 'I' and resid 1695 through 1700 removed outlier: 4.331A pdb=" N GLU I1699 " --> pdb=" O LEU I1695 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP I1700 " --> pdb=" O HIS I1696 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1695 through 1700' Processing helix chain 'I' and resid 1710 through 1714 removed outlier: 3.634A pdb=" N ASP I1713 " --> pdb=" O GLY I1710 " (cutoff:3.500A) Processing helix chain 'I' and resid 1715 through 1719 removed outlier: 3.770A pdb=" N ILE I1718 " --> pdb=" O LEU I1715 " (cutoff:3.500A) Processing helix chain 'I' and resid 1720 through 1732 removed outlier: 3.977A pdb=" N ARG I1725 " --> pdb=" O GLU I1721 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N SER I1726 " --> pdb=" O SER I1722 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER I1729 " --> pdb=" O ARG I1725 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET I1730 " --> pdb=" O SER I1726 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER I1732 " --> pdb=" O ARG I1728 " (cutoff:3.500A) Processing helix chain 'I' and resid 1739 through 1744 removed outlier: 3.550A pdb=" N ALA I1744 " --> pdb=" O PRO I1740 " (cutoff:3.500A) Processing helix chain 'I' and resid 1803 through 1823 removed outlier: 3.879A pdb=" N LEU I1807 " --> pdb=" O PRO I1803 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP I1809 " --> pdb=" O GLU I1805 " (cutoff:3.500A) Processing helix chain 'I' and resid 1833 through 1838 Processing helix chain 'I' and resid 1840 through 1851 removed outlier: 3.542A pdb=" N MET I1851 " --> pdb=" O THR I1847 " (cutoff:3.500A) Processing helix chain 'I' and resid 1855 through 1863 Processing helix chain 'I' and resid 1866 through 1871 Processing helix chain 'I' and resid 1933 through 1977 removed outlier: 4.013A pdb=" N TYR I1945 " --> pdb=" O ASN I1941 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE I1946 " --> pdb=" O LEU I1942 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU I1951 " --> pdb=" O CYS I1947 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU I1963 " --> pdb=" O ALA I1959 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG I1964 " --> pdb=" O ALA I1960 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL I1966 " --> pdb=" O ALA I1962 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN I1972 " --> pdb=" O LYS I1968 " (cutoff:3.500A) Processing helix chain 'I' and resid 1977 through 1982 Processing helix chain 'I' and resid 1989 through 1994 Processing helix chain 'I' and resid 1995 through 1998 Processing helix chain 'I' and resid 2001 through 2012 removed outlier: 3.752A pdb=" N ASN I2007 " --> pdb=" O GLN I2003 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET I2008 " --> pdb=" O GLU I2004 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS I2011 " --> pdb=" O ASN I2007 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE I2012 " --> pdb=" O MET I2008 " (cutoff:3.500A) Processing helix chain 'I' and resid 2029 through 2042 removed outlier: 3.685A pdb=" N LEU I2039 " --> pdb=" O HIS I2035 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA I2040 " --> pdb=" O GLN I2036 " (cutoff:3.500A) Processing helix chain 'I' and resid 2094 through 2108 removed outlier: 3.657A pdb=" N HIS I2100 " --> pdb=" O GLU I2096 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL I2103 " --> pdb=" O SER I2099 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA I2106 " --> pdb=" O VAL I2102 " (cutoff:3.500A) Processing helix chain 'I' and resid 2113 through 2129 removed outlier: 3.928A pdb=" N VAL I2117 " --> pdb=" O SER I2113 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG I2126 " --> pdb=" O SER I2122 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN I2127 " --> pdb=" O LEU I2123 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR I2128 " --> pdb=" O LEU I2124 " (cutoff:3.500A) Processing helix chain 'I' and resid 2129 through 2136 Processing helix chain 'I' and resid 2137 through 2139 No H-bonds generated for 'chain 'I' and resid 2137 through 2139' Processing helix chain 'I' and resid 2149 through 2165 removed outlier: 3.696A pdb=" N GLY I2160 " --> pdb=" O LEU I2156 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN I2161 " --> pdb=" O GLU I2157 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU I2165 " --> pdb=" O GLN I2161 " (cutoff:3.500A) Processing helix chain 'I' and resid 2166 through 2168 No H-bonds generated for 'chain 'I' and resid 2166 through 2168' Processing helix chain 'I' and resid 2171 through 2186 removed outlier: 3.723A pdb=" N ASN I2176 " --> pdb=" O PRO I2172 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU I2177 " --> pdb=" O GLN I2173 " (cutoff:3.500A) Processing helix chain 'I' and resid 2189 through 2194 Processing helix chain 'I' and resid 2194 through 2201 removed outlier: 4.270A pdb=" N MET I2198 " --> pdb=" O HIS I2194 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG I2199 " --> pdb=" O PRO I2195 " (cutoff:3.500A) Processing helix chain 'I' and resid 2202 through 2216 removed outlier: 3.532A pdb=" N VAL I2207 " --> pdb=" O MET I2203 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET I2208 " --> pdb=" O HIS I2204 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN I2213 " --> pdb=" O GLU I2209 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL I2214 " --> pdb=" O VAL I2210 " (cutoff:3.500A) Processing helix chain 'I' and resid 2228 through 2242 removed outlier: 4.042A pdb=" N TYR I2238 " --> pdb=" O ARG I2234 " (cutoff:3.500A) Processing helix chain 'I' and resid 2245 through 2250 Processing helix chain 'I' and resid 2253 through 2261 removed outlier: 3.747A pdb=" N ASN I2260 " --> pdb=" O TYR I2256 " (cutoff:3.500A) Processing helix chain 'I' and resid 2271 through 2279 removed outlier: 3.945A pdb=" N ALA I2276 " --> pdb=" O PRO I2272 " (cutoff:3.500A) Processing helix chain 'I' and resid 2294 through 2306 removed outlier: 3.692A pdb=" N VAL I2299 " --> pdb=" O LEU I2295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER I2300 " --> pdb=" O GLU I2296 " (cutoff:3.500A) Processing helix chain 'I' and resid 2310 through 2315 removed outlier: 4.137A pdb=" N ALA I2315 " --> pdb=" O PRO I2311 " (cutoff:3.500A) Processing helix chain 'I' and resid 2326 through 2331 Processing helix chain 'I' and resid 2332 through 2337 Processing helix chain 'I' and resid 2346 through 2358 removed outlier: 3.998A pdb=" N ALA I2350 " --> pdb=" O VAL I2346 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL I2352 " --> pdb=" O GLU I2348 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL I2353 " --> pdb=" O ASN I2349 " (cutoff:3.500A) Processing helix chain 'I' and resid 2360 through 2364 Processing helix chain 'I' and resid 2375 through 2388 removed outlier: 3.690A pdb=" N ARG I2385 " --> pdb=" O GLU I2381 " (cutoff:3.500A) Processing helix chain 'I' and resid 2389 through 2393 removed outlier: 3.778A pdb=" N ARG I2392 " --> pdb=" O ASP I2389 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP I2393 " --> pdb=" O PRO I2390 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2389 through 2393' Processing helix chain 'I' and resid 2418 through 2436 removed outlier: 3.681A pdb=" N PHE I2425 " --> pdb=" O ALA I2421 " (cutoff:3.500A) Processing helix chain 'I' and resid 2440 through 2445 removed outlier: 4.163A pdb=" N ALA I2445 " --> pdb=" O HIS I2441 " (cutoff:3.500A) Processing helix chain 'I' and resid 2450 through 2461 removed outlier: 3.748A pdb=" N ARG I2454 " --> pdb=" O ALA I2450 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER I2459 " --> pdb=" O ALA I2455 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL I2461 " --> pdb=" O LEU I2457 " (cutoff:3.500A) Processing helix chain 'I' and resid 2466 through 2471 removed outlier: 3.511A pdb=" N SER I2471 " --> pdb=" O VAL I2467 " (cutoff:3.500A) Processing helix chain 'I' and resid 2495 through 2499 removed outlier: 3.516A pdb=" N UNK I2498 " --> pdb=" O UNK I2495 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N UNK I2499 " --> pdb=" O UNK I2496 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2495 through 2499' Processing helix chain 'I' and resid 2502 through 2507 removed outlier: 3.729A pdb=" N UNK I2506 " --> pdb=" O UNK I2502 " (cutoff:3.500A) Processing helix chain 'I' and resid 2516 through 2521 Processing helix chain 'I' and resid 2524 through 2532 removed outlier: 3.920A pdb=" N UNK I2528 " --> pdb=" O UNK I2524 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N UNK I2532 " --> pdb=" O UNK I2528 " (cutoff:3.500A) Processing helix chain 'I' and resid 2542 through 2547 removed outlier: 3.761A pdb=" N UNK I2546 " --> pdb=" O UNK I2542 " (cutoff:3.500A) Processing helix chain 'I' and resid 2551 through 2557 removed outlier: 4.015A pdb=" N UNK I2555 " --> pdb=" O UNK I2551 " (cutoff:3.500A) Processing helix chain 'I' and resid 2567 through 2581 Processing helix chain 'I' and resid 2587 through 2600 removed outlier: 3.665A pdb=" N UNK I2597 " --> pdb=" O UNK I2593 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N UNK I2598 " --> pdb=" O UNK I2594 " (cutoff:3.500A) Processing helix chain 'I' and resid 2610 through 2618 removed outlier: 3.820A pdb=" N UNK I2617 " --> pdb=" O UNK I2613 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N UNK I2618 " --> pdb=" O UNK I2614 " (cutoff:3.500A) Processing helix chain 'I' and resid 2626 through 2640 removed outlier: 3.947A pdb=" N UNK I2630 " --> pdb=" O UNK I2626 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N UNK I2631 " --> pdb=" O UNK I2627 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N UNK I2635 " --> pdb=" O UNK I2631 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N UNK I2636 " --> pdb=" O UNK I2632 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N UNK I2639 " --> pdb=" O UNK I2635 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N UNK I2640 " --> pdb=" O UNK I2636 " (cutoff:3.500A) Processing helix chain 'I' and resid 2641 through 2643 No H-bonds generated for 'chain 'I' and resid 2641 through 2643' Processing helix chain 'I' and resid 2650 through 2666 Processing helix chain 'I' and resid 2667 through 2669 No H-bonds generated for 'chain 'I' and resid 2667 through 2669' Processing helix chain 'I' and resid 2687 through 2691 removed outlier: 3.715A pdb=" N UNK I2690 " --> pdb=" O UNK I2687 " (cutoff:3.500A) Processing helix chain 'I' and resid 2748 through 2773 removed outlier: 3.831A pdb=" N SER I2753 " --> pdb=" O GLU I2749 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE I2754 " --> pdb=" O LYS I2750 " (cutoff:3.500A) Processing helix chain 'I' and resid 2793 through 2797 removed outlier: 3.780A pdb=" N PHE I2797 " --> pdb=" O TYR I2794 " (cutoff:3.500A) Processing helix chain 'I' and resid 2802 through 2806 Processing helix chain 'I' and resid 2809 through 2820 removed outlier: 4.302A pdb=" N ALA I2815 " --> pdb=" O GLU I2811 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE I2817 " --> pdb=" O LEU I2813 " (cutoff:3.500A) Processing helix chain 'I' and resid 2868 through 2895 removed outlier: 4.248A pdb=" N MET I2874 " --> pdb=" O GLU I2870 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA I2875 " --> pdb=" O LEU I2871 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU I2876 " --> pdb=" O GLN I2872 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU I2880 " --> pdb=" O GLU I2876 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TRP I2886 " --> pdb=" O TYR I2882 " (cutoff:3.500A) Processing helix chain 'I' and resid 2907 through 2911 Processing helix chain 'I' and resid 2914 through 2919 removed outlier: 4.092A pdb=" N ARG I2918 " --> pdb=" O LYS I2914 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP I2919 " --> pdb=" O GLU I2915 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2914 through 2919' Processing helix chain 'I' and resid 2920 through 2932 removed outlier: 3.504A pdb=" N PHE I2929 " --> pdb=" O GLU I2925 " (cutoff:3.500A) Processing helix chain 'I' and resid 2950 through 2966 removed outlier: 4.402A pdb=" N UNK I2956 " --> pdb=" O UNK I2952 " (cutoff:3.500A) Processing helix chain 'I' and resid 2966 through 2976 Processing helix chain 'I' and resid 2999 through 3016 removed outlier: 3.775A pdb=" N UNK I3004 " --> pdb=" O UNK I3000 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N UNK I3006 " --> pdb=" O UNK I3002 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N UNK I3009 " --> pdb=" O UNK I3005 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N UNK I3010 " --> pdb=" O UNK I3006 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N UNK I3013 " --> pdb=" O UNK I3009 " (cutoff:3.500A) Processing helix chain 'I' and resid 3017 through 3022 Processing helix chain 'I' and resid 3025 through 3040 removed outlier: 3.539A pdb=" N UNK I3031 " --> pdb=" O UNK I3027 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N UNK I3032 " --> pdb=" O UNK I3028 " (cutoff:3.500A) Processing helix chain 'I' and resid 3052 through 3063 removed outlier: 4.368A pdb=" N UNK I3056 " --> pdb=" O UNK I3052 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N UNK I3057 " --> pdb=" O UNK I3053 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N UNK I3061 " --> pdb=" O UNK I3057 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N UNK I3062 " --> pdb=" O UNK I3058 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N UNK I3063 " --> pdb=" O UNK I3059 " (cutoff:3.500A) Processing helix chain 'I' and resid 3141 through 3151 removed outlier: 3.981A pdb=" N UNK I3148 " --> pdb=" O UNK I3144 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N UNK I3149 " --> pdb=" O UNK I3145 " (cutoff:3.500A) Processing helix chain 'I' and resid 3151 through 3161 removed outlier: 3.507A pdb=" N UNK I3155 " --> pdb=" O UNK I3151 " (cutoff:3.500A) Processing helix chain 'I' and resid 3175 through 3187 removed outlier: 3.539A pdb=" N UNK I3181 " --> pdb=" O UNK I3177 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N UNK I3182 " --> pdb=" O UNK I3178 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N UNK I3183 " --> pdb=" O UNK I3179 " (cutoff:3.500A) Processing helix chain 'I' and resid 3198 through 3212 removed outlier: 3.697A pdb=" N UNK I3205 " --> pdb=" O UNK I3201 " (cutoff:3.500A) Processing helix chain 'I' and resid 3224 through 3230 removed outlier: 3.966A pdb=" N UNK I3228 " --> pdb=" O UNK I3224 " (cutoff:3.500A) Processing helix chain 'I' and resid 3248 through 3254 removed outlier: 3.542A pdb=" N UNK I3252 " --> pdb=" O UNK I3248 " (cutoff:3.500A) Processing helix chain 'I' and resid 3271 through 3285 removed outlier: 3.722A pdb=" N UNK I3281 " --> pdb=" O UNK I3277 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N UNK I3282 " --> pdb=" O UNK I3278 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N UNK I3284 " --> pdb=" O UNK I3280 " (cutoff:3.500A) Processing helix chain 'I' and resid 3305 through 3310 Processing helix chain 'I' and resid 3316 through 3321 removed outlier: 3.618A pdb=" N UNK I3321 " --> pdb=" O UNK I3317 " (cutoff:3.500A) Processing helix chain 'I' and resid 3321 through 3330 removed outlier: 3.704A pdb=" N UNK I3330 " --> pdb=" O UNK I3326 " (cutoff:3.500A) Processing helix chain 'I' and resid 3331 through 3333 No H-bonds generated for 'chain 'I' and resid 3331 through 3333' Processing helix chain 'I' and resid 3344 through 3349 removed outlier: 3.772A pdb=" N UNK I3348 " --> pdb=" O UNK I3344 " (cutoff:3.500A) Processing helix chain 'I' and resid 3361 through 3388 Processing helix chain 'I' and resid 3399 through 3409 removed outlier: 3.822A pdb=" N UNK I3403 " --> pdb=" O UNK I3399 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N UNK I3404 " --> pdb=" O UNK I3400 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N UNK I3405 " --> pdb=" O UNK I3401 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N UNK I3407 " --> pdb=" O UNK I3403 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N UNK I3409 " --> pdb=" O UNK I3405 " (cutoff:3.500A) Processing helix chain 'I' and resid 3410 through 3415 Processing helix chain 'I' and resid 3415 through 3423 removed outlier: 4.373A pdb=" N UNK I3420 " --> pdb=" O UNK I3416 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N UNK I3421 " --> pdb=" O UNK I3417 " (cutoff:3.500A) Processing helix chain 'I' and resid 3425 through 3431 Processing helix chain 'I' and resid 3434 through 3443 removed outlier: 4.013A pdb=" N UNK I3439 " --> pdb=" O UNK I3435 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N UNK I3440 " --> pdb=" O UNK I3436 " (cutoff:3.500A) Processing helix chain 'I' and resid 3445 through 3450 Processing helix chain 'I' and resid 3457 through 3460 Processing helix chain 'I' and resid 3461 through 3466 Processing helix chain 'I' and resid 3518 through 3521 removed outlier: 3.557A pdb=" N UNK I3521 " --> pdb=" O UNK I3518 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3518 through 3521' Processing helix chain 'I' and resid 3522 through 3527 removed outlier: 3.507A pdb=" N UNK I3527 " --> pdb=" O UNK I3523 " (cutoff:3.500A) Processing helix chain 'I' and resid 3551 through 3560 Processing helix chain 'I' and resid 3577 through 3582 Processing helix chain 'I' and resid 3589 through 3611 removed outlier: 4.046A pdb=" N UNK I3595 " --> pdb=" O UNK I3591 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N UNK I3597 " --> pdb=" O UNK I3593 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N UNK I3600 " --> pdb=" O UNK I3596 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N UNK I3601 " --> pdb=" O UNK I3597 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N UNK I3610 " --> pdb=" O UNK I3606 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N UNK I3611 " --> pdb=" O UNK I3607 " (cutoff:3.500A) Processing helix chain 'I' and resid 3645 through 3657 removed outlier: 3.590A pdb=" N ASN I3651 " --> pdb=" O HIS I3647 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET I3652 " --> pdb=" O ARG I3648 " (cutoff:3.500A) Processing helix chain 'I' and resid 3658 through 3661 removed outlier: 3.798A pdb=" N TRP I3661 " --> pdb=" O LYS I3658 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3658 through 3661' Processing helix chain 'I' and resid 3670 through 3680 removed outlier: 3.634A pdb=" N ILE I3674 " --> pdb=" O GLU I3670 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP I3676 " --> pdb=" O ARG I3672 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU I3677 " --> pdb=" O MET I3673 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER I3678 " --> pdb=" O ILE I3674 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA I3680 " --> pdb=" O ASP I3676 " (cutoff:3.500A) Processing helix chain 'I' and resid 3681 through 3683 No H-bonds generated for 'chain 'I' and resid 3681 through 3683' Processing helix chain 'I' and resid 3696 through 3711 removed outlier: 3.595A pdb=" N LEU I3701 " --> pdb=" O PRO I3697 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU I3710 " --> pdb=" O SER I3706 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR I3711 " --> pdb=" O ARG I3707 " (cutoff:3.500A) Processing helix chain 'I' and resid 3719 through 3738 removed outlier: 3.569A pdb=" N MET I3723 " --> pdb=" O ASP I3719 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA I3724 " --> pdb=" O TYR I3720 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR I3725 " --> pdb=" O LEU I3721 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE I3728 " --> pdb=" O ALA I3724 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS I3733 " --> pdb=" O MET I3729 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU I3735 " --> pdb=" O LYS I3731 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU I3736 " --> pdb=" O SER I3732 " (cutoff:3.500A) Processing helix chain 'I' and resid 3752 through 3768 removed outlier: 3.819A pdb=" N LYS I3760 " --> pdb=" O LYS I3756 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG I3762 " --> pdb=" O MET I3758 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU I3763 " --> pdb=" O GLU I3759 " (cutoff:3.500A) Processing helix chain 'I' and resid 3774 through 3778 Processing helix chain 'I' and resid 3791 through 3805 removed outlier: 4.077A pdb=" N LYS I3799 " --> pdb=" O SER I3795 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU I3800 " --> pdb=" O SER I3796 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU I3805 " --> pdb=" O GLY I3801 " (cutoff:3.500A) Processing helix chain 'I' and resid 3809 through 3824 removed outlier: 3.882A pdb=" N TYR I3819 " --> pdb=" O LYS I3815 " (cutoff:3.500A) Processing helix chain 'I' and resid 3828 through 3838 Processing helix chain 'I' and resid 3843 through 3854 removed outlier: 3.525A pdb=" N ARG I3849 " --> pdb=" O ASN I3845 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN I3850 " --> pdb=" O ALA I3846 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN I3851 " --> pdb=" O PHE I3847 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS I3852 " --> pdb=" O GLU I3848 " (cutoff:3.500A) Processing helix chain 'I' and resid 3855 through 3857 No H-bonds generated for 'chain 'I' and resid 3855 through 3857' Processing helix chain 'I' and resid 3880 through 3891 removed outlier: 3.983A pdb=" N PHE I3885 " --> pdb=" O THR I3881 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG I3886 " --> pdb=" O GLN I3882 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE I3887 " --> pdb=" O ASP I3883 " (cutoff:3.500A) Processing helix chain 'I' and resid 3899 through 3905 removed outlier: 3.712A pdb=" N ARG I3904 " --> pdb=" O GLN I3900 " (cutoff:3.500A) Processing helix chain 'I' and resid 3914 through 3938 removed outlier: 3.631A pdb=" N CYS I3918 " --> pdb=" O ASN I3914 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL I3920 " --> pdb=" O ILE I3916 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR I3922 " --> pdb=" O CYS I3918 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER I3929 " --> pdb=" O ARG I3925 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP I3932 " --> pdb=" O GLU I3928 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR I3936 " --> pdb=" O ASP I3932 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR I3937 " --> pdb=" O PHE I3933 " (cutoff:3.500A) Processing helix chain 'I' and resid 3944 through 3967 removed outlier: 3.670A pdb=" N PHE I3951 " --> pdb=" O GLY I3947 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS I3953 " --> pdb=" O ARG I3949 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA I3954 " --> pdb=" O ASN I3950 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA I3958 " --> pdb=" O ALA I3954 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU I3967 " --> pdb=" O ASN I3963 " (cutoff:3.500A) Processing helix chain 'I' and resid 3973 through 3982 Processing helix chain 'I' and resid 3984 through 4003 removed outlier: 3.764A pdb=" N ALA I3988 " --> pdb=" O ARG I3984 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY I3991 " --> pdb=" O ASP I3987 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE I3992 " --> pdb=" O ALA I3988 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU I3993 " --> pdb=" O VAL I3989 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET I4000 " --> pdb=" O PHE I3996 " (cutoff:3.500A) Processing helix chain 'I' and resid 4004 through 4008 removed outlier: 5.473A pdb=" N SER I4007 " --> pdb=" O ALA I4004 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER I4008 " --> pdb=" O GLN I4005 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4004 through 4008' Processing helix chain 'I' and resid 4009 through 4030 removed outlier: 3.809A pdb=" N ASP I4018 " --> pdb=" O LYS I4014 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS I4021 " --> pdb=" O LEU I4017 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL I4024 " --> pdb=" O GLN I4020 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N MET I4026 " --> pdb=" O ASP I4022 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU I4027 " --> pdb=" O MET I4023 " (cutoff:3.500A) Processing helix chain 'I' and resid 4040 through 4051 removed outlier: 3.570A pdb=" N VAL I4045 " --> pdb=" O ALA I4041 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP I4046 " --> pdb=" O ARG I4042 " (cutoff:3.500A) Processing helix chain 'I' and resid 4051 through 4072 removed outlier: 3.791A pdb=" N GLU I4056 " --> pdb=" O SER I4052 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE I4058 " --> pdb=" O ASN I4054 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE I4065 " --> pdb=" O PHE I4061 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU I4066 " --> pdb=" O PHE I4062 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS I4069 " --> pdb=" O PHE I4065 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP I4070 " --> pdb=" O LEU I4066 " (cutoff:3.500A) Processing helix chain 'I' and resid 4074 through 4079 Processing helix chain 'I' and resid 4090 through 4100 removed outlier: 3.704A pdb=" N MET I4097 " --> pdb=" O PHE I4093 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP I4098 " --> pdb=" O GLN I4094 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN I4100 " --> pdb=" O ALA I4096 " (cutoff:3.500A) Processing helix chain 'I' and resid 4104 through 4115 Processing helix chain 'I' and resid 4124 through 4129 removed outlier: 3.513A pdb=" N ALA I4129 " --> pdb=" O PHE I4125 " (cutoff:3.500A) Processing helix chain 'I' and resid 4130 through 4133 Processing helix chain 'I' and resid 4136 through 4154 removed outlier: 4.040A pdb=" N GLY I4140 " --> pdb=" O ALA I4136 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR I4148 " --> pdb=" O ALA I4144 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU I4152 " --> pdb=" O THR I4148 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS I4153 " --> pdb=" O ASN I4149 " (cutoff:3.500A) Processing helix chain 'I' and resid 4157 through 4167 removed outlier: 3.590A pdb=" N ARG I4161 " --> pdb=" O ASP I4157 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN I4162 " --> pdb=" O PRO I4158 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE I4163 " --> pdb=" O ARG I4159 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU I4165 " --> pdb=" O ARG I4161 " (cutoff:3.500A) Processing helix chain 'I' and resid 4167 through 4174 removed outlier: 3.800A pdb=" N LEU I4171 " --> pdb=" O ALA I4167 " (cutoff:3.500A) Processing helix chain 'I' and resid 4200 through 4206 Processing helix chain 'I' and resid 4207 through 4224 removed outlier: 4.022A pdb=" N SER I4213 " --> pdb=" O GLN I4209 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL I4222 " --> pdb=" O ILE I4218 " (cutoff:3.500A) Processing helix chain 'I' and resid 4228 through 4239 removed outlier: 3.623A pdb=" N VAL I4235 " --> pdb=" O MET I4231 " (cutoff:3.500A) Processing helix chain 'I' and resid 4240 through 4249 Processing helix chain 'I' and resid 4543 through 4558 removed outlier: 3.902A pdb=" N VAL I4549 " --> pdb=" O GLU I4545 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR I4554 " --> pdb=" O LYS I4550 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN I4558 " --> pdb=" O TYR I4554 " (cutoff:3.500A) Processing helix chain 'I' and resid 4558 through 4576 removed outlier: 3.840A pdb=" N LEU I4562 " --> pdb=" O ASN I4558 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE I4571 " --> pdb=" O LEU I4567 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA I4572 " --> pdb=" O PHE I4568 " (cutoff:3.500A) Processing helix chain 'I' and resid 4643 through 4665 removed outlier: 3.956A pdb=" N LEU I4648 " --> pdb=" O TRP I4644 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU I4649 " --> pdb=" O CYS I4645 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR I4651 " --> pdb=" O SER I4647 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS I4657 " --> pdb=" O VAL I4653 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE I4659 " --> pdb=" O PHE I4655 " (cutoff:3.500A) Processing helix chain 'I' and resid 4667 through 4683 removed outlier: 3.734A pdb=" N GLU I4676 " --> pdb=" O LYS I4672 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU I4682 " --> pdb=" O ALA I4678 " (cutoff:3.500A) Processing helix chain 'I' and resid 4696 through 4702 removed outlier: 3.536A pdb=" N GLN I4700 " --> pdb=" O ASP I4696 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP I4702 " --> pdb=" O LYS I4698 " (cutoff:3.500A) Processing helix chain 'I' and resid 4703 through 4705 No H-bonds generated for 'chain 'I' and resid 4703 through 4705' Processing helix chain 'I' and resid 4719 through 4728 removed outlier: 3.565A pdb=" N LEU I4725 " --> pdb=" O LYS I4721 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP I4726 " --> pdb=" O ARG I4722 " (cutoff:3.500A) Processing helix chain 'I' and resid 4733 through 4741 Processing helix chain 'I' and resid 4745 through 4753 removed outlier: 4.832A pdb=" N THR I4751 " --> pdb=" O SER I4747 " (cutoff:3.500A) Processing helix chain 'I' and resid 4772 through 4784 Processing helix chain 'I' and resid 4786 through 4802 removed outlier: 3.752A pdb=" N SER I4799 " --> pdb=" O TYR I4795 " (cutoff:3.500A) Processing helix chain 'I' and resid 4811 through 4816 removed outlier: 4.550A pdb=" N ASP I4815 " --> pdb=" O ALA I4811 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE I4816 " --> pdb=" O HIS I4812 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4811 through 4816' Processing helix chain 'I' and resid 4817 through 4819 No H-bonds generated for 'chain 'I' and resid 4817 through 4819' Processing helix chain 'I' and resid 4820 through 4833 removed outlier: 3.622A pdb=" N ARG I4824 " --> pdb=" O VAL I4820 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR I4825 " --> pdb=" O LYS I4821 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER I4829 " --> pdb=" O THR I4825 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL I4830 " --> pdb=" O ILE I4826 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN I4833 " --> pdb=" O SER I4829 " (cutoff:3.500A) Processing helix chain 'I' and resid 4836 through 4858 removed outlier: 3.975A pdb=" N GLY I4842 " --> pdb=" O VAL I4838 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL I4847 " --> pdb=" O LEU I4843 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL I4854 " --> pdb=" O LEU I4850 " (cutoff:3.500A) Processing helix chain 'I' and resid 4859 through 4863 removed outlier: 3.572A pdb=" N PHE I4862 " --> pdb=" O PHE I4859 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR I4863 " --> pdb=" O ARG I4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4859 through 4863' Processing helix chain 'I' and resid 4879 through 4894 removed outlier: 3.643A pdb=" N MET I4887 " --> pdb=" O TYR I4883 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL I4891 " --> pdb=" O MET I4887 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ARG I4892 " --> pdb=" O TYR I4888 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY I4894 " --> pdb=" O GLY I4890 " (cutoff:3.500A) Processing helix chain 'I' and resid 4909 through 4924 removed outlier: 3.614A pdb=" N VAL I4914 " --> pdb=" O GLU I4910 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL I4915 " --> pdb=" O LEU I4911 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL I4924 " --> pdb=" O PHE I4920 " (cutoff:3.500A) Processing helix chain 'I' and resid 4927 through 4933 removed outlier: 4.028A pdb=" N ILE I4932 " --> pdb=" O LEU I4928 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN I4933 " --> pdb=" O LEU I4929 " (cutoff:3.500A) Processing helix chain 'I' and resid 4933 through 4944 removed outlier: 3.535A pdb=" N ILE I4937 " --> pdb=" O GLN I4933 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE I4940 " --> pdb=" O ILE I4936 " (cutoff:3.500A) Processing helix chain 'I' and resid 4947 through 4952 Processing helix chain 'I' and resid 4964 through 4969 removed outlier: 3.875A pdb=" N PHE I4968 " --> pdb=" O GLY I4964 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP I4969 " --> pdb=" O SER I4965 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4964 through 4969' Processing helix chain 'I' and resid 4973 through 4979 Processing helix chain 'I' and resid 4986 through 4997 removed outlier: 3.665A pdb=" N LEU I4992 " --> pdb=" O TYR I4988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE I4996 " --> pdb=" O LEU I4992 " (cutoff:3.500A) Processing helix chain 'I' and resid 4999 through 5003 removed outlier: 3.903A pdb=" N HIS I5003 " --> pdb=" O GLU I5000 " (cutoff:3.500A) Processing helix chain 'I' and resid 5006 through 5017 removed outlier: 3.602A pdb=" N MET I5013 " --> pdb=" O TYR I5009 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 251 through 255 removed outlier: 3.737A pdb=" N THR G 254 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 369 removed outlier: 3.700A pdb=" N LEU G 369 " --> pdb=" O LYS G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 420 removed outlier: 4.023A pdb=" N GLN G 399 " --> pdb=" O GLN G 395 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG G 402 " --> pdb=" O SER G 398 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE G 404 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS G 405 " --> pdb=" O ALA G 401 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN G 413 " --> pdb=" O GLY G 409 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE G 414 " --> pdb=" O LEU G 410 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS G 416 " --> pdb=" O ASN G 412 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY G 417 " --> pdb=" O GLN G 413 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER G 420 " --> pdb=" O LYS G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 452 removed outlier: 3.696A pdb=" N SER G 444 " --> pdb=" O ALA G 440 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY G 450 " --> pdb=" O GLN G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 481 removed outlier: 3.634A pdb=" N SER G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER G 470 " --> pdb=" O SER G 466 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG G 474 " --> pdb=" O SER G 470 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE G 478 " --> pdb=" O ARG G 474 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN G 479 " --> pdb=" O GLN G 475 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU G 480 " --> pdb=" O SER G 476 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU G 481 " --> pdb=" O LEU G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 494 removed outlier: 3.715A pdb=" N CYS G 490 " --> pdb=" O LEU G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 529 removed outlier: 3.728A pdb=" N ILE G 518 " --> pdb=" O SER G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 538 removed outlier: 3.799A pdb=" N CYS G 537 " --> pdb=" O ASN G 533 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA G 538 " --> pdb=" O ARG G 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 533 through 538' Processing helix chain 'G' and resid 539 through 541 No H-bonds generated for 'chain 'G' and resid 539 through 541' Processing helix chain 'G' and resid 543 through 551 removed outlier: 3.555A pdb=" N VAL G 548 " --> pdb=" O LEU G 544 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER G 549 " --> pdb=" O ASP G 545 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS G 550 " --> pdb=" O TRP G 546 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU G 551 " --> pdb=" O VAL G 547 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 571 removed outlier: 3.740A pdb=" N VAL G 567 " --> pdb=" O VAL G 563 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU G 568 " --> pdb=" O LEU G 564 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE G 569 " --> pdb=" O TYR G 565 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU G 570 " --> pdb=" O CYS G 566 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER G 571 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 576 removed outlier: 4.053A pdb=" N LEU G 575 " --> pdb=" O SER G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 594 Processing helix chain 'G' and resid 597 through 608 removed outlier: 3.850A pdb=" N LEU G 603 " --> pdb=" O VAL G 599 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS G 607 " --> pdb=" O LEU G 603 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL G 608 " --> pdb=" O CYS G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 624 removed outlier: 4.002A pdb=" N GLN G 618 " --> pdb=" O VAL G 614 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP G 619 " --> pdb=" O ARG G 615 " (cutoff:3.500A) Processing helix chain 'G' and resid 864 through 888 removed outlier: 3.731A pdb=" N ILE G 870 " --> pdb=" O HIS G 866 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU G 872 " --> pdb=" O GLU G 868 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS G 873 " --> pdb=" O ARG G 869 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS G 879 " --> pdb=" O ALA G 875 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG G 886 " --> pdb=" O TRP G 882 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE G 887 " --> pdb=" O ALA G 883 " (cutoff:3.500A) Processing helix chain 'G' and resid 909 through 913 removed outlier: 3.611A pdb=" N LEU G 913 " --> pdb=" O PHE G 910 " (cutoff:3.500A) Processing helix chain 'G' and resid 914 through 934 removed outlier: 3.667A pdb=" N GLN G 923 " --> pdb=" O ASN G 919 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU G 927 " --> pdb=" O GLN G 923 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA G 934 " --> pdb=" O LYS G 930 " (cutoff:3.500A) Processing helix chain 'G' and resid 980 through 1001 removed outlier: 4.076A pdb=" N ASP G 986 " --> pdb=" O THR G 982 " (cutoff:3.500A) Processing helix chain 'G' and resid 1028 through 1041 removed outlier: 3.952A pdb=" N LYS G1032 " --> pdb=" O ASP G1028 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU G1039 " --> pdb=" O ASN G1035 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN G1041 " --> pdb=" O ASP G1037 " (cutoff:3.500A) Processing helix chain 'G' and resid 1042 through 1049 removed outlier: 3.541A pdb=" N LEU G1046 " --> pdb=" O ALA G1042 " (cutoff:3.500A) Processing helix chain 'G' and resid 1078 through 1082 Processing helix chain 'G' and resid 1575 through 1579 removed outlier: 3.734A pdb=" N MET G1579 " --> pdb=" O SER G1576 " (cutoff:3.500A) Processing helix chain 'G' and resid 1652 through 1657 removed outlier: 3.805A pdb=" N LEU G1657 " --> pdb=" O LEU G1653 " (cutoff:3.500A) Processing helix chain 'G' and resid 1658 through 1674 removed outlier: 4.023A pdb=" N HIS G1665 " --> pdb=" O ARG G1661 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR G1670 " --> pdb=" O THR G1666 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG G1671 " --> pdb=" O LEU G1667 " (cutoff:3.500A) Processing helix chain 'G' and resid 1678 through 1683 Processing helix chain 'G' and resid 1695 through 1700 removed outlier: 4.330A pdb=" N GLU G1699 " --> pdb=" O LEU G1695 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP G1700 " --> pdb=" O HIS G1696 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1695 through 1700' Processing helix chain 'G' and resid 1710 through 1714 removed outlier: 3.634A pdb=" N ASP G1713 " --> pdb=" O GLY G1710 " (cutoff:3.500A) Processing helix chain 'G' and resid 1715 through 1719 removed outlier: 3.769A pdb=" N ILE G1718 " --> pdb=" O LEU G1715 " (cutoff:3.500A) Processing helix chain 'G' and resid 1720 through 1732 removed outlier: 3.976A pdb=" N ARG G1725 " --> pdb=" O GLU G1721 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N SER G1726 " --> pdb=" O SER G1722 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER G1729 " --> pdb=" O ARG G1725 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET G1730 " --> pdb=" O SER G1726 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER G1732 " --> pdb=" O ARG G1728 " (cutoff:3.500A) Processing helix chain 'G' and resid 1739 through 1744 removed outlier: 3.550A pdb=" N ALA G1744 " --> pdb=" O PRO G1740 " (cutoff:3.500A) Processing helix chain 'G' and resid 1803 through 1823 removed outlier: 3.879A pdb=" N LEU G1807 " --> pdb=" O PRO G1803 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP G1809 " --> pdb=" O GLU G1805 " (cutoff:3.500A) Processing helix chain 'G' and resid 1833 through 1838 Processing helix chain 'G' and resid 1840 through 1851 removed outlier: 3.542A pdb=" N MET G1851 " --> pdb=" O THR G1847 " (cutoff:3.500A) Processing helix chain 'G' and resid 1855 through 1863 Processing helix chain 'G' and resid 1866 through 1871 Processing helix chain 'G' and resid 1933 through 1977 removed outlier: 4.014A pdb=" N TYR G1945 " --> pdb=" O ASN G1941 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE G1946 " --> pdb=" O LEU G1942 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU G1951 " --> pdb=" O CYS G1947 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU G1963 " --> pdb=" O ALA G1959 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG G1964 " --> pdb=" O ALA G1960 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL G1966 " --> pdb=" O ALA G1962 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN G1972 " --> pdb=" O LYS G1968 " (cutoff:3.500A) Processing helix chain 'G' and resid 1977 through 1982 Processing helix chain 'G' and resid 1989 through 1994 Processing helix chain 'G' and resid 1995 through 1998 Processing helix chain 'G' and resid 2001 through 2012 removed outlier: 3.751A pdb=" N ASN G2007 " --> pdb=" O GLN G2003 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET G2008 " --> pdb=" O GLU G2004 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS G2011 " --> pdb=" O ASN G2007 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE G2012 " --> pdb=" O MET G2008 " (cutoff:3.500A) Processing helix chain 'G' and resid 2029 through 2042 removed outlier: 3.686A pdb=" N LEU G2039 " --> pdb=" O HIS G2035 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA G2040 " --> pdb=" O GLN G2036 " (cutoff:3.500A) Processing helix chain 'G' and resid 2094 through 2108 removed outlier: 3.657A pdb=" N HIS G2100 " --> pdb=" O GLU G2096 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL G2103 " --> pdb=" O SER G2099 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA G2106 " --> pdb=" O VAL G2102 " (cutoff:3.500A) Processing helix chain 'G' and resid 2113 through 2129 removed outlier: 3.928A pdb=" N VAL G2117 " --> pdb=" O SER G2113 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG G2126 " --> pdb=" O SER G2122 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN G2127 " --> pdb=" O LEU G2123 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR G2128 " --> pdb=" O LEU G2124 " (cutoff:3.500A) Processing helix chain 'G' and resid 2129 through 2136 Processing helix chain 'G' and resid 2137 through 2139 No H-bonds generated for 'chain 'G' and resid 2137 through 2139' Processing helix chain 'G' and resid 2149 through 2165 removed outlier: 3.696A pdb=" N GLY G2160 " --> pdb=" O LEU G2156 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN G2161 " --> pdb=" O GLU G2157 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU G2165 " --> pdb=" O GLN G2161 " (cutoff:3.500A) Processing helix chain 'G' and resid 2166 through 2168 No H-bonds generated for 'chain 'G' and resid 2166 through 2168' Processing helix chain 'G' and resid 2171 through 2186 removed outlier: 3.724A pdb=" N ASN G2176 " --> pdb=" O PRO G2172 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU G2177 " --> pdb=" O GLN G2173 " (cutoff:3.500A) Processing helix chain 'G' and resid 2189 through 2194 Processing helix chain 'G' and resid 2194 through 2201 removed outlier: 4.269A pdb=" N MET G2198 " --> pdb=" O HIS G2194 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG G2199 " --> pdb=" O PRO G2195 " (cutoff:3.500A) Processing helix chain 'G' and resid 2202 through 2216 removed outlier: 3.533A pdb=" N VAL G2207 " --> pdb=" O MET G2203 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET G2208 " --> pdb=" O HIS G2204 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN G2213 " --> pdb=" O GLU G2209 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL G2214 " --> pdb=" O VAL G2210 " (cutoff:3.500A) Processing helix chain 'G' and resid 2228 through 2242 removed outlier: 4.042A pdb=" N TYR G2238 " --> pdb=" O ARG G2234 " (cutoff:3.500A) Processing helix chain 'G' and resid 2245 through 2250 Processing helix chain 'G' and resid 2253 through 2261 removed outlier: 3.747A pdb=" N ASN G2260 " --> pdb=" O TYR G2256 " (cutoff:3.500A) Processing helix chain 'G' and resid 2271 through 2279 removed outlier: 3.945A pdb=" N ALA G2276 " --> pdb=" O PRO G2272 " (cutoff:3.500A) Processing helix chain 'G' and resid 2294 through 2306 removed outlier: 3.693A pdb=" N VAL G2299 " --> pdb=" O LEU G2295 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER G2300 " --> pdb=" O GLU G2296 " (cutoff:3.500A) Processing helix chain 'G' and resid 2310 through 2315 removed outlier: 4.138A pdb=" N ALA G2315 " --> pdb=" O PRO G2311 " (cutoff:3.500A) Processing helix chain 'G' and resid 2326 through 2331 Processing helix chain 'G' and resid 2332 through 2337 Processing helix chain 'G' and resid 2346 through 2358 removed outlier: 3.998A pdb=" N ALA G2350 " --> pdb=" O VAL G2346 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL G2352 " --> pdb=" O GLU G2348 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL G2353 " --> pdb=" O ASN G2349 " (cutoff:3.500A) Processing helix chain 'G' and resid 2360 through 2364 Processing helix chain 'G' and resid 2375 through 2388 removed outlier: 3.690A pdb=" N ARG G2385 " --> pdb=" O GLU G2381 " (cutoff:3.500A) Processing helix chain 'G' and resid 2389 through 2393 removed outlier: 3.778A pdb=" N ARG G2392 " --> pdb=" O ASP G2389 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP G2393 " --> pdb=" O PRO G2390 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2389 through 2393' Processing helix chain 'G' and resid 2418 through 2436 removed outlier: 3.681A pdb=" N PHE G2425 " --> pdb=" O ALA G2421 " (cutoff:3.500A) Processing helix chain 'G' and resid 2440 through 2445 removed outlier: 4.164A pdb=" N ALA G2445 " --> pdb=" O HIS G2441 " (cutoff:3.500A) Processing helix chain 'G' and resid 2450 through 2461 removed outlier: 3.748A pdb=" N ARG G2454 " --> pdb=" O ALA G2450 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER G2459 " --> pdb=" O ALA G2455 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL G2461 " --> pdb=" O LEU G2457 " (cutoff:3.500A) Processing helix chain 'G' and resid 2466 through 2471 removed outlier: 3.511A pdb=" N SER G2471 " --> pdb=" O VAL G2467 " (cutoff:3.500A) Processing helix chain 'G' and resid 2495 through 2499 removed outlier: 3.524A pdb=" N UNK G2498 " --> pdb=" O UNK G2495 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N UNK G2499 " --> pdb=" O UNK G2496 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2495 through 2499' Processing helix chain 'G' and resid 2502 through 2507 removed outlier: 3.733A pdb=" N UNK G2506 " --> pdb=" O UNK G2502 " (cutoff:3.500A) Processing helix chain 'G' and resid 2516 through 2521 Processing helix chain 'G' and resid 2524 through 2532 removed outlier: 3.915A pdb=" N UNK G2528 " --> pdb=" O UNK G2524 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N UNK G2532 " --> pdb=" O UNK G2528 " (cutoff:3.500A) Processing helix chain 'G' and resid 2542 through 2547 removed outlier: 3.759A pdb=" N UNK G2546 " --> pdb=" O UNK G2542 " (cutoff:3.500A) Processing helix chain 'G' and resid 2551 through 2557 removed outlier: 4.019A pdb=" N UNK G2555 " --> pdb=" O UNK G2551 " (cutoff:3.500A) Processing helix chain 'G' and resid 2567 through 2581 Processing helix chain 'G' and resid 2587 through 2600 removed outlier: 3.661A pdb=" N UNK G2597 " --> pdb=" O UNK G2593 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N UNK G2598 " --> pdb=" O UNK G2594 " (cutoff:3.500A) Processing helix chain 'G' and resid 2610 through 2618 removed outlier: 3.815A pdb=" N UNK G2617 " --> pdb=" O UNK G2613 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N UNK G2618 " --> pdb=" O UNK G2614 " (cutoff:3.500A) Processing helix chain 'G' and resid 2626 through 2640 removed outlier: 3.947A pdb=" N UNK G2630 " --> pdb=" O UNK G2626 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N UNK G2631 " --> pdb=" O UNK G2627 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N UNK G2635 " --> pdb=" O UNK G2631 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N UNK G2636 " --> pdb=" O UNK G2632 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N UNK G2639 " --> pdb=" O UNK G2635 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N UNK G2640 " --> pdb=" O UNK G2636 " (cutoff:3.500A) Processing helix chain 'G' and resid 2641 through 2643 No H-bonds generated for 'chain 'G' and resid 2641 through 2643' Processing helix chain 'G' and resid 2650 through 2666 Processing helix chain 'G' and resid 2667 through 2669 No H-bonds generated for 'chain 'G' and resid 2667 through 2669' Processing helix chain 'G' and resid 2687 through 2691 removed outlier: 3.715A pdb=" N UNK G2690 " --> pdb=" O UNK G2687 " (cutoff:3.500A) Processing helix chain 'G' and resid 2748 through 2773 removed outlier: 3.830A pdb=" N SER G2753 " --> pdb=" O GLU G2749 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE G2754 " --> pdb=" O LYS G2750 " (cutoff:3.500A) Processing helix chain 'G' and resid 2793 through 2797 removed outlier: 3.780A pdb=" N PHE G2797 " --> pdb=" O TYR G2794 " (cutoff:3.500A) Processing helix chain 'G' and resid 2809 through 2820 removed outlier: 4.302A pdb=" N ALA G2815 " --> pdb=" O GLU G2811 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE G2817 " --> pdb=" O LEU G2813 " (cutoff:3.500A) Processing helix chain 'G' and resid 2868 through 2895 removed outlier: 4.248A pdb=" N MET G2874 " --> pdb=" O GLU G2870 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA G2875 " --> pdb=" O LEU G2871 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU G2876 " --> pdb=" O GLN G2872 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU G2880 " --> pdb=" O GLU G2876 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TRP G2886 " --> pdb=" O TYR G2882 " (cutoff:3.500A) Processing helix chain 'G' and resid 2907 through 2911 Processing helix chain 'G' and resid 2914 through 2919 removed outlier: 4.092A pdb=" N ARG G2918 " --> pdb=" O LYS G2914 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP G2919 " --> pdb=" O GLU G2915 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2914 through 2919' Processing helix chain 'G' and resid 2920 through 2932 removed outlier: 3.504A pdb=" N PHE G2929 " --> pdb=" O GLU G2925 " (cutoff:3.500A) Processing helix chain 'G' and resid 2950 through 2966 removed outlier: 4.404A pdb=" N UNK G2956 " --> pdb=" O UNK G2952 " (cutoff:3.500A) Processing helix chain 'G' and resid 2966 through 2976 Processing helix chain 'G' and resid 2999 through 3016 removed outlier: 3.777A pdb=" N UNK G3004 " --> pdb=" O UNK G3000 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N UNK G3006 " --> pdb=" O UNK G3002 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N UNK G3009 " --> pdb=" O UNK G3005 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N UNK G3010 " --> pdb=" O UNK G3006 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N UNK G3013 " --> pdb=" O UNK G3009 " (cutoff:3.500A) Processing helix chain 'G' and resid 3017 through 3022 Processing helix chain 'G' and resid 3025 through 3040 removed outlier: 3.538A pdb=" N UNK G3031 " --> pdb=" O UNK G3027 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N UNK G3032 " --> pdb=" O UNK G3028 " (cutoff:3.500A) Processing helix chain 'G' and resid 3052 through 3063 removed outlier: 4.371A pdb=" N UNK G3056 " --> pdb=" O UNK G3052 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N UNK G3057 " --> pdb=" O UNK G3053 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N UNK G3061 " --> pdb=" O UNK G3057 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N UNK G3062 " --> pdb=" O UNK G3058 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N UNK G3063 " --> pdb=" O UNK G3059 " (cutoff:3.500A) Processing helix chain 'G' and resid 3141 through 3151 removed outlier: 3.981A pdb=" N UNK G3148 " --> pdb=" O UNK G3144 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N UNK G3149 " --> pdb=" O UNK G3145 " (cutoff:3.500A) Processing helix chain 'G' and resid 3151 through 3161 removed outlier: 3.508A pdb=" N UNK G3155 " --> pdb=" O UNK G3151 " (cutoff:3.500A) Processing helix chain 'G' and resid 3175 through 3187 removed outlier: 3.537A pdb=" N UNK G3181 " --> pdb=" O UNK G3177 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N UNK G3182 " --> pdb=" O UNK G3178 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N UNK G3183 " --> pdb=" O UNK G3179 " (cutoff:3.500A) Processing helix chain 'G' and resid 3198 through 3212 removed outlier: 3.702A pdb=" N UNK G3205 " --> pdb=" O UNK G3201 " (cutoff:3.500A) Processing helix chain 'G' and resid 3224 through 3230 removed outlier: 3.965A pdb=" N UNK G3228 " --> pdb=" O UNK G3224 " (cutoff:3.500A) Processing helix chain 'G' and resid 3248 through 3254 removed outlier: 3.539A pdb=" N UNK G3252 " --> pdb=" O UNK G3248 " (cutoff:3.500A) Processing helix chain 'G' and resid 3271 through 3285 removed outlier: 3.717A pdb=" N UNK G3281 " --> pdb=" O UNK G3277 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N UNK G3282 " --> pdb=" O UNK G3278 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N UNK G3284 " --> pdb=" O UNK G3280 " (cutoff:3.500A) Processing helix chain 'G' and resid 3305 through 3310 Processing helix chain 'G' and resid 3316 through 3321 removed outlier: 3.619A pdb=" N UNK G3321 " --> pdb=" O UNK G3317 " (cutoff:3.500A) Processing helix chain 'G' and resid 3321 through 3330 removed outlier: 3.701A pdb=" N UNK G3330 " --> pdb=" O UNK G3326 " (cutoff:3.500A) Processing helix chain 'G' and resid 3331 through 3333 No H-bonds generated for 'chain 'G' and resid 3331 through 3333' Processing helix chain 'G' and resid 3344 through 3349 removed outlier: 3.771A pdb=" N UNK G3348 " --> pdb=" O UNK G3344 " (cutoff:3.500A) Processing helix chain 'G' and resid 3361 through 3388 Processing helix chain 'G' and resid 3399 through 3409 removed outlier: 3.823A pdb=" N UNK G3403 " --> pdb=" O UNK G3399 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N UNK G3404 " --> pdb=" O UNK G3400 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N UNK G3405 " --> pdb=" O UNK G3401 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N UNK G3407 " --> pdb=" O UNK G3403 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N UNK G3409 " --> pdb=" O UNK G3405 " (cutoff:3.500A) Processing helix chain 'G' and resid 3410 through 3415 Processing helix chain 'G' and resid 3415 through 3423 removed outlier: 4.374A pdb=" N UNK G3420 " --> pdb=" O UNK G3416 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N UNK G3421 " --> pdb=" O UNK G3417 " (cutoff:3.500A) Processing helix chain 'G' and resid 3425 through 3431 Processing helix chain 'G' and resid 3434 through 3443 removed outlier: 4.014A pdb=" N UNK G3439 " --> pdb=" O UNK G3435 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N UNK G3440 " --> pdb=" O UNK G3436 " (cutoff:3.500A) Processing helix chain 'G' and resid 3445 through 3450 Processing helix chain 'G' and resid 3457 through 3460 Processing helix chain 'G' and resid 3461 through 3466 Processing helix chain 'G' and resid 3518 through 3521 removed outlier: 3.552A pdb=" N UNK G3521 " --> pdb=" O UNK G3518 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 3518 through 3521' Processing helix chain 'G' and resid 3522 through 3527 removed outlier: 3.505A pdb=" N UNK G3527 " --> pdb=" O UNK G3523 " (cutoff:3.500A) Processing helix chain 'G' and resid 3551 through 3560 Processing helix chain 'G' and resid 3577 through 3582 Processing helix chain 'G' and resid 3589 through 3611 removed outlier: 4.045A pdb=" N UNK G3595 " --> pdb=" O UNK G3591 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N UNK G3597 " --> pdb=" O UNK G3593 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N UNK G3600 " --> pdb=" O UNK G3596 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N UNK G3601 " --> pdb=" O UNK G3597 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N UNK G3610 " --> pdb=" O UNK G3606 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N UNK G3611 " --> pdb=" O UNK G3607 " (cutoff:3.500A) Processing helix chain 'G' and resid 3645 through 3657 removed outlier: 3.589A pdb=" N ASN G3651 " --> pdb=" O HIS G3647 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET G3652 " --> pdb=" O ARG G3648 " (cutoff:3.500A) Processing helix chain 'G' and resid 3658 through 3661 removed outlier: 3.798A pdb=" N TRP G3661 " --> pdb=" O LYS G3658 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 3658 through 3661' Processing helix chain 'G' and resid 3670 through 3680 removed outlier: 3.634A pdb=" N ILE G3674 " --> pdb=" O GLU G3670 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP G3676 " --> pdb=" O ARG G3672 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU G3677 " --> pdb=" O MET G3673 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER G3678 " --> pdb=" O ILE G3674 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA G3680 " --> pdb=" O ASP G3676 " (cutoff:3.500A) Processing helix chain 'G' and resid 3681 through 3683 No H-bonds generated for 'chain 'G' and resid 3681 through 3683' Processing helix chain 'G' and resid 3696 through 3711 removed outlier: 3.594A pdb=" N LEU G3701 " --> pdb=" O PRO G3697 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU G3710 " --> pdb=" O SER G3706 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR G3711 " --> pdb=" O ARG G3707 " (cutoff:3.500A) Processing helix chain 'G' and resid 3719 through 3738 removed outlier: 3.569A pdb=" N MET G3723 " --> pdb=" O ASP G3719 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA G3724 " --> pdb=" O TYR G3720 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR G3725 " --> pdb=" O LEU G3721 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE G3728 " --> pdb=" O ALA G3724 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS G3733 " --> pdb=" O MET G3729 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU G3735 " --> pdb=" O LYS G3731 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU G3736 " --> pdb=" O SER G3732 " (cutoff:3.500A) Processing helix chain 'G' and resid 3752 through 3768 removed outlier: 3.819A pdb=" N LYS G3760 " --> pdb=" O LYS G3756 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG G3762 " --> pdb=" O MET G3758 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU G3763 " --> pdb=" O GLU G3759 " (cutoff:3.500A) Processing helix chain 'G' and resid 3774 through 3778 Processing helix chain 'G' and resid 3791 through 3805 removed outlier: 4.078A pdb=" N LYS G3799 " --> pdb=" O SER G3795 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU G3800 " --> pdb=" O SER G3796 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU G3805 " --> pdb=" O GLY G3801 " (cutoff:3.500A) Processing helix chain 'G' and resid 3809 through 3824 removed outlier: 3.882A pdb=" N TYR G3819 " --> pdb=" O LYS G3815 " (cutoff:3.500A) Processing helix chain 'G' and resid 3828 through 3838 Processing helix chain 'G' and resid 3843 through 3854 removed outlier: 3.525A pdb=" N ARG G3849 " --> pdb=" O ASN G3845 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN G3850 " --> pdb=" O ALA G3846 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN G3851 " --> pdb=" O PHE G3847 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS G3852 " --> pdb=" O GLU G3848 " (cutoff:3.500A) Processing helix chain 'G' and resid 3855 through 3857 No H-bonds generated for 'chain 'G' and resid 3855 through 3857' Processing helix chain 'G' and resid 3880 through 3891 removed outlier: 3.982A pdb=" N PHE G3885 " --> pdb=" O THR G3881 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG G3886 " --> pdb=" O GLN G3882 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE G3887 " --> pdb=" O ASP G3883 " (cutoff:3.500A) Processing helix chain 'G' and resid 3899 through 3905 removed outlier: 3.711A pdb=" N ARG G3904 " --> pdb=" O GLN G3900 " (cutoff:3.500A) Processing helix chain 'G' and resid 3914 through 3938 removed outlier: 3.629A pdb=" N CYS G3918 " --> pdb=" O ASN G3914 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL G3920 " --> pdb=" O ILE G3916 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR G3922 " --> pdb=" O CYS G3918 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER G3929 " --> pdb=" O ARG G3925 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP G3932 " --> pdb=" O GLU G3928 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR G3936 " --> pdb=" O ASP G3932 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR G3937 " --> pdb=" O PHE G3933 " (cutoff:3.500A) Processing helix chain 'G' and resid 3944 through 3967 removed outlier: 3.669A pdb=" N PHE G3951 " --> pdb=" O GLY G3947 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS G3953 " --> pdb=" O ARG G3949 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA G3954 " --> pdb=" O ASN G3950 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA G3958 " --> pdb=" O ALA G3954 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU G3967 " --> pdb=" O ASN G3963 " (cutoff:3.500A) Processing helix chain 'G' and resid 3973 through 3982 Processing helix chain 'G' and resid 3984 through 4003 removed outlier: 3.764A pdb=" N ALA G3988 " --> pdb=" O ARG G3984 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY G3991 " --> pdb=" O ASP G3987 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE G3992 " --> pdb=" O ALA G3988 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU G3993 " --> pdb=" O VAL G3989 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET G4000 " --> pdb=" O PHE G3996 " (cutoff:3.500A) Processing helix chain 'G' and resid 4004 through 4008 removed outlier: 5.473A pdb=" N SER G4007 " --> pdb=" O ALA G4004 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N SER G4008 " --> pdb=" O GLN G4005 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4004 through 4008' Processing helix chain 'G' and resid 4009 through 4030 removed outlier: 3.808A pdb=" N ASP G4018 " --> pdb=" O LYS G4014 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS G4021 " --> pdb=" O LEU G4017 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL G4024 " --> pdb=" O GLN G4020 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N MET G4026 " --> pdb=" O ASP G4022 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU G4027 " --> pdb=" O MET G4023 " (cutoff:3.500A) Processing helix chain 'G' and resid 4040 through 4051 removed outlier: 3.570A pdb=" N VAL G4045 " --> pdb=" O ALA G4041 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP G4046 " --> pdb=" O ARG G4042 " (cutoff:3.500A) Processing helix chain 'G' and resid 4051 through 4072 removed outlier: 3.790A pdb=" N GLU G4056 " --> pdb=" O SER G4052 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE G4058 " --> pdb=" O ASN G4054 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE G4065 " --> pdb=" O PHE G4061 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU G4066 " --> pdb=" O PHE G4062 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS G4069 " --> pdb=" O PHE G4065 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP G4070 " --> pdb=" O LEU G4066 " (cutoff:3.500A) Processing helix chain 'G' and resid 4074 through 4079 Processing helix chain 'G' and resid 4090 through 4100 removed outlier: 3.704A pdb=" N MET G4097 " --> pdb=" O PHE G4093 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP G4098 " --> pdb=" O GLN G4094 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN G4100 " --> pdb=" O ALA G4096 " (cutoff:3.500A) Processing helix chain 'G' and resid 4104 through 4115 Processing helix chain 'G' and resid 4124 through 4129 removed outlier: 3.514A pdb=" N ALA G4129 " --> pdb=" O PHE G4125 " (cutoff:3.500A) Processing helix chain 'G' and resid 4130 through 4133 Processing helix chain 'G' and resid 4136 through 4154 removed outlier: 4.040A pdb=" N GLY G4140 " --> pdb=" O ALA G4136 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR G4148 " --> pdb=" O ALA G4144 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU G4152 " --> pdb=" O THR G4148 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS G4153 " --> pdb=" O ASN G4149 " (cutoff:3.500A) Processing helix chain 'G' and resid 4157 through 4167 removed outlier: 3.590A pdb=" N ARG G4161 " --> pdb=" O ASP G4157 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN G4162 " --> pdb=" O PRO G4158 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE G4163 " --> pdb=" O ARG G4159 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU G4165 " --> pdb=" O ARG G4161 " (cutoff:3.500A) Processing helix chain 'G' and resid 4167 through 4174 removed outlier: 3.800A pdb=" N LEU G4171 " --> pdb=" O ALA G4167 " (cutoff:3.500A) Processing helix chain 'G' and resid 4200 through 4206 Processing helix chain 'G' and resid 4207 through 4224 removed outlier: 4.021A pdb=" N SER G4213 " --> pdb=" O GLN G4209 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL G4222 " --> pdb=" O ILE G4218 " (cutoff:3.500A) Processing helix chain 'G' and resid 4228 through 4239 removed outlier: 3.623A pdb=" N VAL G4235 " --> pdb=" O MET G4231 " (cutoff:3.500A) Processing helix chain 'G' and resid 4240 through 4249 Processing helix chain 'G' and resid 4543 through 4558 removed outlier: 3.902A pdb=" N VAL G4549 " --> pdb=" O GLU G4545 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR G4554 " --> pdb=" O LYS G4550 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN G4558 " --> pdb=" O TYR G4554 " (cutoff:3.500A) Processing helix chain 'G' and resid 4558 through 4576 removed outlier: 3.840A pdb=" N LEU G4562 " --> pdb=" O ASN G4558 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE G4571 " --> pdb=" O LEU G4567 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA G4572 " --> pdb=" O PHE G4568 " (cutoff:3.500A) Processing helix chain 'G' and resid 4643 through 4665 removed outlier: 3.954A pdb=" N LEU G4648 " --> pdb=" O TRP G4644 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU G4649 " --> pdb=" O CYS G4645 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR G4651 " --> pdb=" O SER G4647 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS G4657 " --> pdb=" O VAL G4653 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE G4659 " --> pdb=" O PHE G4655 " (cutoff:3.500A) Processing helix chain 'G' and resid 4667 through 4683 removed outlier: 3.733A pdb=" N GLU G4676 " --> pdb=" O LYS G4672 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU G4682 " --> pdb=" O ALA G4678 " (cutoff:3.500A) Processing helix chain 'G' and resid 4696 through 4702 removed outlier: 3.536A pdb=" N GLN G4700 " --> pdb=" O ASP G4696 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP G4702 " --> pdb=" O LYS G4698 " (cutoff:3.500A) Processing helix chain 'G' and resid 4703 through 4705 No H-bonds generated for 'chain 'G' and resid 4703 through 4705' Processing helix chain 'G' and resid 4719 through 4728 removed outlier: 3.565A pdb=" N LEU G4725 " --> pdb=" O LYS G4721 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP G4726 " --> pdb=" O ARG G4722 " (cutoff:3.500A) Processing helix chain 'G' and resid 4733 through 4741 Processing helix chain 'G' and resid 4745 through 4753 removed outlier: 4.833A pdb=" N THR G4751 " --> pdb=" O SER G4747 " (cutoff:3.500A) Processing helix chain 'G' and resid 4772 through 4784 Processing helix chain 'G' and resid 4786 through 4802 removed outlier: 3.752A pdb=" N SER G4799 " --> pdb=" O TYR G4795 " (cutoff:3.500A) Processing helix chain 'G' and resid 4811 through 4816 removed outlier: 4.551A pdb=" N ASP G4815 " --> pdb=" O ALA G4811 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE G4816 " --> pdb=" O HIS G4812 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4811 through 4816' Processing helix chain 'G' and resid 4817 through 4819 No H-bonds generated for 'chain 'G' and resid 4817 through 4819' Processing helix chain 'G' and resid 4820 through 4833 removed outlier: 3.622A pdb=" N ARG G4824 " --> pdb=" O VAL G4820 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR G4825 " --> pdb=" O LYS G4821 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER G4829 " --> pdb=" O THR G4825 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL G4830 " --> pdb=" O ILE G4826 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN G4833 " --> pdb=" O SER G4829 " (cutoff:3.500A) Processing helix chain 'G' and resid 4836 through 4858 removed outlier: 3.975A pdb=" N GLY G4842 " --> pdb=" O VAL G4838 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL G4847 " --> pdb=" O LEU G4843 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL G4854 " --> pdb=" O LEU G4850 " (cutoff:3.500A) Processing helix chain 'G' and resid 4859 through 4863 removed outlier: 3.572A pdb=" N PHE G4862 " --> pdb=" O PHE G4859 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR G4863 " --> pdb=" O ARG G4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4859 through 4863' Processing helix chain 'G' and resid 4879 through 4894 removed outlier: 3.642A pdb=" N MET G4887 " --> pdb=" O TYR G4883 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL G4891 " --> pdb=" O MET G4887 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ARG G4892 " --> pdb=" O TYR G4888 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY G4894 " --> pdb=" O GLY G4890 " (cutoff:3.500A) Processing helix chain 'G' and resid 4909 through 4924 removed outlier: 3.614A pdb=" N VAL G4914 " --> pdb=" O GLU G4910 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL G4915 " --> pdb=" O LEU G4911 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL G4924 " --> pdb=" O PHE G4920 " (cutoff:3.500A) Processing helix chain 'G' and resid 4927 through 4933 removed outlier: 4.028A pdb=" N ILE G4932 " --> pdb=" O LEU G4928 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN G4933 " --> pdb=" O LEU G4929 " (cutoff:3.500A) Processing helix chain 'G' and resid 4933 through 4944 removed outlier: 3.536A pdb=" N ILE G4937 " --> pdb=" O GLN G4933 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE G4940 " --> pdb=" O ILE G4936 " (cutoff:3.500A) Processing helix chain 'G' and resid 4947 through 4952 Processing helix chain 'G' and resid 4964 through 4969 removed outlier: 3.876A pdb=" N PHE G4968 " --> pdb=" O GLY G4964 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP G4969 " --> pdb=" O SER G4965 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4964 through 4969' Processing helix chain 'G' and resid 4973 through 4979 Processing helix chain 'G' and resid 4986 through 4997 removed outlier: 3.665A pdb=" N LEU G4992 " --> pdb=" O TYR G4988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE G4996 " --> pdb=" O LEU G4992 " (cutoff:3.500A) Processing helix chain 'G' and resid 4999 through 5003 removed outlier: 3.903A pdb=" N HIS G5003 " --> pdb=" O GLU G5000 " (cutoff:3.500A) Processing helix chain 'G' and resid 5006 through 5017 removed outlier: 3.602A pdb=" N MET G5013 " --> pdb=" O TYR G5009 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'F' and resid 27 through 30 removed outlier: 3.729A pdb=" N VAL F 101 " --> pdb=" O ALA F 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AA4, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.728A pdb=" N VAL A 101 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 21 through 22 Processing sheet with id=AA6, first strand: chain 'H' and resid 27 through 30 removed outlier: 3.729A pdb=" N VAL H 101 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 21 through 22 Processing sheet with id=AA8, first strand: chain 'J' and resid 27 through 30 removed outlier: 3.729A pdb=" N VAL J 101 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 51 removed outlier: 5.201A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU B 69 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG B 110 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN B 71 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 172 " --> pdb=" O THR B 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.560A pdb=" N MET B 116 " --> pdb=" O HIS B 111 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN B 71 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG B 110 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU B 69 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU B 19 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL B 21 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLN B 23 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N MET B 202 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AB3, first strand: chain 'B' and resid 299 through 302 removed outlier: 5.494A pdb=" N ILE B 282 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N LEU B 293 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 14.064A pdb=" N LEU B 280 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 391 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 389 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 230 through 233 removed outlier: 3.604A pdb=" N THR B 232 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL B 245 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 376 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS B 374 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 314 through 317 Processing sheet with id=AB6, first strand: chain 'B' and resid 634 through 639 removed outlier: 3.961A pdb=" N GLN B 634 " --> pdb=" O HIS B1640 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN B 636 " --> pdb=" O ALA B1638 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B1638 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B1646 " --> pdb=" O ILE B1641 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 713 through 716 removed outlier: 3.909A pdb=" N VAL B 781 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 644 " --> pdb=" O VAL B 781 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 763 through 769 removed outlier: 6.263A pdb=" N VAL B 764 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE B 759 " --> pdb=" O VAL B 764 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLY B 766 " --> pdb=" O PHE B 757 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 757 " --> pdb=" O GLY B 766 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 742 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 744 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 666 " --> pdb=" O VAL B 744 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 830 through 831 Processing sheet with id=AC1, first strand: chain 'B' and resid 938 through 941 Processing sheet with id=AC2, first strand: chain 'B' and resid 1136 through 1138 removed outlier: 3.501A pdb=" N VAL B1123 " --> pdb=" O TRP B1132 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B1604 " --> pdb=" O LYS B1240 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1167 through 1168 Processing sheet with id=AC4, first strand: chain 'B' and resid 1255 through 1259 removed outlier: 4.061A pdb=" N GLU B1256 " --> pdb=" O ALA B1273 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1287 through 1288 removed outlier: 3.516A pdb=" N UNK B1288 " --> pdb=" O GLN B1598 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1293 through 1294 Processing sheet with id=AC7, first strand: chain 'B' and resid 1734 through 1736 Processing sheet with id=AC8, first strand: chain 'B' and resid 4178 through 4184 Processing sheet with id=AC9, first strand: chain 'B' and resid 4580 through 4583 Processing sheet with id=AD1, first strand: chain 'E' and resid 48 through 51 removed outlier: 5.201A pdb=" N LEU E 22 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU E 69 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG E 110 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN E 71 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL E 172 " --> pdb=" O THR E 149 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 116 through 117 removed outlier: 3.561A pdb=" N MET E 116 " --> pdb=" O HIS E 111 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN E 71 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG E 110 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU E 69 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU E 19 " --> pdb=" O CYS E 206 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL E 21 " --> pdb=" O PRO E 204 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLN E 23 " --> pdb=" O MET E 202 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N MET E 202 " --> pdb=" O GLN E 23 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 181 through 184 Processing sheet with id=AD4, first strand: chain 'E' and resid 299 through 302 removed outlier: 5.494A pdb=" N ILE E 282 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N LEU E 293 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 14.065A pdb=" N LEU E 280 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR E 391 " --> pdb=" O ARG E 221 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE E 389 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 230 through 233 removed outlier: 3.605A pdb=" N THR E 232 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL E 245 " --> pdb=" O ALA E 376 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA E 376 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS E 374 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 314 through 317 Processing sheet with id=AD7, first strand: chain 'E' and resid 634 through 639 removed outlier: 3.961A pdb=" N GLN E 634 " --> pdb=" O HIS E1640 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN E 636 " --> pdb=" O ALA E1638 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA E1638 " --> pdb=" O ASN E 636 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG E1646 " --> pdb=" O ILE E1641 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 713 through 716 removed outlier: 3.909A pdb=" N VAL E 781 " --> pdb=" O ILE E 644 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE E 644 " --> pdb=" O VAL E 781 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 763 through 769 removed outlier: 6.263A pdb=" N VAL E 764 " --> pdb=" O ILE E 759 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE E 759 " --> pdb=" O VAL E 764 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLY E 766 " --> pdb=" O PHE E 757 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE E 757 " --> pdb=" O GLY E 766 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP E 742 " --> pdb=" O VAL E 668 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL E 744 " --> pdb=" O VAL E 666 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E 666 " --> pdb=" O VAL E 744 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 830 through 831 Processing sheet with id=AE2, first strand: chain 'E' and resid 938 through 941 Processing sheet with id=AE3, first strand: chain 'E' and resid 1136 through 1138 removed outlier: 3.501A pdb=" N VAL E1123 " --> pdb=" O TRP E1132 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE E1074 " --> pdb=" O SER E1239 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER E1604 " --> pdb=" O LYS E1240 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 1167 through 1168 Processing sheet with id=AE5, first strand: chain 'E' and resid 1255 through 1259 removed outlier: 4.062A pdb=" N GLU E1256 " --> pdb=" O ALA E1273 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N UNK E1472 " --> pdb=" O LEU E1270 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 1287 through 1288 removed outlier: 3.520A pdb=" N UNK E1288 " --> pdb=" O GLN E1598 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 1293 through 1294 Processing sheet with id=AE8, first strand: chain 'E' and resid 1734 through 1736 Processing sheet with id=AE9, first strand: chain 'E' and resid 4178 through 4184 Processing sheet with id=AF1, first strand: chain 'E' and resid 4580 through 4583 Processing sheet with id=AF2, first strand: chain 'I' and resid 48 through 51 removed outlier: 5.201A pdb=" N LEU I 22 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU I 69 " --> pdb=" O ARG I 110 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG I 110 " --> pdb=" O LEU I 69 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN I 71 " --> pdb=" O LEU I 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL I 172 " --> pdb=" O THR I 149 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 116 through 117 removed outlier: 3.560A pdb=" N MET I 116 " --> pdb=" O HIS I 111 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN I 71 " --> pdb=" O LEU I 108 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG I 110 " --> pdb=" O LEU I 69 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU I 69 " --> pdb=" O ARG I 110 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU I 19 " --> pdb=" O CYS I 206 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL I 21 " --> pdb=" O PRO I 204 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLN I 23 " --> pdb=" O MET I 202 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N MET I 202 " --> pdb=" O GLN I 23 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 181 through 184 Processing sheet with id=AF5, first strand: chain 'I' and resid 299 through 302 removed outlier: 5.495A pdb=" N ILE I 282 " --> pdb=" O LEU I 291 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N LEU I 293 " --> pdb=" O LEU I 280 " (cutoff:3.500A) removed outlier: 14.064A pdb=" N LEU I 280 " --> pdb=" O LEU I 293 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR I 391 " --> pdb=" O ARG I 221 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE I 389 " --> pdb=" O PHE I 223 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 230 through 233 removed outlier: 3.604A pdb=" N THR I 232 " --> pdb=" O TYR I 246 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL I 245 " --> pdb=" O ALA I 376 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA I 376 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS I 374 " --> pdb=" O TYR I 247 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 314 through 317 Processing sheet with id=AF8, first strand: chain 'I' and resid 634 through 639 removed outlier: 3.961A pdb=" N GLN I 634 " --> pdb=" O HIS I1640 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN I 636 " --> pdb=" O ALA I1638 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA I1638 " --> pdb=" O ASN I 636 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG I1646 " --> pdb=" O ILE I1641 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 713 through 716 removed outlier: 3.909A pdb=" N VAL I 781 " --> pdb=" O ILE I 644 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE I 644 " --> pdb=" O VAL I 781 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 763 through 769 removed outlier: 6.263A pdb=" N VAL I 764 " --> pdb=" O ILE I 759 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE I 759 " --> pdb=" O VAL I 764 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLY I 766 " --> pdb=" O PHE I 757 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE I 757 " --> pdb=" O GLY I 766 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP I 742 " --> pdb=" O VAL I 668 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL I 744 " --> pdb=" O VAL I 666 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL I 666 " --> pdb=" O VAL I 744 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 830 through 831 Processing sheet with id=AG3, first strand: chain 'I' and resid 938 through 941 Processing sheet with id=AG4, first strand: chain 'I' and resid 1136 through 1138 removed outlier: 3.501A pdb=" N VAL I1123 " --> pdb=" O TRP I1132 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE I1074 " --> pdb=" O SER I1239 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER I1604 " --> pdb=" O LYS I1240 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 1167 through 1168 Processing sheet with id=AG6, first strand: chain 'I' and resid 1255 through 1259 removed outlier: 4.061A pdb=" N GLU I1256 " --> pdb=" O ALA I1273 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N UNK I1472 " --> pdb=" O LEU I1270 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 1287 through 1288 removed outlier: 3.514A pdb=" N UNK I1288 " --> pdb=" O GLN I1598 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 1293 through 1294 Processing sheet with id=AG9, first strand: chain 'I' and resid 1734 through 1736 Processing sheet with id=AH1, first strand: chain 'I' and resid 4178 through 4184 Processing sheet with id=AH2, first strand: chain 'I' and resid 4580 through 4583 Processing sheet with id=AH3, first strand: chain 'G' and resid 48 through 51 removed outlier: 5.200A pdb=" N LEU G 22 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU G 69 " --> pdb=" O ARG G 110 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG G 110 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN G 71 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL G 172 " --> pdb=" O THR G 149 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 116 through 117 removed outlier: 3.560A pdb=" N MET G 116 " --> pdb=" O HIS G 111 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN G 71 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG G 110 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU G 69 " --> pdb=" O ARG G 110 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU G 19 " --> pdb=" O CYS G 206 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL G 21 " --> pdb=" O PRO G 204 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLN G 23 " --> pdb=" O MET G 202 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N MET G 202 " --> pdb=" O GLN G 23 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 181 through 184 Processing sheet with id=AH6, first strand: chain 'G' and resid 299 through 302 removed outlier: 5.495A pdb=" N ILE G 282 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 10.806A pdb=" N LEU G 293 " --> pdb=" O LEU G 280 " (cutoff:3.500A) removed outlier: 14.064A pdb=" N LEU G 280 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR G 391 " --> pdb=" O ARG G 221 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE G 389 " --> pdb=" O PHE G 223 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 230 through 233 removed outlier: 3.604A pdb=" N THR G 232 " --> pdb=" O TYR G 246 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL G 245 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA G 376 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS G 374 " --> pdb=" O TYR G 247 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 314 through 317 Processing sheet with id=AH9, first strand: chain 'G' and resid 634 through 639 removed outlier: 3.961A pdb=" N GLN G 634 " --> pdb=" O HIS G1640 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN G 636 " --> pdb=" O ALA G1638 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA G1638 " --> pdb=" O ASN G 636 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG G1646 " --> pdb=" O ILE G1641 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 713 through 716 removed outlier: 3.909A pdb=" N VAL G 781 " --> pdb=" O ILE G 644 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE G 644 " --> pdb=" O VAL G 781 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 763 through 769 removed outlier: 6.263A pdb=" N VAL G 764 " --> pdb=" O ILE G 759 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE G 759 " --> pdb=" O VAL G 764 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLY G 766 " --> pdb=" O PHE G 757 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE G 757 " --> pdb=" O GLY G 766 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP G 742 " --> pdb=" O VAL G 668 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL G 744 " --> pdb=" O VAL G 666 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL G 666 " --> pdb=" O VAL G 744 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 830 through 831 Processing sheet with id=AI4, first strand: chain 'G' and resid 938 through 941 Processing sheet with id=AI5, first strand: chain 'G' and resid 1136 through 1138 removed outlier: 3.502A pdb=" N VAL G1123 " --> pdb=" O TRP G1132 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE G1074 " --> pdb=" O SER G1239 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER G1604 " --> pdb=" O LYS G1240 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 1167 through 1168 Processing sheet with id=AI7, first strand: chain 'G' and resid 1255 through 1259 removed outlier: 4.061A pdb=" N GLU G1256 " --> pdb=" O ALA G1273 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N UNK G1472 " --> pdb=" O LEU G1270 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'G' and resid 1287 through 1288 removed outlier: 3.521A pdb=" N UNK G1288 " --> pdb=" O GLN G1598 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'G' and resid 1293 through 1294 Processing sheet with id=AJ1, first strand: chain 'G' and resid 1734 through 1736 Processing sheet with id=AJ2, first strand: chain 'G' and resid 4178 through 4184 Processing sheet with id=AJ3, first strand: chain 'G' and resid 4580 through 4583 4641 hydrogen bonds defined for protein. 13332 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: 95.34 Time building geometry restraints manager: 34.96 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: 39557 1.34 - 1.46: 20992 1.46 - 1.58: 61483 1.58 - 1.70: 0 1.70 - 1.82: 1020 Bond restraints: 123052 Sorted by residual: bond pdb=" C ILE G2476 " pdb=" N PRO G2477 " ideal model delta sigma weight residual 1.334 1.424 -0.090 2.34e-02 1.83e+03 1.49e+01 bond pdb=" C ILE B2476 " pdb=" N PRO B2477 " ideal model delta sigma weight residual 1.334 1.424 -0.090 2.34e-02 1.83e+03 1.47e+01 bond pdb=" C ILE I2476 " pdb=" N PRO I2477 " ideal model delta sigma weight residual 1.334 1.424 -0.090 2.34e-02 1.83e+03 1.47e+01 bond pdb=" C ILE E2476 " pdb=" N PRO E2477 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.34e-02 1.83e+03 1.45e+01 bond pdb=" C LEU I1242 " pdb=" N PRO I1243 " ideal model delta sigma weight residual 1.334 1.248 0.086 2.34e-02 1.83e+03 1.36e+01 ... (remaining 123047 not shown) Histogram of bond angle deviations from ideal: 95.50 - 104.12: 1878 104.12 - 112.73: 65364 112.73 - 121.35: 67437 121.35 - 129.96: 32322 129.96 - 138.58: 775 Bond angle restraints: 167776 Sorted by residual: angle pdb=" CA TYR G1712 " pdb=" CB TYR G1712 " pdb=" CG TYR G1712 " ideal model delta sigma weight residual 113.90 102.02 11.88 1.80e+00 3.09e-01 4.35e+01 angle pdb=" CA TYR I1712 " pdb=" CB TYR I1712 " pdb=" CG TYR I1712 " ideal model delta sigma weight residual 113.90 102.03 11.87 1.80e+00 3.09e-01 4.35e+01 angle pdb=" CA TYR B1712 " pdb=" CB TYR B1712 " pdb=" CG TYR B1712 " ideal model delta sigma weight residual 113.90 102.06 11.84 1.80e+00 3.09e-01 4.33e+01 angle pdb=" CA TYR E1712 " pdb=" CB TYR E1712 " pdb=" CG TYR E1712 " ideal model delta sigma weight residual 113.90 102.07 11.83 1.80e+00 3.09e-01 4.32e+01 angle pdb=" C MET E4639 " pdb=" N GLU E4640 " pdb=" CA GLU E4640 " ideal model delta sigma weight residual 121.80 137.21 -15.41 2.44e+00 1.68e-01 3.99e+01 ... (remaining 167771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 69629 15.45 - 30.91: 2967 30.91 - 46.36: 676 46.36 - 61.82: 68 61.82 - 77.27: 108 Dihedral angle restraints: 73448 sinusoidal: 23656 harmonic: 49792 Sorted by residual: dihedral pdb=" CA GLY B2343 " pdb=" C GLY B2343 " pdb=" N GLU B2344 " pdb=" CA GLU B2344 " ideal model delta harmonic sigma weight residual -180.00 -127.18 -52.82 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA GLY E2343 " pdb=" C GLY E2343 " pdb=" N GLU E2344 " pdb=" CA GLU E2344 " ideal model delta harmonic sigma weight residual -180.00 -127.20 -52.80 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA GLY I2343 " pdb=" C GLY I2343 " pdb=" N GLU I2344 " pdb=" CA GLU I2344 " ideal model delta harmonic sigma weight residual 180.00 -127.23 -52.77 0 5.00e+00 4.00e-02 1.11e+02 ... (remaining 73445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 17374 0.081 - 0.162: 1983 0.162 - 0.243: 208 0.243 - 0.324: 27 0.324 - 0.405: 16 Chirality restraints: 19608 Sorted by residual: chirality pdb=" CG LEU E1676 " pdb=" CB LEU E1676 " pdb=" CD1 LEU E1676 " pdb=" CD2 LEU E1676 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CG LEU B1676 " pdb=" CB LEU B1676 " pdb=" CD1 LEU B1676 " pdb=" CD2 LEU B1676 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CG LEU G1676 " pdb=" CB LEU G1676 " pdb=" CD1 LEU G1676 " pdb=" CD2 LEU G1676 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 19605 not shown) Planarity restraints: 22100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B4666 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO B4667 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO B4667 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B4667 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I4666 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO I4667 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO I4667 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO I4667 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G4666 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO G4667 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO G4667 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO G4667 " -0.056 5.00e-02 4.00e+02 ... (remaining 22097 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 12 2.08 - 2.78: 31049 2.78 - 3.49: 152210 3.49 - 4.19: 262484 4.19 - 4.90: 440272 Nonbonded interactions: 886027 Sorted by model distance: nonbonded pdb=" O UNK G3557 " pdb=" CB UNK G3561 " model vdw 1.373 3.440 nonbonded pdb=" O UNK B3557 " pdb=" CB UNK B3561 " model vdw 1.373 3.440 nonbonded pdb=" O UNK E3557 " pdb=" CB UNK E3561 " model vdw 1.373 3.440 nonbonded pdb=" CB UNK B1297 " pdb=" O UNK B1452 " model vdw 1.374 3.440 nonbonded pdb=" CB UNK G1297 " pdb=" O UNK G1452 " model vdw 1.374 3.440 ... (remaining 886022 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 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'I' } 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.540 Construct map_model_manager: 0.140 Extract box with map and model: 17.240 Check model and map are aligned: 1.290 Set scattering table: 0.840 Process input model: 292.590 Find NCS groups from input model: 6.100 Set up NCS constraints: 0.630 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 324.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 0.095 123052 Z= 0.454 Angle : 1.010 17.174 167776 Z= 0.526 Chirality : 0.054 0.405 19608 Planarity : 0.007 0.102 22100 Dihedral : 10.369 77.275 41072 Min Nonbonded Distance : 1.373 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.49 % Favored : 88.24 % Rotamer: Outliers : 0.45 % Allowed : 3.04 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 4.27 % Twisted General : 0.56 % 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: -5.71 (0.05), residues: 13364 helix: -4.29 (0.03), residues: 5796 sheet: -2.45 (0.14), residues: 1248 loop : -3.53 (0.06), residues: 6320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E 515 HIS 0.011 0.002 HIS B1133 PHE 0.037 0.003 PHE B3962 TYR 0.042 0.003 TYR G3657 ARG 0.019 0.001 ARG B4913 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2100 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 2054 time to evaluate : 8.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 MET cc_start: 0.7645 (tpp) cc_final: 0.7252 (tpt) REVERT: F 47 LYS cc_start: 0.9157 (mttt) cc_final: 0.8943 (mmtt) REVERT: F 73 LYS cc_start: 0.8943 (tttm) cc_final: 0.8412 (tmtt) REVERT: F 91 ILE cc_start: 0.8750 (mm) cc_final: 0.8436 (mp) REVERT: A 29 MET cc_start: 0.7590 (tpp) cc_final: 0.7156 (tpt) REVERT: A 40 ARG cc_start: 0.7992 (mmm160) cc_final: 0.7670 (tpp80) REVERT: A 47 LYS cc_start: 0.9136 (mttt) cc_final: 0.8919 (mmtt) REVERT: A 73 LYS cc_start: 0.8955 (tttm) cc_final: 0.8343 (tmtt) REVERT: A 91 ILE cc_start: 0.8852 (mm) cc_final: 0.8551 (mp) REVERT: H 13 ARG cc_start: 0.8169 (ptt-90) cc_final: 0.7930 (ptp90) REVERT: H 29 MET cc_start: 0.7558 (tpp) cc_final: 0.7276 (tpt) REVERT: H 73 LYS cc_start: 0.9039 (tttm) cc_final: 0.8624 (tmtt) REVERT: H 91 ILE cc_start: 0.8798 (mm) cc_final: 0.8550 (mp) REVERT: J 29 MET cc_start: 0.7619 (tpp) cc_final: 0.7176 (tpt) REVERT: J 40 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7674 (tpp80) REVERT: J 73 LYS cc_start: 0.8936 (tttm) cc_final: 0.8324 (tmtt) REVERT: J 91 ILE cc_start: 0.8826 (mm) cc_final: 0.8511 (mp) REVERT: B 36 CYS cc_start: 0.8338 (m) cc_final: 0.7890 (p) REVERT: B 158 SER cc_start: 0.9085 (m) cc_final: 0.8824 (m) REVERT: B 205 ILE cc_start: 0.9385 (tp) cc_final: 0.8981 (tp) REVERT: B 385 ASP cc_start: 0.5865 (p0) cc_final: 0.4496 (t0) REVERT: B 470 SER cc_start: 0.9087 (m) cc_final: 0.8791 (p) REVERT: B 686 TRP cc_start: 0.7339 (m100) cc_final: 0.6798 (m100) REVERT: B 961 MET cc_start: 0.3821 (mmp) cc_final: 0.2225 (mmt) REVERT: B 1152 MET cc_start: 0.8526 (mtt) cc_final: 0.8324 (mtp) REVERT: B 1713 ASP cc_start: 0.7768 (t70) cc_final: 0.7295 (t70) REVERT: B 1865 MET cc_start: 0.8095 (mpt) cc_final: 0.7861 (mpt) REVERT: B 2032 GLN cc_start: 0.8474 (tp40) cc_final: 0.7993 (tm-30) REVERT: B 2430 ILE cc_start: 0.9565 (mm) cc_final: 0.9309 (mt) REVERT: B 3652 MET cc_start: 0.8429 (tpp) cc_final: 0.8101 (tpt) REVERT: B 3711 THR cc_start: 0.8733 (m) cc_final: 0.8451 (p) REVERT: B 3805 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8980 (pp) REVERT: B 3893 GLU cc_start: 0.8388 (tp30) cc_final: 0.8001 (tp30) REVERT: B 4220 ASP cc_start: 0.8349 (m-30) cc_final: 0.7381 (m-30) REVERT: B 4231 MET cc_start: 0.8955 (mmt) cc_final: 0.8688 (mmm) REVERT: B 4647 SER cc_start: 0.8683 (p) cc_final: 0.8387 (t) REVERT: E 36 CYS cc_start: 0.8252 (m) cc_final: 0.7873 (p) REVERT: E 158 SER cc_start: 0.9086 (m) cc_final: 0.8814 (m) REVERT: E 205 ILE cc_start: 0.9427 (tp) cc_final: 0.9075 (tp) REVERT: E 385 ASP cc_start: 0.5829 (p0) cc_final: 0.5090 (p0) REVERT: E 470 SER cc_start: 0.9098 (m) cc_final: 0.8787 (p) REVERT: E 686 TRP cc_start: 0.7421 (m100) cc_final: 0.6717 (m100) REVERT: E 961 MET cc_start: 0.3932 (mmp) cc_final: 0.2313 (mmt) REVERT: E 1152 MET cc_start: 0.8529 (mtt) cc_final: 0.8283 (mtp) REVERT: E 1713 ASP cc_start: 0.7764 (t70) cc_final: 0.7315 (t70) REVERT: E 2032 GLN cc_start: 0.8482 (tp40) cc_final: 0.7942 (tm-30) REVERT: E 2430 ILE cc_start: 0.9564 (mm) cc_final: 0.9313 (mt) REVERT: E 2816 MET cc_start: 0.1096 (mtp) cc_final: 0.0896 (mmm) REVERT: E 3652 MET cc_start: 0.8436 (tpp) cc_final: 0.8099 (tpt) REVERT: E 3711 THR cc_start: 0.8719 (m) cc_final: 0.8430 (p) REVERT: E 3805 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8985 (pp) REVERT: E 3893 GLU cc_start: 0.8408 (tp30) cc_final: 0.8053 (tp30) REVERT: E 4220 ASP cc_start: 0.8385 (m-30) cc_final: 0.7433 (m-30) REVERT: E 4231 MET cc_start: 0.8969 (mmt) cc_final: 0.8710 (mmm) REVERT: E 4647 SER cc_start: 0.8706 (p) cc_final: 0.8420 (t) REVERT: I 36 CYS cc_start: 0.8351 (m) cc_final: 0.7887 (p) REVERT: I 158 SER cc_start: 0.9087 (m) cc_final: 0.8845 (m) REVERT: I 205 ILE cc_start: 0.9365 (tp) cc_final: 0.8995 (tp) REVERT: I 385 ASP cc_start: 0.5841 (p0) cc_final: 0.4499 (t0) REVERT: I 470 SER cc_start: 0.9102 (m) cc_final: 0.8793 (p) REVERT: I 686 TRP cc_start: 0.7391 (m100) cc_final: 0.6813 (m100) REVERT: I 961 MET cc_start: 0.3729 (mmp) cc_final: 0.2098 (mmt) REVERT: I 1152 MET cc_start: 0.8532 (mtt) cc_final: 0.8279 (mtp) REVERT: I 1713 ASP cc_start: 0.7760 (t70) cc_final: 0.7306 (t70) REVERT: I 1865 MET cc_start: 0.8082 (mpt) cc_final: 0.7876 (mpt) REVERT: I 2032 GLN cc_start: 0.8486 (tp40) cc_final: 0.7998 (tm-30) REVERT: I 2430 ILE cc_start: 0.9560 (mm) cc_final: 0.9302 (mt) REVERT: I 3652 MET cc_start: 0.8450 (tpp) cc_final: 0.8106 (tpt) REVERT: I 3711 THR cc_start: 0.8746 (m) cc_final: 0.8459 (p) REVERT: I 3805 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8992 (pp) REVERT: I 3893 GLU cc_start: 0.8392 (tp30) cc_final: 0.8008 (tp30) REVERT: I 4220 ASP cc_start: 0.8362 (m-30) cc_final: 0.7407 (m-30) REVERT: I 4231 MET cc_start: 0.8992 (mmt) cc_final: 0.8739 (mmm) REVERT: I 4647 SER cc_start: 0.8687 (p) cc_final: 0.8397 (t) REVERT: G 36 CYS cc_start: 0.8338 (m) cc_final: 0.7889 (p) REVERT: G 158 SER cc_start: 0.9082 (m) cc_final: 0.8819 (m) REVERT: G 205 ILE cc_start: 0.9359 (tp) cc_final: 0.8988 (tp) REVERT: G 385 ASP cc_start: 0.5825 (p0) cc_final: 0.5320 (p0) REVERT: G 470 SER cc_start: 0.9099 (m) cc_final: 0.8783 (p) REVERT: G 686 TRP cc_start: 0.7351 (m100) cc_final: 0.6728 (m100) REVERT: G 961 MET cc_start: 0.3790 (mmp) cc_final: 0.2224 (mmt) REVERT: G 1152 MET cc_start: 0.8528 (mtt) cc_final: 0.8267 (mtp) REVERT: G 1713 ASP cc_start: 0.7797 (t70) cc_final: 0.7341 (t70) REVERT: G 1865 MET cc_start: 0.8137 (mpt) cc_final: 0.7934 (mpt) REVERT: G 3652 MET cc_start: 0.8464 (tpp) cc_final: 0.8117 (tpt) REVERT: G 3711 THR cc_start: 0.8749 (m) cc_final: 0.8464 (p) REVERT: G 3805 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8996 (pp) REVERT: G 3893 GLU cc_start: 0.8406 (tp30) cc_final: 0.8017 (tp30) REVERT: G 4220 ASP cc_start: 0.8329 (m-30) cc_final: 0.7368 (m-30) REVERT: G 4231 MET cc_start: 0.8952 (mmt) cc_final: 0.8688 (mmm) REVERT: G 4647 SER cc_start: 0.8677 (p) cc_final: 0.8392 (t) outliers start: 46 outliers final: 10 residues processed: 2096 average time/residue: 1.1415 time to fit residues: 4138.7301 Evaluate side-chains 1084 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1070 time to evaluate : 8.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 3663 LEU Chi-restraints excluded: chain B residue 3805 LEU Chi-restraints excluded: chain B residue 4081 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 3805 LEU Chi-restraints excluded: chain E residue 4081 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 3805 LEU Chi-restraints excluded: chain I residue 4081 VAL Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 3663 LEU Chi-restraints excluded: chain G residue 3805 LEU Chi-restraints excluded: chain G residue 4081 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 98 HIS B 111 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS B 224 HIS B 379 HIS B 383 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 ASN B1158 ASN B1254 HIS B1598 GLN B1663 HIS B1688 HIS B1837 GLN B1928 GLN B1952 GLN B1972 ASN B2005 GLN B2127 GLN B2161 GLN ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2881 ASN B2884 ASN B2931 GLN B3647 HIS B3781 GLN ** B3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3897 ASN ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3994 HIS B4034 ASN B4120 ASN B4142 ASN B4153 HIS ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4691 GLN B4728 HIS ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN E 98 HIS E 111 HIS E 181 HIS E 224 HIS E 379 HIS E 383 HIS ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 GLN ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 520 ASN ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 921 ASN E 949 ASN E1158 ASN E1254 HIS E1598 GLN E1663 HIS E1688 HIS E1837 GLN E1928 GLN E1952 GLN E1972 ASN E2005 GLN E2127 GLN E2161 GLN ** E2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2881 ASN E2884 ASN E2931 GLN E3647 HIS ** E3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3897 ASN ** E3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3994 HIS E4034 ASN E4120 ASN E4142 ASN E4153 HIS E4246 GLN ** E4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4691 GLN E4728 HIS ** E4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 ASN I 98 HIS I 111 HIS I 181 HIS I 224 HIS I 379 HIS I 383 HIS ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 460 GLN ** I 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 520 ASN ** I 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 921 ASN I 949 ASN I1158 ASN I1254 HIS I1598 GLN I1663 HIS I1688 HIS I1837 GLN I1928 GLN I1952 GLN I1972 ASN I2005 GLN I2127 GLN I2161 GLN ** I2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2881 ASN I2884 ASN I2931 GLN I3647 HIS I3897 ASN ** I3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3994 HIS I4034 ASN I4120 ASN I4153 HIS ** I4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I4691 GLN I4728 HIS ** I4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 ASN G 98 HIS G 111 HIS G 181 HIS G 224 HIS G 379 HIS G 383 HIS ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 460 GLN ** G 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 520 ASN ** G 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 949 ASN G1158 ASN G1254 HIS G1598 GLN G1663 HIS G1688 HIS G1837 GLN G1928 GLN G1972 ASN G2005 GLN G2127 GLN G2161 GLN ** G2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2881 ASN G2884 ASN G2931 GLN G3647 HIS G3897 ASN ** G3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3994 HIS G4034 ASN G4120 ASN G4142 ASN G4153 HIS ** G4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4691 GLN G4728 HIS ** G4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 123052 Z= 0.523 Angle : 0.904 15.559 167776 Z= 0.463 Chirality : 0.047 0.256 19608 Planarity : 0.007 0.089 22100 Dihedral : 6.788 50.516 18088 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.82 % Favored : 86.97 % Rotamer: Outliers : 3.04 % Allowed : 9.56 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.66 % Twisted General : 0.38 % 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: -4.11 (0.06), residues: 13364 helix: -2.43 (0.05), residues: 5960 sheet: -1.91 (0.15), residues: 1200 loop : -3.19 (0.07), residues: 6204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP I 891 HIS 0.008 0.002 HIS I5003 PHE 0.034 0.003 PHE G4807 TYR 0.043 0.002 TYR E1712 ARG 0.019 0.001 ARG G2888 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1352 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 1038 time to evaluate : 9.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 MET cc_start: 0.7505 (tpp) cc_final: 0.7203 (tpp) REVERT: F 30 LEU cc_start: 0.9086 (tt) cc_final: 0.8851 (tt) REVERT: F 73 LYS cc_start: 0.8962 (tttm) cc_final: 0.8475 (tmtt) REVERT: F 91 ILE cc_start: 0.8908 (mm) cc_final: 0.8690 (mp) REVERT: A 29 MET cc_start: 0.7490 (tpp) cc_final: 0.7166 (tpp) REVERT: A 30 LEU cc_start: 0.9075 (tt) cc_final: 0.8836 (tt) REVERT: A 73 LYS cc_start: 0.8956 (tttm) cc_final: 0.8507 (tmtt) REVERT: H 29 MET cc_start: 0.7455 (tpp) cc_final: 0.7244 (tpp) REVERT: H 73 LYS cc_start: 0.9021 (tttm) cc_final: 0.8595 (tmtt) REVERT: J 29 MET cc_start: 0.7494 (tpp) cc_final: 0.7197 (tpp) REVERT: J 30 LEU cc_start: 0.9107 (tt) cc_final: 0.8766 (mp) REVERT: J 91 ILE cc_start: 0.8798 (mm) cc_final: 0.8577 (mp) REVERT: B 158 SER cc_start: 0.9106 (m) cc_final: 0.8895 (t) REVERT: B 205 ILE cc_start: 0.9521 (tp) cc_final: 0.9053 (tp) REVERT: B 483 MET cc_start: 0.8477 (mmm) cc_final: 0.8175 (mmm) REVERT: B 1713 ASP cc_start: 0.7584 (t70) cc_final: 0.7327 (t70) REVERT: B 1865 MET cc_start: 0.7859 (mpt) cc_final: 0.7573 (mpt) REVERT: B 2032 GLN cc_start: 0.8334 (tp40) cc_final: 0.7774 (tm-30) REVERT: B 2205 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8390 (mp0) REVERT: B 2211 MET cc_start: 0.8856 (ttp) cc_final: 0.8593 (tmm) REVERT: B 3652 MET cc_start: 0.8613 (tpp) cc_final: 0.8170 (tpt) REVERT: B 3711 THR cc_start: 0.8789 (m) cc_final: 0.8424 (p) REVERT: B 3805 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9056 (pp) REVERT: B 4647 SER cc_start: 0.8774 (p) cc_final: 0.8530 (t) REVERT: E 205 ILE cc_start: 0.9509 (tp) cc_final: 0.9020 (tp) REVERT: E 1713 ASP cc_start: 0.7513 (t70) cc_final: 0.7276 (t70) REVERT: E 2032 GLN cc_start: 0.8340 (tp40) cc_final: 0.7763 (tm-30) REVERT: E 2211 MET cc_start: 0.8856 (ttp) cc_final: 0.8592 (tmm) REVERT: E 2816 MET cc_start: 0.0557 (mtp) cc_final: 0.0015 (mmm) REVERT: E 3652 MET cc_start: 0.8561 (tpp) cc_final: 0.8144 (tpt) REVERT: E 3711 THR cc_start: 0.8820 (m) cc_final: 0.8444 (p) REVERT: E 3805 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9041 (pp) REVERT: E 4026 MET cc_start: 0.9287 (ttp) cc_final: 0.8900 (ttm) REVERT: E 4647 SER cc_start: 0.8819 (p) cc_final: 0.8564 (t) REVERT: I 205 ILE cc_start: 0.9507 (tp) cc_final: 0.9025 (tp) REVERT: I 348 VAL cc_start: 0.9114 (t) cc_final: 0.8914 (m) REVERT: I 1713 ASP cc_start: 0.7565 (t70) cc_final: 0.7295 (t70) REVERT: I 1865 MET cc_start: 0.7773 (mpt) cc_final: 0.7500 (mpt) REVERT: I 2032 GLN cc_start: 0.8431 (tp40) cc_final: 0.7799 (tm-30) REVERT: I 2211 MET cc_start: 0.8853 (ttp) cc_final: 0.8588 (tmm) REVERT: I 3652 MET cc_start: 0.8618 (tpp) cc_final: 0.8172 (tpt) REVERT: I 3711 THR cc_start: 0.8787 (m) cc_final: 0.8407 (p) REVERT: I 3805 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9058 (pp) REVERT: I 4026 MET cc_start: 0.9287 (ttp) cc_final: 0.8903 (ttm) REVERT: I 4647 SER cc_start: 0.8776 (p) cc_final: 0.8534 (t) REVERT: G 205 ILE cc_start: 0.9517 (tp) cc_final: 0.9041 (tp) REVERT: G 1652 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7831 (mt-10) REVERT: G 1713 ASP cc_start: 0.7590 (t70) cc_final: 0.7331 (t70) REVERT: G 1865 MET cc_start: 0.7825 (mpt) cc_final: 0.7597 (mpt) REVERT: G 2211 MET cc_start: 0.8857 (ttp) cc_final: 0.8602 (tmm) REVERT: G 3652 MET cc_start: 0.8623 (tpp) cc_final: 0.8213 (tpt) REVERT: G 3711 THR cc_start: 0.8817 (m) cc_final: 0.8443 (p) REVERT: G 3805 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9048 (pp) REVERT: G 4026 MET cc_start: 0.9289 (ttp) cc_final: 0.8905 (ttm) REVERT: G 4647 SER cc_start: 0.8768 (p) cc_final: 0.8533 (t) outliers start: 314 outliers final: 192 residues processed: 1291 average time/residue: 0.9408 time to fit residues: 2162.1987 Evaluate side-chains 1080 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 884 time to evaluate : 8.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 664 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 1217 CYS Chi-restraints excluded: chain B residue 1595 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1703 LEU Chi-restraints excluded: chain B residue 1711 TYR Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1720 LEU Chi-restraints excluded: chain B residue 1944 GLU Chi-restraints excluded: chain B residue 1966 VAL Chi-restraints excluded: chain B residue 2031 LEU Chi-restraints excluded: chain B residue 2252 ASP Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2342 ASN Chi-restraints excluded: chain B residue 2466 LEU Chi-restraints excluded: chain B residue 3679 LYS Chi-restraints excluded: chain B residue 3805 LEU Chi-restraints excluded: chain B residue 3944 GLU Chi-restraints excluded: chain B residue 4023 MET Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4044 MET Chi-restraints excluded: chain B residue 4081 VAL Chi-restraints excluded: chain B residue 4145 VAL Chi-restraints excluded: chain B residue 4181 ILE Chi-restraints excluded: chain B residue 4197 ILE Chi-restraints excluded: chain B residue 4233 LEU Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4645 CYS Chi-restraints excluded: chain B residue 4688 ILE Chi-restraints excluded: chain B residue 4690 GLU Chi-restraints excluded: chain B residue 4814 LEU Chi-restraints excluded: chain B residue 4891 VAL Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4950 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 605 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 635 THR Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 826 ILE Chi-restraints excluded: chain E residue 920 TYR Chi-restraints excluded: chain E residue 1161 ILE Chi-restraints excluded: chain E residue 1217 CYS Chi-restraints excluded: chain E residue 1595 LEU Chi-restraints excluded: chain E residue 1657 LEU Chi-restraints excluded: chain E residue 1676 LEU Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1711 TYR Chi-restraints excluded: chain E residue 1720 LEU Chi-restraints excluded: chain E residue 1944 GLU Chi-restraints excluded: chain E residue 1966 VAL Chi-restraints excluded: chain E residue 2031 LEU Chi-restraints excluded: chain E residue 2252 ASP Chi-restraints excluded: chain E residue 2258 LEU Chi-restraints excluded: chain E residue 2342 ASN Chi-restraints excluded: chain E residue 3679 LYS Chi-restraints excluded: chain E residue 3805 LEU Chi-restraints excluded: chain E residue 3944 GLU Chi-restraints excluded: chain E residue 4023 MET Chi-restraints excluded: chain E residue 4036 VAL Chi-restraints excluded: chain E residue 4044 MET Chi-restraints excluded: chain E residue 4081 VAL Chi-restraints excluded: chain E residue 4145 VAL Chi-restraints excluded: chain E residue 4181 ILE Chi-restraints excluded: chain E residue 4197 ILE Chi-restraints excluded: chain E residue 4233 LEU Chi-restraints excluded: chain E residue 4247 ILE Chi-restraints excluded: chain E residue 4645 CYS Chi-restraints excluded: chain E residue 4688 ILE Chi-restraints excluded: chain E residue 4690 GLU Chi-restraints excluded: chain E residue 4807 PHE Chi-restraints excluded: chain E residue 4814 LEU Chi-restraints excluded: chain E residue 4891 VAL Chi-restraints excluded: chain E residue 4929 LEU Chi-restraints excluded: chain E residue 4950 VAL Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 605 SER Chi-restraints excluded: chain I residue 608 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 647 ASN Chi-restraints excluded: chain I residue 664 PHE Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain I residue 791 PHE Chi-restraints excluded: chain I residue 826 ILE Chi-restraints excluded: chain I residue 920 TYR Chi-restraints excluded: chain I residue 1217 CYS Chi-restraints excluded: chain I residue 1595 LEU Chi-restraints excluded: chain I residue 1657 LEU Chi-restraints excluded: chain I residue 1676 LEU Chi-restraints excluded: chain I residue 1703 LEU Chi-restraints excluded: chain I residue 1711 TYR Chi-restraints excluded: chain I residue 1850 VAL Chi-restraints excluded: chain I residue 1944 GLU Chi-restraints excluded: chain I residue 1966 VAL Chi-restraints excluded: chain I residue 2031 LEU Chi-restraints excluded: chain I residue 2252 ASP Chi-restraints excluded: chain I residue 2258 LEU Chi-restraints excluded: chain I residue 2342 ASN Chi-restraints excluded: chain I residue 3679 LYS Chi-restraints excluded: chain I residue 3805 LEU Chi-restraints excluded: chain I residue 3944 GLU Chi-restraints excluded: chain I residue 4023 MET Chi-restraints excluded: chain I residue 4036 VAL Chi-restraints excluded: chain I residue 4044 MET Chi-restraints excluded: chain I residue 4081 VAL Chi-restraints excluded: chain I residue 4145 VAL Chi-restraints excluded: chain I residue 4181 ILE Chi-restraints excluded: chain I residue 4197 ILE Chi-restraints excluded: chain I residue 4233 LEU Chi-restraints excluded: chain I residue 4247 ILE Chi-restraints excluded: chain I residue 4645 CYS Chi-restraints excluded: chain I residue 4688 ILE Chi-restraints excluded: chain I residue 4690 GLU Chi-restraints excluded: chain I residue 4814 LEU Chi-restraints excluded: chain I residue 4891 VAL Chi-restraints excluded: chain I residue 4929 LEU Chi-restraints excluded: chain I residue 4950 VAL Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 564 LEU Chi-restraints excluded: chain G residue 605 SER Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 635 THR Chi-restraints excluded: chain G residue 647 ASN Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 791 PHE Chi-restraints excluded: chain G residue 826 ILE Chi-restraints excluded: chain G residue 920 TYR Chi-restraints excluded: chain G residue 1217 CYS Chi-restraints excluded: chain G residue 1595 LEU Chi-restraints excluded: chain G residue 1676 LEU Chi-restraints excluded: chain G residue 1703 LEU Chi-restraints excluded: chain G residue 1711 TYR Chi-restraints excluded: chain G residue 1850 VAL Chi-restraints excluded: chain G residue 1944 GLU Chi-restraints excluded: chain G residue 1966 VAL Chi-restraints excluded: chain G residue 2031 LEU Chi-restraints excluded: chain G residue 2252 ASP Chi-restraints excluded: chain G residue 2342 ASN Chi-restraints excluded: chain G residue 2466 LEU Chi-restraints excluded: chain G residue 3679 LYS Chi-restraints excluded: chain G residue 3805 LEU Chi-restraints excluded: chain G residue 3944 GLU Chi-restraints excluded: chain G residue 4023 MET Chi-restraints excluded: chain G residue 4036 VAL Chi-restraints excluded: chain G residue 4044 MET Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4145 VAL Chi-restraints excluded: chain G residue 4181 ILE Chi-restraints excluded: chain G residue 4197 ILE Chi-restraints excluded: chain G residue 4233 LEU Chi-restraints excluded: chain G residue 4247 ILE Chi-restraints excluded: chain G residue 4645 CYS Chi-restraints excluded: chain G residue 4688 ILE Chi-restraints excluded: chain G residue 4690 GLU Chi-restraints excluded: chain G residue 4814 LEU Chi-restraints excluded: chain G residue 4891 VAL Chi-restraints excluded: chain G residue 4929 LEU Chi-restraints excluded: chain G residue 4950 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 0.3980 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 ASN F 70 GLN A 43 ASN A 70 GLN H 43 ASN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 ASN J 70 GLN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1660 GLN B1693 GLN ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2763 HIS ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3896 ASN B3897 ASN ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3976 ASN ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4806 ASN ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 877 ASN E 904 HIS E1660 GLN E1693 GLN ** E1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2763 HIS ** E3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3896 ASN E3897 ASN ** E3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3976 ASN ** E4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4806 ASN I 156 GLN ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 465 GLN ** I 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1660 GLN I1693 GLN ** I1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2763 HIS ** I3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3897 ASN ** I3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3976 ASN I4142 ASN ** I4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I4806 ASN G 156 GLN ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN ** G 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1660 GLN G1693 GLN ** G1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1952 GLN ** G2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2763 HIS ** G3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3897 ASN ** G3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3976 ASN ** G4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4806 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 123052 Z= 0.183 Angle : 0.657 12.222 167776 Z= 0.331 Chirality : 0.039 0.232 19608 Planarity : 0.005 0.082 22100 Dihedral : 5.968 50.852 18084 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.15 % Favored : 89.67 % Rotamer: Outliers : 2.52 % Allowed : 10.96 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.66 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.07), residues: 13364 helix: -1.31 (0.06), residues: 5908 sheet: -1.54 (0.15), residues: 1196 loop : -2.96 (0.07), residues: 6260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E2886 HIS 0.010 0.001 HIS E 879 PHE 0.023 0.001 PHE E 389 TYR 0.032 0.001 TYR I1712 ARG 0.010 0.001 ARG J 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1378 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1118 time to evaluate : 8.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 MET cc_start: 0.7449 (tpp) cc_final: 0.7188 (tpp) REVERT: F 30 LEU cc_start: 0.9041 (tt) cc_final: 0.8758 (mp) REVERT: F 91 ILE cc_start: 0.8733 (mm) cc_final: 0.8493 (mp) REVERT: F 94 ASN cc_start: 0.8182 (t0) cc_final: 0.7801 (p0) REVERT: A 29 MET cc_start: 0.7428 (tpp) cc_final: 0.7037 (tpp) REVERT: A 30 LEU cc_start: 0.9014 (tt) cc_final: 0.8640 (mp) REVERT: A 94 ASN cc_start: 0.8173 (t0) cc_final: 0.7825 (p0) REVERT: H 29 MET cc_start: 0.7484 (tpp) cc_final: 0.7274 (tpp) REVERT: J 29 MET cc_start: 0.7465 (tpp) cc_final: 0.7203 (tpp) REVERT: J 30 LEU cc_start: 0.9041 (tt) cc_final: 0.8824 (mp) REVERT: J 91 ILE cc_start: 0.8748 (mm) cc_final: 0.8513 (mp) REVERT: J 94 ASN cc_start: 0.8183 (t0) cc_final: 0.7839 (p0) REVERT: B 158 SER cc_start: 0.9031 (m) cc_final: 0.8827 (t) REVERT: B 205 ILE cc_start: 0.9486 (tp) cc_final: 0.9023 (tp) REVERT: B 483 MET cc_start: 0.8355 (mmm) cc_final: 0.8059 (mmm) REVERT: B 1713 ASP cc_start: 0.7226 (t70) cc_final: 0.7011 (t70) REVERT: B 2032 GLN cc_start: 0.8381 (tp40) cc_final: 0.7752 (tm-30) REVERT: B 2188 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7646 (p0) REVERT: B 2211 MET cc_start: 0.8841 (ttp) cc_final: 0.8580 (tmm) REVERT: B 3652 MET cc_start: 0.8288 (tpp) cc_final: 0.7917 (tpt) REVERT: B 3711 THR cc_start: 0.8678 (m) cc_final: 0.8321 (p) REVERT: B 3805 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9039 (pp) REVERT: B 4216 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8493 (tm-30) REVERT: B 4647 SER cc_start: 0.8685 (p) cc_final: 0.8479 (t) REVERT: E 205 ILE cc_start: 0.9486 (tp) cc_final: 0.9016 (tp) REVERT: E 1652 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7489 (mt-10) REVERT: E 1713 ASP cc_start: 0.7231 (t70) cc_final: 0.7019 (t70) REVERT: E 2032 GLN cc_start: 0.8393 (tp40) cc_final: 0.7768 (tm-30) REVERT: E 2178 MET cc_start: 0.8831 (tmm) cc_final: 0.7942 (tmm) REVERT: E 2188 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7631 (p0) REVERT: E 2211 MET cc_start: 0.8849 (ttp) cc_final: 0.8589 (tmm) REVERT: E 3652 MET cc_start: 0.8284 (tpp) cc_final: 0.7916 (tpt) REVERT: E 3711 THR cc_start: 0.8703 (m) cc_final: 0.8338 (p) REVERT: E 3805 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9056 (pp) REVERT: E 4026 MET cc_start: 0.9129 (ttp) cc_final: 0.8632 (ttm) REVERT: E 4216 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8519 (tm-30) REVERT: E 4647 SER cc_start: 0.8714 (p) cc_final: 0.8513 (t) REVERT: I 205 ILE cc_start: 0.9482 (tp) cc_final: 0.9016 (tp) REVERT: I 1652 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7376 (mt-10) REVERT: I 1713 ASP cc_start: 0.7248 (t70) cc_final: 0.7041 (t70) REVERT: I 2032 GLN cc_start: 0.8389 (tp40) cc_final: 0.7758 (tm-30) REVERT: I 2178 MET cc_start: 0.8802 (tmm) cc_final: 0.7892 (tmm) REVERT: I 2188 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7627 (p0) REVERT: I 2211 MET cc_start: 0.8846 (ttp) cc_final: 0.8582 (tmm) REVERT: I 3652 MET cc_start: 0.8296 (tpp) cc_final: 0.7916 (tpt) REVERT: I 3711 THR cc_start: 0.8698 (m) cc_final: 0.8329 (p) REVERT: I 3805 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9014 (pp) REVERT: I 4026 MET cc_start: 0.9129 (ttp) cc_final: 0.8640 (ttm) REVERT: I 4647 SER cc_start: 0.8686 (p) cc_final: 0.8483 (t) REVERT: G 205 ILE cc_start: 0.9483 (tp) cc_final: 0.9013 (tp) REVERT: G 1713 ASP cc_start: 0.7254 (t70) cc_final: 0.7046 (t70) REVERT: G 2178 MET cc_start: 0.8826 (tmm) cc_final: 0.7911 (tmm) REVERT: G 2188 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7614 (p0) REVERT: G 2211 MET cc_start: 0.8843 (ttp) cc_final: 0.8593 (tmm) REVERT: G 3652 MET cc_start: 0.8311 (tpp) cc_final: 0.7919 (tpt) REVERT: G 3711 THR cc_start: 0.8696 (m) cc_final: 0.8336 (p) REVERT: G 3805 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9062 (pp) REVERT: G 4026 MET cc_start: 0.9129 (ttp) cc_final: 0.8636 (ttm) REVERT: G 4216 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8470 (tm-30) REVERT: G 4647 SER cc_start: 0.8680 (p) cc_final: 0.8479 (t) outliers start: 260 outliers final: 159 residues processed: 1322 average time/residue: 0.9205 time to fit residues: 2180.7946 Evaluate side-chains 1115 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 948 time to evaluate : 8.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 664 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 772 ASN Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 1217 CYS Chi-restraints excluded: chain B residue 1657 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1702 HIS Chi-restraints excluded: chain B residue 1711 TYR Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1720 LEU Chi-restraints excluded: chain B residue 1802 ILE Chi-restraints excluded: chain B residue 1850 VAL Chi-restraints excluded: chain B residue 1937 LEU Chi-restraints excluded: chain B residue 1944 GLU Chi-restraints excluded: chain B residue 2188 ASN Chi-restraints excluded: chain B residue 2223 ILE Chi-restraints excluded: chain B residue 2252 ASP Chi-restraints excluded: chain B residue 2461 VAL Chi-restraints excluded: chain B residue 3717 ASP Chi-restraints excluded: chain B residue 3781 GLN Chi-restraints excluded: chain B residue 3805 LEU Chi-restraints excluded: chain B residue 3832 ILE Chi-restraints excluded: chain B residue 3938 SER Chi-restraints excluded: chain B residue 4023 MET Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4081 VAL Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4645 CYS Chi-restraints excluded: chain B residue 4688 ILE Chi-restraints excluded: chain B residue 4690 GLU Chi-restraints excluded: chain B residue 4787 ASN Chi-restraints excluded: chain B residue 4801 LEU Chi-restraints excluded: chain B residue 4807 PHE Chi-restraints excluded: chain B residue 4891 VAL Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 599 VAL Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 664 PHE Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain E residue 772 ASN Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 826 ILE Chi-restraints excluded: chain E residue 920 TYR Chi-restraints excluded: chain E residue 1217 CYS Chi-restraints excluded: chain E residue 1676 LEU Chi-restraints excluded: chain E residue 1702 HIS Chi-restraints excluded: chain E residue 1720 LEU Chi-restraints excluded: chain E residue 1802 ILE Chi-restraints excluded: chain E residue 1850 VAL Chi-restraints excluded: chain E residue 1937 LEU Chi-restraints excluded: chain E residue 1944 GLU Chi-restraints excluded: chain E residue 2188 ASN Chi-restraints excluded: chain E residue 2223 ILE Chi-restraints excluded: chain E residue 2252 ASP Chi-restraints excluded: chain E residue 2461 VAL Chi-restraints excluded: chain E residue 2466 LEU Chi-restraints excluded: chain E residue 3717 ASP Chi-restraints excluded: chain E residue 3805 LEU Chi-restraints excluded: chain E residue 3832 ILE Chi-restraints excluded: chain E residue 3938 SER Chi-restraints excluded: chain E residue 4036 VAL Chi-restraints excluded: chain E residue 4081 VAL Chi-restraints excluded: chain E residue 4247 ILE Chi-restraints excluded: chain E residue 4551 PHE Chi-restraints excluded: chain E residue 4645 CYS Chi-restraints excluded: chain E residue 4688 ILE Chi-restraints excluded: chain E residue 4690 GLU Chi-restraints excluded: chain E residue 4787 ASN Chi-restraints excluded: chain E residue 4801 LEU Chi-restraints excluded: chain E residue 4807 PHE Chi-restraints excluded: chain E residue 4891 VAL Chi-restraints excluded: chain E residue 4952 GLU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 608 VAL Chi-restraints excluded: chain I residue 664 PHE Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain I residue 674 PHE Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 772 ASN Chi-restraints excluded: chain I residue 791 PHE Chi-restraints excluded: chain I residue 826 ILE Chi-restraints excluded: chain I residue 920 TYR Chi-restraints excluded: chain I residue 1217 CYS Chi-restraints excluded: chain I residue 1676 LEU Chi-restraints excluded: chain I residue 1702 HIS Chi-restraints excluded: chain I residue 1937 LEU Chi-restraints excluded: chain I residue 1944 GLU Chi-restraints excluded: chain I residue 2188 ASN Chi-restraints excluded: chain I residue 2223 ILE Chi-restraints excluded: chain I residue 2252 ASP Chi-restraints excluded: chain I residue 2461 VAL Chi-restraints excluded: chain I residue 2466 LEU Chi-restraints excluded: chain I residue 3717 ASP Chi-restraints excluded: chain I residue 3805 LEU Chi-restraints excluded: chain I residue 3832 ILE Chi-restraints excluded: chain I residue 3938 SER Chi-restraints excluded: chain I residue 4036 VAL Chi-restraints excluded: chain I residue 4081 VAL Chi-restraints excluded: chain I residue 4247 ILE Chi-restraints excluded: chain I residue 4645 CYS Chi-restraints excluded: chain I residue 4688 ILE Chi-restraints excluded: chain I residue 4690 GLU Chi-restraints excluded: chain I residue 4787 ASN Chi-restraints excluded: chain I residue 4801 LEU Chi-restraints excluded: chain I residue 4807 PHE Chi-restraints excluded: chain I residue 4891 VAL Chi-restraints excluded: chain I residue 4952 GLU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 564 LEU Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 647 ASN Chi-restraints excluded: chain G residue 664 PHE Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 749 ASP Chi-restraints excluded: chain G residue 772 ASN Chi-restraints excluded: chain G residue 791 PHE Chi-restraints excluded: chain G residue 826 ILE Chi-restraints excluded: chain G residue 920 TYR Chi-restraints excluded: chain G residue 1120 LEU Chi-restraints excluded: chain G residue 1217 CYS Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1676 LEU Chi-restraints excluded: chain G residue 1702 HIS Chi-restraints excluded: chain G residue 1711 TYR Chi-restraints excluded: chain G residue 1937 LEU Chi-restraints excluded: chain G residue 1944 GLU Chi-restraints excluded: chain G residue 2188 ASN Chi-restraints excluded: chain G residue 2223 ILE Chi-restraints excluded: chain G residue 2252 ASP Chi-restraints excluded: chain G residue 2461 VAL Chi-restraints excluded: chain G residue 2466 LEU Chi-restraints excluded: chain G residue 3717 ASP Chi-restraints excluded: chain G residue 3805 LEU Chi-restraints excluded: chain G residue 3832 ILE Chi-restraints excluded: chain G residue 3938 SER Chi-restraints excluded: chain G residue 4036 VAL Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4247 ILE Chi-restraints excluded: chain G residue 4645 CYS Chi-restraints excluded: chain G residue 4688 ILE Chi-restraints excluded: chain G residue 4690 GLU Chi-restraints excluded: chain G residue 4787 ASN Chi-restraints excluded: chain G residue 4801 LEU Chi-restraints excluded: chain G residue 4807 PHE Chi-restraints excluded: chain G residue 4891 VAL Chi-restraints excluded: chain G residue 4952 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2349 ASN B3781 GLN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3896 ASN B3897 ASN ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3976 ASN B4553 ASN ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2349 ASN ** E3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3896 ASN E3897 ASN ** E3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3976 ASN E4553 ASN ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 904 HIS I1691 GLN I2349 ASN ** I3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3896 ASN I3897 ASN ** I3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3976 ASN I4553 ASN G 151 HIS ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 624 ASN G1691 GLN ** G1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1775 HIS G2349 ASN ** G3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3896 ASN G3897 ASN ** G3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3976 ASN G4553 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 123052 Z= 0.148 Angle : 0.608 11.519 167776 Z= 0.303 Chirality : 0.037 0.211 19608 Planarity : 0.005 0.079 22100 Dihedral : 5.448 44.033 18084 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.23 % Favored : 89.59 % Rotamer: Outliers : 2.36 % Allowed : 12.54 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.66 % Twisted General : 0.16 % 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: -2.50 (0.07), residues: 13364 helix: -0.67 (0.07), residues: 5888 sheet: -1.21 (0.16), residues: 1196 loop : -2.78 (0.07), residues: 6280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G2766 HIS 0.006 0.001 HIS E 911 PHE 0.034 0.001 PHE E1748 TYR 0.027 0.001 TYR G1712 ARG 0.006 0.000 ARG G 493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1349 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1105 time to evaluate : 8.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 MET cc_start: 0.7425 (tpp) cc_final: 0.7055 (tpp) REVERT: F 30 LEU cc_start: 0.9009 (tt) cc_final: 0.8669 (mp) REVERT: F 91 ILE cc_start: 0.8709 (mm) cc_final: 0.8444 (mp) REVERT: A 29 MET cc_start: 0.7450 (tpp) cc_final: 0.7057 (tpp) REVERT: A 30 LEU cc_start: 0.9019 (tt) cc_final: 0.8674 (mp) REVERT: A 52 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8652 (mmmt) REVERT: H 30 LEU cc_start: 0.8876 (tt) cc_final: 0.8490 (mp) REVERT: J 29 MET cc_start: 0.7459 (tpp) cc_final: 0.7059 (tpp) REVERT: J 30 LEU cc_start: 0.9001 (tt) cc_final: 0.8687 (mp) REVERT: J 91 ILE cc_start: 0.8717 (mm) cc_final: 0.8456 (mp) REVERT: B 158 SER cc_start: 0.9028 (m) cc_final: 0.8804 (t) REVERT: B 205 ILE cc_start: 0.9336 (tp) cc_final: 0.8833 (tp) REVERT: B 483 MET cc_start: 0.8277 (mmm) cc_final: 0.8022 (mmm) REVERT: B 723 THR cc_start: 0.9316 (OUTLIER) cc_final: 0.9096 (m) REVERT: B 791 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.6323 (t80) REVERT: B 1711 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.8927 (m-10) REVERT: B 2032 GLN cc_start: 0.8451 (tp40) cc_final: 0.7820 (tm-30) REVERT: B 2211 MET cc_start: 0.8876 (ttp) cc_final: 0.8662 (tmm) REVERT: B 3652 MET cc_start: 0.8249 (tpp) cc_final: 0.7823 (tpt) REVERT: B 3711 THR cc_start: 0.8624 (m) cc_final: 0.8187 (p) REVERT: B 3805 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9010 (pp) REVERT: B 3896 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7637 (m110) REVERT: B 4216 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8415 (tm-30) REVERT: E 205 ILE cc_start: 0.9338 (tp) cc_final: 0.8830 (tp) REVERT: E 723 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9088 (m) REVERT: E 791 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6458 (t80) REVERT: E 1652 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7359 (mt-10) REVERT: E 2032 GLN cc_start: 0.8468 (tp40) cc_final: 0.7831 (tm-30) REVERT: E 3652 MET cc_start: 0.8281 (tpp) cc_final: 0.7863 (tpt) REVERT: E 3711 THR cc_start: 0.8653 (m) cc_final: 0.8199 (p) REVERT: E 3805 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8964 (pp) REVERT: E 3896 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7656 (m110) REVERT: E 4102 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7340 (pm20) REVERT: E 4216 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8438 (tm-30) REVERT: I 205 ILE cc_start: 0.9334 (tp) cc_final: 0.8828 (tp) REVERT: I 723 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9083 (m) REVERT: I 791 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6326 (t80) REVERT: I 1652 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7317 (mt-10) REVERT: I 2032 GLN cc_start: 0.8465 (tp40) cc_final: 0.7819 (tm-30) REVERT: I 3652 MET cc_start: 0.8282 (tpp) cc_final: 0.7865 (tpt) REVERT: I 3711 THR cc_start: 0.8634 (m) cc_final: 0.8197 (p) REVERT: I 3805 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.8989 (pp) REVERT: I 5013 MET cc_start: 0.7849 (mtt) cc_final: 0.7180 (mtt) REVERT: G 205 ILE cc_start: 0.9335 (tp) cc_final: 0.8826 (tp) REVERT: G 723 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.9077 (m) REVERT: G 961 MET cc_start: 0.3323 (mmp) cc_final: 0.2712 (mmt) REVERT: G 2211 MET cc_start: 0.8875 (ttp) cc_final: 0.8662 (tmm) REVERT: G 3652 MET cc_start: 0.8265 (tpp) cc_final: 0.7835 (tpt) REVERT: G 3711 THR cc_start: 0.8643 (m) cc_final: 0.8202 (p) REVERT: G 3805 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9006 (pp) REVERT: G 4216 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8424 (tm-30) REVERT: G 5013 MET cc_start: 0.7854 (mtt) cc_final: 0.7112 (mtt) outliers start: 244 outliers final: 136 residues processed: 1289 average time/residue: 0.9257 time to fit residues: 2159.4724 Evaluate side-chains 1119 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 968 time to evaluate : 8.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 664 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 772 ASN Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 1217 CYS Chi-restraints excluded: chain B residue 1657 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1702 HIS Chi-restraints excluded: chain B residue 1711 TYR Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1736 VAL Chi-restraints excluded: chain B residue 1839 VAL Chi-restraints excluded: chain B residue 1850 VAL Chi-restraints excluded: chain B residue 1944 GLU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2131 LEU Chi-restraints excluded: chain B residue 2153 MET Chi-restraints excluded: chain B residue 2461 VAL Chi-restraints excluded: chain B residue 3717 ASP Chi-restraints excluded: chain B residue 3781 GLN Chi-restraints excluded: chain B residue 3787 LYS Chi-restraints excluded: chain B residue 3805 LEU Chi-restraints excluded: chain B residue 3896 ASN Chi-restraints excluded: chain B residue 3903 LEU Chi-restraints excluded: chain B residue 3942 VAL Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4081 VAL Chi-restraints excluded: chain B residue 4102 GLN Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4645 CYS Chi-restraints excluded: chain B residue 4688 ILE Chi-restraints excluded: chain B residue 4807 PHE Chi-restraints excluded: chain B residue 4891 VAL Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 664 PHE Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain E residue 772 ASN Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 826 ILE Chi-restraints excluded: chain E residue 920 TYR Chi-restraints excluded: chain E residue 1217 CYS Chi-restraints excluded: chain E residue 1657 LEU Chi-restraints excluded: chain E residue 1676 LEU Chi-restraints excluded: chain E residue 1702 HIS Chi-restraints excluded: chain E residue 1839 VAL Chi-restraints excluded: chain E residue 1850 VAL Chi-restraints excluded: chain E residue 1944 GLU Chi-restraints excluded: chain E residue 2038 LEU Chi-restraints excluded: chain E residue 2153 MET Chi-restraints excluded: chain E residue 2346 VAL Chi-restraints excluded: chain E residue 2461 VAL Chi-restraints excluded: chain E residue 2466 LEU Chi-restraints excluded: chain E residue 3717 ASP Chi-restraints excluded: chain E residue 3787 LYS Chi-restraints excluded: chain E residue 3805 LEU Chi-restraints excluded: chain E residue 3896 ASN Chi-restraints excluded: chain E residue 3903 LEU Chi-restraints excluded: chain E residue 3942 VAL Chi-restraints excluded: chain E residue 4036 VAL Chi-restraints excluded: chain E residue 4081 VAL Chi-restraints excluded: chain E residue 4102 GLN Chi-restraints excluded: chain E residue 4207 MET Chi-restraints excluded: chain E residue 4645 CYS Chi-restraints excluded: chain E residue 4688 ILE Chi-restraints excluded: chain E residue 4787 ASN Chi-restraints excluded: chain E residue 4807 PHE Chi-restraints excluded: chain E residue 4891 VAL Chi-restraints excluded: chain E residue 4952 GLU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 608 VAL Chi-restraints excluded: chain I residue 647 ASN Chi-restraints excluded: chain I residue 664 PHE Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain I residue 674 PHE Chi-restraints excluded: chain I residue 723 THR Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 772 ASN Chi-restraints excluded: chain I residue 791 PHE Chi-restraints excluded: chain I residue 826 ILE Chi-restraints excluded: chain I residue 920 TYR Chi-restraints excluded: chain I residue 1217 CYS Chi-restraints excluded: chain I residue 1657 LEU Chi-restraints excluded: chain I residue 1676 LEU Chi-restraints excluded: chain I residue 1702 HIS Chi-restraints excluded: chain I residue 1703 LEU Chi-restraints excluded: chain I residue 1839 VAL Chi-restraints excluded: chain I residue 1944 GLU Chi-restraints excluded: chain I residue 2038 LEU Chi-restraints excluded: chain I residue 2346 VAL Chi-restraints excluded: chain I residue 2461 VAL Chi-restraints excluded: chain I residue 2466 LEU Chi-restraints excluded: chain I residue 3717 ASP Chi-restraints excluded: chain I residue 3787 LYS Chi-restraints excluded: chain I residue 3805 LEU Chi-restraints excluded: chain I residue 3903 LEU Chi-restraints excluded: chain I residue 4036 VAL Chi-restraints excluded: chain I residue 4081 VAL Chi-restraints excluded: chain I residue 4207 MET Chi-restraints excluded: chain I residue 4551 PHE Chi-restraints excluded: chain I residue 4645 CYS Chi-restraints excluded: chain I residue 4688 ILE Chi-restraints excluded: chain I residue 4807 PHE Chi-restraints excluded: chain I residue 4891 VAL Chi-restraints excluded: chain I residue 4952 GLU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 664 PHE Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 749 ASP Chi-restraints excluded: chain G residue 772 ASN Chi-restraints excluded: chain G residue 791 PHE Chi-restraints excluded: chain G residue 826 ILE Chi-restraints excluded: chain G residue 920 TYR Chi-restraints excluded: chain G residue 1217 CYS Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1676 LEU Chi-restraints excluded: chain G residue 1702 HIS Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1839 VAL Chi-restraints excluded: chain G residue 1944 GLU Chi-restraints excluded: chain G residue 2038 LEU Chi-restraints excluded: chain G residue 2131 LEU Chi-restraints excluded: chain G residue 2461 VAL Chi-restraints excluded: chain G residue 2466 LEU Chi-restraints excluded: chain G residue 3787 LYS Chi-restraints excluded: chain G residue 3805 LEU Chi-restraints excluded: chain G residue 3903 LEU Chi-restraints excluded: chain G residue 4036 VAL Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4207 MET Chi-restraints excluded: chain G residue 4645 CYS Chi-restraints excluded: chain G residue 4677 LEU Chi-restraints excluded: chain G residue 4688 ILE Chi-restraints excluded: chain G residue 4807 PHE Chi-restraints excluded: chain G residue 4891 VAL Chi-restraints excluded: chain G residue 4952 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 GLN B1972 ASN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3896 ASN B3897 ASN ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 HIS ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 765 GLN E1972 ASN E2763 HIS ** E3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3896 ASN E3897 ASN ** E3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 765 GLN I1972 ASN ** I3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3896 ASN I3897 ASN ** I3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 765 GLN G1972 ASN ** G2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G3781 GLN ** G3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3896 ASN G3897 ASN ** G3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 123052 Z= 0.353 Angle : 0.722 18.057 167776 Z= 0.361 Chirality : 0.042 0.367 19608 Planarity : 0.005 0.082 22100 Dihedral : 5.682 42.359 18084 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.94 % Favored : 87.86 % Rotamer: Outliers : 3.26 % Allowed : 13.40 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.66 % Twisted General : 0.16 % 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: -2.36 (0.07), residues: 13364 helix: -0.49 (0.07), residues: 5896 sheet: -1.09 (0.16), residues: 1176 loop : -2.79 (0.07), residues: 6292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I3661 HIS 0.012 0.001 HIS G1719 PHE 0.019 0.002 PHE B4559 TYR 0.034 0.002 TYR B1712 ARG 0.007 0.001 ARG G4137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 931 time to evaluate : 9.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 MET cc_start: 0.7484 (tpp) cc_final: 0.7231 (tpp) REVERT: F 30 LEU cc_start: 0.9059 (tt) cc_final: 0.8803 (mp) REVERT: F 91 ILE cc_start: 0.8764 (mm) cc_final: 0.8530 (mp) REVERT: A 29 MET cc_start: 0.7454 (tpp) cc_final: 0.7195 (tpp) REVERT: A 30 LEU cc_start: 0.9070 (tt) cc_final: 0.8829 (mp) REVERT: H 73 LYS cc_start: 0.8912 (tttm) cc_final: 0.8525 (tmtt) REVERT: J 29 MET cc_start: 0.7466 (tpp) cc_final: 0.7198 (tpp) REVERT: J 91 ILE cc_start: 0.8817 (mm) cc_final: 0.8581 (mp) REVERT: B 205 ILE cc_start: 0.9473 (tp) cc_final: 0.9026 (tp) REVERT: B 483 MET cc_start: 0.8616 (mmm) cc_final: 0.8348 (mmm) REVERT: B 723 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9156 (m) REVERT: B 1170 MET cc_start: 0.7504 (mmp) cc_final: 0.7155 (mmp) REVERT: B 1242 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8708 (tt) REVERT: B 2032 GLN cc_start: 0.8435 (tp40) cc_final: 0.7817 (tm-30) REVERT: B 2211 MET cc_start: 0.8909 (ttp) cc_final: 0.8700 (tmm) REVERT: B 3652 MET cc_start: 0.8452 (tpp) cc_final: 0.8044 (tpt) REVERT: B 3662 ILE cc_start: 0.5644 (OUTLIER) cc_final: 0.5342 (pp) REVERT: B 3711 THR cc_start: 0.8698 (m) cc_final: 0.8350 (p) REVERT: B 3805 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9014 (pp) REVERT: B 4216 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8547 (tm-30) REVERT: E 205 ILE cc_start: 0.9471 (tp) cc_final: 0.9021 (tp) REVERT: E 723 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.9152 (m) REVERT: E 1170 MET cc_start: 0.7550 (mmp) cc_final: 0.7209 (mmp) REVERT: E 1242 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8731 (tt) REVERT: E 2032 GLN cc_start: 0.8421 (tp40) cc_final: 0.7785 (tm-30) REVERT: E 3652 MET cc_start: 0.8457 (tpp) cc_final: 0.8042 (tpt) REVERT: E 3662 ILE cc_start: 0.5747 (OUTLIER) cc_final: 0.5336 (pp) REVERT: E 3805 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9012 (pp) REVERT: E 4026 MET cc_start: 0.9147 (ttp) cc_final: 0.8613 (ttm) REVERT: E 4216 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8564 (tm-30) REVERT: E 4769 MET cc_start: 0.8212 (ppp) cc_final: 0.7974 (ppp) REVERT: I 205 ILE cc_start: 0.9469 (tp) cc_final: 0.9019 (tp) REVERT: I 723 THR cc_start: 0.9379 (OUTLIER) cc_final: 0.9158 (m) REVERT: I 1170 MET cc_start: 0.7565 (mmp) cc_final: 0.7219 (mmp) REVERT: I 1242 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8719 (tt) REVERT: I 2032 GLN cc_start: 0.8443 (tp40) cc_final: 0.7821 (tm-30) REVERT: I 3652 MET cc_start: 0.8461 (tpp) cc_final: 0.8045 (tpt) REVERT: I 3662 ILE cc_start: 0.5817 (OUTLIER) cc_final: 0.5398 (pp) REVERT: I 3711 THR cc_start: 0.8837 (m) cc_final: 0.8403 (p) REVERT: I 3805 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9021 (pp) REVERT: I 3896 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.7945 (m110) REVERT: I 4026 MET cc_start: 0.9148 (ttp) cc_final: 0.8625 (ttm) REVERT: G 205 ILE cc_start: 0.9471 (tp) cc_final: 0.9018 (tp) REVERT: G 723 THR cc_start: 0.9376 (OUTLIER) cc_final: 0.9153 (m) REVERT: G 961 MET cc_start: 0.3470 (mmp) cc_final: 0.3016 (mmt) REVERT: G 1170 MET cc_start: 0.7496 (mmp) cc_final: 0.7147 (mmp) REVERT: G 1242 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8715 (tt) REVERT: G 1786 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6217 (pp) REVERT: G 2211 MET cc_start: 0.8909 (ttp) cc_final: 0.8703 (tmm) REVERT: G 3652 MET cc_start: 0.8492 (tpp) cc_final: 0.8097 (tpt) REVERT: G 3662 ILE cc_start: 0.5582 (OUTLIER) cc_final: 0.5282 (pp) REVERT: G 3711 THR cc_start: 0.8845 (m) cc_final: 0.8436 (p) REVERT: G 3805 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9016 (pp) REVERT: G 3896 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.7938 (m110) REVERT: G 4026 MET cc_start: 0.9148 (ttp) cc_final: 0.8611 (ttm) REVERT: G 4216 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8540 (tm-30) REVERT: G 4769 MET cc_start: 0.8157 (ppp) cc_final: 0.7925 (ppp) outliers start: 337 outliers final: 234 residues processed: 1217 average time/residue: 0.9080 time to fit residues: 2003.2974 Evaluate side-chains 1163 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 910 time to evaluate : 9.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 664 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 772 ASN Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 1095 VAL Chi-restraints excluded: chain B residue 1217 CYS Chi-restraints excluded: chain B residue 1242 LEU Chi-restraints excluded: chain B residue 1595 LEU Chi-restraints excluded: chain B residue 1641 ILE Chi-restraints excluded: chain B residue 1657 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1702 HIS Chi-restraints excluded: chain B residue 1711 TYR Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1736 VAL Chi-restraints excluded: chain B residue 1839 VAL Chi-restraints excluded: chain B residue 1850 VAL Chi-restraints excluded: chain B residue 1944 GLU Chi-restraints excluded: chain B residue 1966 VAL Chi-restraints excluded: chain B residue 2031 LEU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2188 ASN Chi-restraints excluded: chain B residue 2223 ILE Chi-restraints excluded: chain B residue 2461 VAL Chi-restraints excluded: chain B residue 3662 ILE Chi-restraints excluded: chain B residue 3781 GLN Chi-restraints excluded: chain B residue 3787 LYS Chi-restraints excluded: chain B residue 3805 LEU Chi-restraints excluded: chain B residue 3883 ASP Chi-restraints excluded: chain B residue 3903 LEU Chi-restraints excluded: chain B residue 3913 ILE Chi-restraints excluded: chain B residue 3915 ILE Chi-restraints excluded: chain B residue 3938 SER Chi-restraints excluded: chain B residue 3942 VAL Chi-restraints excluded: chain B residue 3955 MET Chi-restraints excluded: chain B residue 4000 MET Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4081 VAL Chi-restraints excluded: chain B residue 4104 THR Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4551 PHE Chi-restraints excluded: chain B residue 4645 CYS Chi-restraints excluded: chain B residue 4688 ILE Chi-restraints excluded: chain B residue 4690 GLU Chi-restraints excluded: chain B residue 4807 PHE Chi-restraints excluded: chain B residue 4814 LEU Chi-restraints excluded: chain B residue 4891 VAL Chi-restraints excluded: chain B residue 4950 VAL Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 664 PHE Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain E residue 750 LEU Chi-restraints excluded: chain E residue 772 ASN Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 826 ILE Chi-restraints excluded: chain E residue 920 TYR Chi-restraints excluded: chain E residue 1095 VAL Chi-restraints excluded: chain E residue 1217 CYS Chi-restraints excluded: chain E residue 1242 LEU Chi-restraints excluded: chain E residue 1595 LEU Chi-restraints excluded: chain E residue 1641 ILE Chi-restraints excluded: chain E residue 1657 LEU Chi-restraints excluded: chain E residue 1676 LEU Chi-restraints excluded: chain E residue 1702 HIS Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1736 VAL Chi-restraints excluded: chain E residue 1839 VAL Chi-restraints excluded: chain E residue 1850 VAL Chi-restraints excluded: chain E residue 1944 GLU Chi-restraints excluded: chain E residue 1966 VAL Chi-restraints excluded: chain E residue 2031 LEU Chi-restraints excluded: chain E residue 2038 LEU Chi-restraints excluded: chain E residue 2188 ASN Chi-restraints excluded: chain E residue 2223 ILE Chi-restraints excluded: chain E residue 2461 VAL Chi-restraints excluded: chain E residue 2466 LEU Chi-restraints excluded: chain E residue 3662 ILE Chi-restraints excluded: chain E residue 3787 LYS Chi-restraints excluded: chain E residue 3805 LEU Chi-restraints excluded: chain E residue 3903 LEU Chi-restraints excluded: chain E residue 3913 ILE Chi-restraints excluded: chain E residue 3915 ILE Chi-restraints excluded: chain E residue 3938 SER Chi-restraints excluded: chain E residue 3942 VAL Chi-restraints excluded: chain E residue 3955 MET Chi-restraints excluded: chain E residue 4000 MET Chi-restraints excluded: chain E residue 4036 VAL Chi-restraints excluded: chain E residue 4081 VAL Chi-restraints excluded: chain E residue 4104 THR Chi-restraints excluded: chain E residue 4207 MET Chi-restraints excluded: chain E residue 4247 ILE Chi-restraints excluded: chain E residue 4551 PHE Chi-restraints excluded: chain E residue 4645 CYS Chi-restraints excluded: chain E residue 4688 ILE Chi-restraints excluded: chain E residue 4690 GLU Chi-restraints excluded: chain E residue 4807 PHE Chi-restraints excluded: chain E residue 4814 LEU Chi-restraints excluded: chain E residue 4891 VAL Chi-restraints excluded: chain E residue 4950 VAL Chi-restraints excluded: chain E residue 4952 GLU Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 583 ILE Chi-restraints excluded: chain I residue 608 VAL Chi-restraints excluded: chain I residue 647 ASN Chi-restraints excluded: chain I residue 664 PHE Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain I residue 674 PHE Chi-restraints excluded: chain I residue 723 THR Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 772 ASN Chi-restraints excluded: chain I residue 791 PHE Chi-restraints excluded: chain I residue 826 ILE Chi-restraints excluded: chain I residue 920 TYR Chi-restraints excluded: chain I residue 1095 VAL Chi-restraints excluded: chain I residue 1217 CYS Chi-restraints excluded: chain I residue 1242 LEU Chi-restraints excluded: chain I residue 1595 LEU Chi-restraints excluded: chain I residue 1641 ILE Chi-restraints excluded: chain I residue 1657 LEU Chi-restraints excluded: chain I residue 1676 LEU Chi-restraints excluded: chain I residue 1702 HIS Chi-restraints excluded: chain I residue 1703 LEU Chi-restraints excluded: chain I residue 1717 SER Chi-restraints excluded: chain I residue 1736 VAL Chi-restraints excluded: chain I residue 1839 VAL Chi-restraints excluded: chain I residue 1850 VAL Chi-restraints excluded: chain I residue 1944 GLU Chi-restraints excluded: chain I residue 1966 VAL Chi-restraints excluded: chain I residue 2031 LEU Chi-restraints excluded: chain I residue 2038 LEU Chi-restraints excluded: chain I residue 2188 ASN Chi-restraints excluded: chain I residue 2223 ILE Chi-restraints excluded: chain I residue 2461 VAL Chi-restraints excluded: chain I residue 2466 LEU Chi-restraints excluded: chain I residue 3662 ILE Chi-restraints excluded: chain I residue 3787 LYS Chi-restraints excluded: chain I residue 3805 LEU Chi-restraints excluded: chain I residue 3883 ASP Chi-restraints excluded: chain I residue 3896 ASN Chi-restraints excluded: chain I residue 3903 LEU Chi-restraints excluded: chain I residue 3913 ILE Chi-restraints excluded: chain I residue 3915 ILE Chi-restraints excluded: chain I residue 3938 SER Chi-restraints excluded: chain I residue 3942 VAL Chi-restraints excluded: chain I residue 3955 MET Chi-restraints excluded: chain I residue 4000 MET Chi-restraints excluded: chain I residue 4036 VAL Chi-restraints excluded: chain I residue 4044 MET Chi-restraints excluded: chain I residue 4081 VAL Chi-restraints excluded: chain I residue 4104 THR Chi-restraints excluded: chain I residue 4207 MET Chi-restraints excluded: chain I residue 4247 ILE Chi-restraints excluded: chain I residue 4551 PHE Chi-restraints excluded: chain I residue 4645 CYS Chi-restraints excluded: chain I residue 4688 ILE Chi-restraints excluded: chain I residue 4690 GLU Chi-restraints excluded: chain I residue 4807 PHE Chi-restraints excluded: chain I residue 4891 VAL Chi-restraints excluded: chain I residue 4950 VAL Chi-restraints excluded: chain I residue 4952 GLU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 575 LEU Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 647 ASN Chi-restraints excluded: chain G residue 664 PHE Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 749 ASP Chi-restraints excluded: chain G residue 772 ASN Chi-restraints excluded: chain G residue 791 PHE Chi-restraints excluded: chain G residue 826 ILE Chi-restraints excluded: chain G residue 920 TYR Chi-restraints excluded: chain G residue 1217 CYS Chi-restraints excluded: chain G residue 1242 LEU Chi-restraints excluded: chain G residue 1595 LEU Chi-restraints excluded: chain G residue 1641 ILE Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1676 LEU Chi-restraints excluded: chain G residue 1702 HIS Chi-restraints excluded: chain G residue 1703 LEU Chi-restraints excluded: chain G residue 1711 TYR Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1786 LEU Chi-restraints excluded: chain G residue 1839 VAL Chi-restraints excluded: chain G residue 1850 VAL Chi-restraints excluded: chain G residue 1944 GLU Chi-restraints excluded: chain G residue 1966 VAL Chi-restraints excluded: chain G residue 2031 LEU Chi-restraints excluded: chain G residue 2038 LEU Chi-restraints excluded: chain G residue 2188 ASN Chi-restraints excluded: chain G residue 2223 ILE Chi-restraints excluded: chain G residue 2461 VAL Chi-restraints excluded: chain G residue 2466 LEU Chi-restraints excluded: chain G residue 3662 ILE Chi-restraints excluded: chain G residue 3717 ASP Chi-restraints excluded: chain G residue 3781 GLN Chi-restraints excluded: chain G residue 3787 LYS Chi-restraints excluded: chain G residue 3805 LEU Chi-restraints excluded: chain G residue 3883 ASP Chi-restraints excluded: chain G residue 3896 ASN Chi-restraints excluded: chain G residue 3903 LEU Chi-restraints excluded: chain G residue 3913 ILE Chi-restraints excluded: chain G residue 3915 ILE Chi-restraints excluded: chain G residue 3938 SER Chi-restraints excluded: chain G residue 3942 VAL Chi-restraints excluded: chain G residue 3955 MET Chi-restraints excluded: chain G residue 4036 VAL Chi-restraints excluded: chain G residue 4044 MET Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4104 THR Chi-restraints excluded: chain G residue 4207 MET Chi-restraints excluded: chain G residue 4245 MET Chi-restraints excluded: chain G residue 4247 ILE Chi-restraints excluded: chain G residue 4645 CYS Chi-restraints excluded: chain G residue 4688 ILE Chi-restraints excluded: chain G residue 4690 GLU Chi-restraints excluded: chain G residue 4807 PHE Chi-restraints excluded: chain G residue 4814 LEU Chi-restraints excluded: chain G residue 4891 VAL Chi-restraints excluded: chain G residue 4950 VAL Chi-restraints excluded: chain G residue 4952 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 0.0870 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 GLN B1691 GLN B1972 ASN B3781 GLN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3897 ASN ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3976 ASN ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 765 GLN E1691 GLN E1972 ASN ** E3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3897 ASN ** E3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3976 ASN ** I 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 765 GLN I1972 ASN ** I3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3896 ASN I3897 ASN ** I3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3976 ASN ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 765 GLN G1972 ASN G2763 HIS ** G3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3896 ASN G3897 ASN ** G3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3976 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 123052 Z= 0.214 Angle : 0.643 16.252 167776 Z= 0.319 Chirality : 0.039 0.377 19608 Planarity : 0.005 0.077 22100 Dihedral : 5.465 40.959 18084 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.62 % Favored : 89.20 % Rotamer: Outliers : 2.96 % Allowed : 14.09 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.66 % Twisted General : 0.13 % 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: -2.08 (0.07), residues: 13364 helix: -0.19 (0.07), residues: 5868 sheet: -0.94 (0.16), residues: 1220 loop : -2.72 (0.08), residues: 6276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B4767 HIS 0.012 0.001 HIS E1719 PHE 0.049 0.001 PHE B1748 TYR 0.031 0.001 TYR G1712 ARG 0.006 0.000 ARG E 871 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1292 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 986 time to evaluate : 8.933 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: F 29 MET cc_start: 0.7447 (tpp) cc_final: 0.7197 (tpp) REVERT: F 91 ILE cc_start: 0.8720 (mm) cc_final: 0.8481 (mp) REVERT: F 94 ASN cc_start: 0.8215 (t0) cc_final: 0.7792 (p0) REVERT: A 29 MET cc_start: 0.7454 (tpp) cc_final: 0.7190 (tpp) REVERT: A 94 ASN cc_start: 0.8187 (t0) cc_final: 0.7756 (p0) REVERT: J 29 MET cc_start: 0.7463 (tpp) cc_final: 0.7034 (tpp) REVERT: J 73 LYS cc_start: 0.8824 (tttt) cc_final: 0.8489 (ttpp) REVERT: J 91 ILE cc_start: 0.8710 (mm) cc_final: 0.8497 (mp) REVERT: J 94 ASN cc_start: 0.8204 (t0) cc_final: 0.7831 (p0) REVERT: B 205 ILE cc_start: 0.9453 (tp) cc_final: 0.8985 (tp) REVERT: B 301 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8676 (m) REVERT: B 483 MET cc_start: 0.8538 (mmm) cc_final: 0.8265 (mmm) REVERT: B 1170 MET cc_start: 0.7477 (mmp) cc_final: 0.7107 (mmp) REVERT: B 1242 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8654 (tt) REVERT: B 1786 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6209 (pp) REVERT: B 2032 GLN cc_start: 0.8464 (tp40) cc_final: 0.7817 (tm-30) REVERT: B 2211 MET cc_start: 0.8906 (ttp) cc_final: 0.8697 (tmm) REVERT: B 3652 MET cc_start: 0.8408 (tpp) cc_final: 0.7879 (tpt) REVERT: B 3711 THR cc_start: 0.8759 (m) cc_final: 0.8399 (p) REVERT: B 3805 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.8978 (pp) REVERT: B 4216 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8534 (tm-30) REVERT: B 4232 GLU cc_start: 0.8461 (tp30) cc_final: 0.7928 (tp30) REVERT: E 205 ILE cc_start: 0.9441 (tp) cc_final: 0.9005 (tp) REVERT: E 301 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8689 (m) REVERT: E 1170 MET cc_start: 0.7584 (mmp) cc_final: 0.7227 (mmp) REVERT: E 1652 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7747 (mt-10) REVERT: E 1786 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.6216 (pp) REVERT: E 2032 GLN cc_start: 0.8473 (tp40) cc_final: 0.7832 (tm-30) REVERT: E 2816 MET cc_start: 0.1208 (ppp) cc_final: 0.0446 (mmm) REVERT: E 3652 MET cc_start: 0.8362 (tpp) cc_final: 0.7959 (tpt) REVERT: E 3805 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8971 (pp) REVERT: E 4216 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8545 (tm-30) REVERT: E 4232 GLU cc_start: 0.8470 (tp30) cc_final: 0.7937 (tp30) REVERT: E 4769 MET cc_start: 0.8309 (ppp) cc_final: 0.8010 (ppp) REVERT: I 205 ILE cc_start: 0.9443 (tp) cc_final: 0.9007 (tp) REVERT: I 1170 MET cc_start: 0.7462 (mmp) cc_final: 0.7091 (mmp) REVERT: I 1242 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8671 (tt) REVERT: I 1786 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6206 (pp) REVERT: I 2032 GLN cc_start: 0.8471 (tp40) cc_final: 0.7819 (tm-30) REVERT: I 2140 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.7750 (mtp-110) REVERT: I 3652 MET cc_start: 0.8403 (tpp) cc_final: 0.7968 (tpt) REVERT: I 3805 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.8981 (pp) REVERT: I 4216 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8592 (tm-30) REVERT: I 4232 GLU cc_start: 0.8451 (tp30) cc_final: 0.7929 (tp30) REVERT: G 205 ILE cc_start: 0.9443 (tp) cc_final: 0.9010 (tp) REVERT: G 301 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8695 (m) REVERT: G 723 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.9165 (m) REVERT: G 961 MET cc_start: 0.4184 (mmp) cc_final: 0.3892 (mmt) REVERT: G 1170 MET cc_start: 0.7523 (mmp) cc_final: 0.7163 (mmp) REVERT: G 1786 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6279 (pp) REVERT: G 2211 MET cc_start: 0.8904 (ttp) cc_final: 0.8700 (tmm) REVERT: G 2347 GLU cc_start: 0.7874 (pm20) cc_final: 0.7638 (pm20) REVERT: G 3652 MET cc_start: 0.8420 (tpp) cc_final: 0.7879 (tpt) REVERT: G 3711 THR cc_start: 0.8688 (m) cc_final: 0.8331 (p) REVERT: G 3805 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8978 (pp) REVERT: G 4216 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8521 (tm-30) REVERT: G 4232 GLU cc_start: 0.8449 (tp30) cc_final: 0.7927 (tp30) REVERT: G 4769 MET cc_start: 0.8128 (ppp) cc_final: 0.7864 (ppp) outliers start: 306 outliers final: 224 residues processed: 1226 average time/residue: 0.9914 time to fit residues: 2205.0968 Evaluate side-chains 1176 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 938 time to evaluate : 8.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 664 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 772 ASN Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 1217 CYS Chi-restraints excluded: chain B residue 1234 VAL Chi-restraints excluded: chain B residue 1242 LEU Chi-restraints excluded: chain B residue 1657 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1702 HIS Chi-restraints excluded: chain B residue 1703 LEU Chi-restraints excluded: chain B residue 1711 TYR Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1736 VAL Chi-restraints excluded: chain B residue 1786 LEU Chi-restraints excluded: chain B residue 1839 VAL Chi-restraints excluded: chain B residue 1850 VAL Chi-restraints excluded: chain B residue 1944 GLU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2188 ASN Chi-restraints excluded: chain B residue 2342 ASN Chi-restraints excluded: chain B residue 2461 VAL Chi-restraints excluded: chain B residue 3717 ASP Chi-restraints excluded: chain B residue 3781 GLN Chi-restraints excluded: chain B residue 3787 LYS Chi-restraints excluded: chain B residue 3805 LEU Chi-restraints excluded: chain B residue 3832 ILE Chi-restraints excluded: chain B residue 3883 ASP Chi-restraints excluded: chain B residue 3903 LEU Chi-restraints excluded: chain B residue 3913 ILE Chi-restraints excluded: chain B residue 3915 ILE Chi-restraints excluded: chain B residue 3938 SER Chi-restraints excluded: chain B residue 3942 VAL Chi-restraints excluded: chain B residue 3955 MET Chi-restraints excluded: chain B residue 4000 MET Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4044 MET Chi-restraints excluded: chain B residue 4081 VAL Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4551 PHE Chi-restraints excluded: chain B residue 4645 CYS Chi-restraints excluded: chain B residue 4688 ILE Chi-restraints excluded: chain B residue 4690 GLU Chi-restraints excluded: chain B residue 4807 PHE Chi-restraints excluded: chain B residue 4891 VAL Chi-restraints excluded: chain B residue 4950 VAL Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 664 PHE Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 671 VAL Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain E residue 772 ASN Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 826 ILE Chi-restraints excluded: chain E residue 920 TYR Chi-restraints excluded: chain E residue 1095 VAL Chi-restraints excluded: chain E residue 1217 CYS Chi-restraints excluded: chain E residue 1234 VAL Chi-restraints excluded: chain E residue 1657 LEU Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1676 LEU Chi-restraints excluded: chain E residue 1702 HIS Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1736 VAL Chi-restraints excluded: chain E residue 1786 LEU Chi-restraints excluded: chain E residue 1839 VAL Chi-restraints excluded: chain E residue 1850 VAL Chi-restraints excluded: chain E residue 1944 GLU Chi-restraints excluded: chain E residue 2038 LEU Chi-restraints excluded: chain E residue 2188 ASN Chi-restraints excluded: chain E residue 2461 VAL Chi-restraints excluded: chain E residue 2466 LEU Chi-restraints excluded: chain E residue 3717 ASP Chi-restraints excluded: chain E residue 3781 GLN Chi-restraints excluded: chain E residue 3787 LYS Chi-restraints excluded: chain E residue 3805 LEU Chi-restraints excluded: chain E residue 3832 ILE Chi-restraints excluded: chain E residue 3903 LEU Chi-restraints excluded: chain E residue 3913 ILE Chi-restraints excluded: chain E residue 3915 ILE Chi-restraints excluded: chain E residue 3938 SER Chi-restraints excluded: chain E residue 3942 VAL Chi-restraints excluded: chain E residue 3955 MET Chi-restraints excluded: chain E residue 4000 MET Chi-restraints excluded: chain E residue 4036 VAL Chi-restraints excluded: chain E residue 4044 MET Chi-restraints excluded: chain E residue 4081 VAL Chi-restraints excluded: chain E residue 4207 MET Chi-restraints excluded: chain E residue 4247 ILE Chi-restraints excluded: chain E residue 4551 PHE Chi-restraints excluded: chain E residue 4645 CYS Chi-restraints excluded: chain E residue 4688 ILE Chi-restraints excluded: chain E residue 4690 GLU Chi-restraints excluded: chain E residue 4807 PHE Chi-restraints excluded: chain E residue 4891 VAL Chi-restraints excluded: chain E residue 4950 VAL Chi-restraints excluded: chain E residue 4952 GLU Chi-restraints excluded: chain I residue 65 CYS Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 608 VAL Chi-restraints excluded: chain I residue 647 ASN Chi-restraints excluded: chain I residue 664 PHE Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain I residue 671 VAL Chi-restraints excluded: chain I residue 674 PHE Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 772 ASN Chi-restraints excluded: chain I residue 781 VAL Chi-restraints excluded: chain I residue 791 PHE Chi-restraints excluded: chain I residue 826 ILE Chi-restraints excluded: chain I residue 920 TYR Chi-restraints excluded: chain I residue 1095 VAL Chi-restraints excluded: chain I residue 1217 CYS Chi-restraints excluded: chain I residue 1234 VAL Chi-restraints excluded: chain I residue 1242 LEU Chi-restraints excluded: chain I residue 1657 LEU Chi-restraints excluded: chain I residue 1667 LEU Chi-restraints excluded: chain I residue 1676 LEU Chi-restraints excluded: chain I residue 1702 HIS Chi-restraints excluded: chain I residue 1717 SER Chi-restraints excluded: chain I residue 1736 VAL Chi-restraints excluded: chain I residue 1786 LEU Chi-restraints excluded: chain I residue 1839 VAL Chi-restraints excluded: chain I residue 1850 VAL Chi-restraints excluded: chain I residue 1865 MET Chi-restraints excluded: chain I residue 1944 GLU Chi-restraints excluded: chain I residue 2038 LEU Chi-restraints excluded: chain I residue 2188 ASN Chi-restraints excluded: chain I residue 2342 ASN Chi-restraints excluded: chain I residue 2461 VAL Chi-restraints excluded: chain I residue 2466 LEU Chi-restraints excluded: chain I residue 3717 ASP Chi-restraints excluded: chain I residue 3781 GLN Chi-restraints excluded: chain I residue 3787 LYS Chi-restraints excluded: chain I residue 3805 LEU Chi-restraints excluded: chain I residue 3832 ILE Chi-restraints excluded: chain I residue 3883 ASP Chi-restraints excluded: chain I residue 3903 LEU Chi-restraints excluded: chain I residue 3913 ILE Chi-restraints excluded: chain I residue 3915 ILE Chi-restraints excluded: chain I residue 3938 SER Chi-restraints excluded: chain I residue 3942 VAL Chi-restraints excluded: chain I residue 3955 MET Chi-restraints excluded: chain I residue 4000 MET Chi-restraints excluded: chain I residue 4036 VAL Chi-restraints excluded: chain I residue 4044 MET Chi-restraints excluded: chain I residue 4081 VAL Chi-restraints excluded: chain I residue 4187 SER Chi-restraints excluded: chain I residue 4207 MET Chi-restraints excluded: chain I residue 4247 ILE Chi-restraints excluded: chain I residue 4551 PHE Chi-restraints excluded: chain I residue 4645 CYS Chi-restraints excluded: chain I residue 4688 ILE Chi-restraints excluded: chain I residue 4690 GLU Chi-restraints excluded: chain I residue 4807 PHE Chi-restraints excluded: chain I residue 4891 VAL Chi-restraints excluded: chain I residue 4950 VAL Chi-restraints excluded: chain I residue 4952 GLU Chi-restraints excluded: chain G residue 65 CYS Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 664 PHE Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 671 VAL Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 749 ASP Chi-restraints excluded: chain G residue 772 ASN Chi-restraints excluded: chain G residue 791 PHE Chi-restraints excluded: chain G residue 826 ILE Chi-restraints excluded: chain G residue 920 TYR Chi-restraints excluded: chain G residue 1095 VAL Chi-restraints excluded: chain G residue 1217 CYS Chi-restraints excluded: chain G residue 1234 VAL Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1676 LEU Chi-restraints excluded: chain G residue 1702 HIS Chi-restraints excluded: chain G residue 1703 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1786 LEU Chi-restraints excluded: chain G residue 1839 VAL Chi-restraints excluded: chain G residue 1850 VAL Chi-restraints excluded: chain G residue 1865 MET Chi-restraints excluded: chain G residue 1944 GLU Chi-restraints excluded: chain G residue 2038 LEU Chi-restraints excluded: chain G residue 2188 ASN Chi-restraints excluded: chain G residue 2252 ASP Chi-restraints excluded: chain G residue 2342 ASN Chi-restraints excluded: chain G residue 2461 VAL Chi-restraints excluded: chain G residue 2466 LEU Chi-restraints excluded: chain G residue 3717 ASP Chi-restraints excluded: chain G residue 3787 LYS Chi-restraints excluded: chain G residue 3805 LEU Chi-restraints excluded: chain G residue 3832 ILE Chi-restraints excluded: chain G residue 3883 ASP Chi-restraints excluded: chain G residue 3903 LEU Chi-restraints excluded: chain G residue 3913 ILE Chi-restraints excluded: chain G residue 3915 ILE Chi-restraints excluded: chain G residue 3938 SER Chi-restraints excluded: chain G residue 3942 VAL Chi-restraints excluded: chain G residue 3955 MET Chi-restraints excluded: chain G residue 4000 MET Chi-restraints excluded: chain G residue 4036 VAL Chi-restraints excluded: chain G residue 4044 MET Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4207 MET Chi-restraints excluded: chain G residue 4245 MET Chi-restraints excluded: chain G residue 4645 CYS Chi-restraints excluded: chain G residue 4688 ILE Chi-restraints excluded: chain G residue 4690 GLU Chi-restraints excluded: chain G residue 4807 PHE Chi-restraints excluded: chain G residue 4891 VAL Chi-restraints excluded: chain G residue 4950 VAL Chi-restraints excluded: chain G residue 4952 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 ASN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3897 ASN ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3976 ASN ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1972 ASN ** E3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3897 ASN ** E3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3976 ASN ** I 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1691 GLN ** I3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3976 ASN ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1972 ASN ** G3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3976 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 123052 Z= 0.210 Angle : 0.641 17.015 167776 Z= 0.317 Chirality : 0.039 0.349 19608 Planarity : 0.005 0.081 22100 Dihedral : 5.368 40.713 18084 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.20 % Favored : 88.62 % Rotamer: Outliers : 3.33 % Allowed : 14.15 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.66 % Twisted General : 0.06 % 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: -1.90 (0.07), residues: 13364 helix: 0.01 (0.07), residues: 5824 sheet: -0.92 (0.16), residues: 1216 loop : -2.64 (0.08), residues: 6324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I1143 HIS 0.010 0.001 HIS B 879 PHE 0.019 0.001 PHE E 389 TYR 0.029 0.001 TYR B1712 ARG 0.007 0.000 ARG G1128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1317 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 973 time to evaluate : 9.014 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: F 29 MET cc_start: 0.7472 (tpp) cc_final: 0.7046 (tpp) REVERT: F 91 ILE cc_start: 0.8718 (mm) cc_final: 0.8494 (mp) REVERT: F 94 ASN cc_start: 0.8296 (t0) cc_final: 0.7870 (p0) REVERT: A 29 MET cc_start: 0.7478 (tpp) cc_final: 0.7045 (tpp) REVERT: A 94 ASN cc_start: 0.8308 (t0) cc_final: 0.7885 (p0) REVERT: J 29 MET cc_start: 0.7429 (tpp) cc_final: 0.7048 (tpp) REVERT: J 94 ASN cc_start: 0.8293 (t0) cc_final: 0.7903 (p0) REVERT: B 205 ILE cc_start: 0.9447 (tp) cc_final: 0.8992 (tp) REVERT: B 301 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8680 (m) REVERT: B 345 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7890 (mm) REVERT: B 394 GLN cc_start: 0.2495 (OUTLIER) cc_final: 0.1252 (pm20) REVERT: B 483 MET cc_start: 0.8543 (mmm) cc_final: 0.8315 (mmm) REVERT: B 924 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6604 (ptp) REVERT: B 1170 MET cc_start: 0.7479 (mmp) cc_final: 0.7106 (mmp) REVERT: B 1242 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8663 (tt) REVERT: B 1786 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6194 (pp) REVERT: B 2032 GLN cc_start: 0.8505 (tp40) cc_final: 0.7875 (tm-30) REVERT: B 3652 MET cc_start: 0.8405 (tpp) cc_final: 0.7864 (tpt) REVERT: B 3711 THR cc_start: 0.8682 (m) cc_final: 0.8353 (p) REVERT: B 3805 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.8965 (pp) REVERT: B 4216 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8632 (tm-30) REVERT: B 4232 GLU cc_start: 0.8452 (tp30) cc_final: 0.7902 (tp30) REVERT: B 4839 MET cc_start: 0.7668 (mmt) cc_final: 0.7433 (tpp) REVERT: E 205 ILE cc_start: 0.9443 (tp) cc_final: 0.8984 (tp) REVERT: E 301 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8685 (m) REVERT: E 345 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7930 (mm) REVERT: E 394 GLN cc_start: 0.2454 (OUTLIER) cc_final: 0.1252 (pm20) REVERT: E 467 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8679 (ttmm) REVERT: E 1170 MET cc_start: 0.7510 (mmp) cc_final: 0.7147 (mmp) REVERT: E 1242 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8681 (tt) REVERT: E 1652 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7737 (mt-10) REVERT: E 1786 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6202 (pp) REVERT: E 2032 GLN cc_start: 0.8493 (tp40) cc_final: 0.7846 (tm-30) REVERT: E 2816 MET cc_start: 0.1499 (ppp) cc_final: 0.0656 (mmm) REVERT: E 3652 MET cc_start: 0.8417 (tpp) cc_final: 0.7871 (tpt) REVERT: E 3782 MET cc_start: 0.8683 (tpp) cc_final: 0.8398 (mmm) REVERT: E 3805 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.8969 (pp) REVERT: E 4216 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8629 (tm-30) REVERT: E 4232 GLU cc_start: 0.8460 (tp30) cc_final: 0.7908 (tp30) REVERT: E 4769 MET cc_start: 0.8294 (ppp) cc_final: 0.7983 (ppp) REVERT: E 4839 MET cc_start: 0.7709 (mmt) cc_final: 0.7471 (tpp) REVERT: I 205 ILE cc_start: 0.9480 (tp) cc_final: 0.9008 (tp) REVERT: I 345 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7935 (mm) REVERT: I 394 GLN cc_start: 0.2684 (OUTLIER) cc_final: 0.1339 (pm20) REVERT: I 941 MET cc_start: 0.7063 (mmt) cc_final: 0.6742 (mmt) REVERT: I 1170 MET cc_start: 0.7467 (mmp) cc_final: 0.7089 (mmp) REVERT: I 1242 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8680 (tt) REVERT: I 1786 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6210 (pp) REVERT: I 2032 GLN cc_start: 0.8542 (tp40) cc_final: 0.7907 (tm-30) REVERT: I 2140 ARG cc_start: 0.8371 (mtm-85) cc_final: 0.7802 (mtp-110) REVERT: I 3652 MET cc_start: 0.8420 (tpp) cc_final: 0.7874 (tpt) REVERT: I 3805 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8977 (pp) REVERT: I 4216 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8605 (tm-30) REVERT: I 4232 GLU cc_start: 0.8444 (tp30) cc_final: 0.7900 (tp30) REVERT: G 205 ILE cc_start: 0.9485 (tp) cc_final: 0.9013 (tp) REVERT: G 301 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8686 (m) REVERT: G 345 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7939 (mm) REVERT: G 394 GLN cc_start: 0.2686 (OUTLIER) cc_final: 0.1331 (pm20) REVERT: G 961 MET cc_start: 0.4175 (mmp) cc_final: 0.3907 (mmt) REVERT: G 1170 MET cc_start: 0.7475 (mmp) cc_final: 0.7098 (mmp) REVERT: G 1242 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8672 (tt) REVERT: G 1786 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6299 (pp) REVERT: G 2342 ASN cc_start: 0.5983 (OUTLIER) cc_final: 0.5630 (p0) REVERT: G 2347 GLU cc_start: 0.7826 (pm20) cc_final: 0.7565 (pm20) REVERT: G 3652 MET cc_start: 0.8424 (tpp) cc_final: 0.7868 (tpt) REVERT: G 3711 THR cc_start: 0.8766 (m) cc_final: 0.8379 (p) REVERT: G 3805 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8979 (pp) REVERT: G 4216 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8534 (tm-30) REVERT: G 4232 GLU cc_start: 0.8447 (tp30) cc_final: 0.7900 (tp30) REVERT: G 4769 MET cc_start: 0.8265 (ppp) cc_final: 0.7946 (ppp) outliers start: 344 outliers final: 257 residues processed: 1239 average time/residue: 0.9156 time to fit residues: 2059.8522 Evaluate side-chains 1212 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 929 time to evaluate : 8.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 664 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 772 ASN Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 924 MET Chi-restraints excluded: chain B residue 1095 VAL Chi-restraints excluded: chain B residue 1217 CYS Chi-restraints excluded: chain B residue 1234 VAL Chi-restraints excluded: chain B residue 1242 LEU Chi-restraints excluded: chain B residue 1595 LEU Chi-restraints excluded: chain B residue 1641 ILE Chi-restraints excluded: chain B residue 1657 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1702 HIS Chi-restraints excluded: chain B residue 1703 LEU Chi-restraints excluded: chain B residue 1711 TYR Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1736 VAL Chi-restraints excluded: chain B residue 1786 LEU Chi-restraints excluded: chain B residue 1839 VAL Chi-restraints excluded: chain B residue 1850 VAL Chi-restraints excluded: chain B residue 1944 GLU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2188 ASN Chi-restraints excluded: chain B residue 2461 VAL Chi-restraints excluded: chain B residue 3717 ASP Chi-restraints excluded: chain B residue 3781 GLN Chi-restraints excluded: chain B residue 3787 LYS Chi-restraints excluded: chain B residue 3805 LEU Chi-restraints excluded: chain B residue 3832 ILE Chi-restraints excluded: chain B residue 3883 ASP Chi-restraints excluded: chain B residue 3903 LEU Chi-restraints excluded: chain B residue 3913 ILE Chi-restraints excluded: chain B residue 3915 ILE Chi-restraints excluded: chain B residue 3942 VAL Chi-restraints excluded: chain B residue 3955 MET Chi-restraints excluded: chain B residue 4000 MET Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4044 MET Chi-restraints excluded: chain B residue 4081 VAL Chi-restraints excluded: chain B residue 4187 SER Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4551 PHE Chi-restraints excluded: chain B residue 4645 CYS Chi-restraints excluded: chain B residue 4688 ILE Chi-restraints excluded: chain B residue 4690 GLU Chi-restraints excluded: chain B residue 4807 PHE Chi-restraints excluded: chain B residue 4891 VAL Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4950 VAL Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 394 GLN Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 635 THR Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 664 PHE Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 671 VAL Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain E residue 750 LEU Chi-restraints excluded: chain E residue 772 ASN Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 826 ILE Chi-restraints excluded: chain E residue 920 TYR Chi-restraints excluded: chain E residue 1095 VAL Chi-restraints excluded: chain E residue 1186 ASP Chi-restraints excluded: chain E residue 1217 CYS Chi-restraints excluded: chain E residue 1234 VAL Chi-restraints excluded: chain E residue 1242 LEU Chi-restraints excluded: chain E residue 1595 LEU Chi-restraints excluded: chain E residue 1601 MET Chi-restraints excluded: chain E residue 1641 ILE Chi-restraints excluded: chain E residue 1657 LEU Chi-restraints excluded: chain E residue 1676 LEU Chi-restraints excluded: chain E residue 1702 HIS Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1736 VAL Chi-restraints excluded: chain E residue 1786 LEU Chi-restraints excluded: chain E residue 1839 VAL Chi-restraints excluded: chain E residue 1850 VAL Chi-restraints excluded: chain E residue 1944 GLU Chi-restraints excluded: chain E residue 2038 LEU Chi-restraints excluded: chain E residue 2188 ASN Chi-restraints excluded: chain E residue 2342 ASN Chi-restraints excluded: chain E residue 2461 VAL Chi-restraints excluded: chain E residue 2466 LEU Chi-restraints excluded: chain E residue 2874 MET Chi-restraints excluded: chain E residue 3717 ASP Chi-restraints excluded: chain E residue 3781 GLN Chi-restraints excluded: chain E residue 3787 LYS Chi-restraints excluded: chain E residue 3805 LEU Chi-restraints excluded: chain E residue 3832 ILE Chi-restraints excluded: chain E residue 3883 ASP Chi-restraints excluded: chain E residue 3903 LEU Chi-restraints excluded: chain E residue 3913 ILE Chi-restraints excluded: chain E residue 3915 ILE Chi-restraints excluded: chain E residue 3938 SER Chi-restraints excluded: chain E residue 3942 VAL Chi-restraints excluded: chain E residue 3955 MET Chi-restraints excluded: chain E residue 4000 MET Chi-restraints excluded: chain E residue 4036 VAL Chi-restraints excluded: chain E residue 4044 MET Chi-restraints excluded: chain E residue 4081 VAL Chi-restraints excluded: chain E residue 4181 ILE Chi-restraints excluded: chain E residue 4187 SER Chi-restraints excluded: chain E residue 4207 MET Chi-restraints excluded: chain E residue 4551 PHE Chi-restraints excluded: chain E residue 4645 CYS Chi-restraints excluded: chain E residue 4688 ILE Chi-restraints excluded: chain E residue 4690 GLU Chi-restraints excluded: chain E residue 4807 PHE Chi-restraints excluded: chain E residue 4891 VAL Chi-restraints excluded: chain E residue 4950 VAL Chi-restraints excluded: chain E residue 4952 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 65 CYS Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 394 GLN Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 608 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 647 ASN Chi-restraints excluded: chain I residue 664 PHE Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain I residue 671 VAL Chi-restraints excluded: chain I residue 674 PHE Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 772 ASN Chi-restraints excluded: chain I residue 781 VAL Chi-restraints excluded: chain I residue 791 PHE Chi-restraints excluded: chain I residue 826 ILE Chi-restraints excluded: chain I residue 920 TYR Chi-restraints excluded: chain I residue 1095 VAL Chi-restraints excluded: chain I residue 1209 SER Chi-restraints excluded: chain I residue 1217 CYS Chi-restraints excluded: chain I residue 1234 VAL Chi-restraints excluded: chain I residue 1242 LEU Chi-restraints excluded: chain I residue 1595 LEU Chi-restraints excluded: chain I residue 1641 ILE Chi-restraints excluded: chain I residue 1657 LEU Chi-restraints excluded: chain I residue 1667 LEU Chi-restraints excluded: chain I residue 1676 LEU Chi-restraints excluded: chain I residue 1702 HIS Chi-restraints excluded: chain I residue 1717 SER Chi-restraints excluded: chain I residue 1736 VAL Chi-restraints excluded: chain I residue 1786 LEU Chi-restraints excluded: chain I residue 1839 VAL Chi-restraints excluded: chain I residue 1850 VAL Chi-restraints excluded: chain I residue 1865 MET Chi-restraints excluded: chain I residue 1944 GLU Chi-restraints excluded: chain I residue 2038 LEU Chi-restraints excluded: chain I residue 2188 ASN Chi-restraints excluded: chain I residue 2461 VAL Chi-restraints excluded: chain I residue 2466 LEU Chi-restraints excluded: chain I residue 3717 ASP Chi-restraints excluded: chain I residue 3781 GLN Chi-restraints excluded: chain I residue 3787 LYS Chi-restraints excluded: chain I residue 3793 MET Chi-restraints excluded: chain I residue 3805 LEU Chi-restraints excluded: chain I residue 3832 ILE Chi-restraints excluded: chain I residue 3883 ASP Chi-restraints excluded: chain I residue 3903 LEU Chi-restraints excluded: chain I residue 3913 ILE Chi-restraints excluded: chain I residue 3915 ILE Chi-restraints excluded: chain I residue 3938 SER Chi-restraints excluded: chain I residue 3942 VAL Chi-restraints excluded: chain I residue 3955 MET Chi-restraints excluded: chain I residue 4000 MET Chi-restraints excluded: chain I residue 4036 VAL Chi-restraints excluded: chain I residue 4044 MET Chi-restraints excluded: chain I residue 4081 VAL Chi-restraints excluded: chain I residue 4207 MET Chi-restraints excluded: chain I residue 4551 PHE Chi-restraints excluded: chain I residue 4645 CYS Chi-restraints excluded: chain I residue 4688 ILE Chi-restraints excluded: chain I residue 4690 GLU Chi-restraints excluded: chain I residue 4807 PHE Chi-restraints excluded: chain I residue 4891 VAL Chi-restraints excluded: chain I residue 4929 LEU Chi-restraints excluded: chain I residue 4950 VAL Chi-restraints excluded: chain I residue 4952 GLU Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 65 CYS Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 394 GLN Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 635 THR Chi-restraints excluded: chain G residue 647 ASN Chi-restraints excluded: chain G residue 664 PHE Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 671 VAL Chi-restraints excluded: chain G residue 749 ASP Chi-restraints excluded: chain G residue 772 ASN Chi-restraints excluded: chain G residue 791 PHE Chi-restraints excluded: chain G residue 826 ILE Chi-restraints excluded: chain G residue 920 TYR Chi-restraints excluded: chain G residue 1095 VAL Chi-restraints excluded: chain G residue 1217 CYS Chi-restraints excluded: chain G residue 1234 VAL Chi-restraints excluded: chain G residue 1242 LEU Chi-restraints excluded: chain G residue 1595 LEU Chi-restraints excluded: chain G residue 1641 ILE Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1676 LEU Chi-restraints excluded: chain G residue 1702 HIS Chi-restraints excluded: chain G residue 1703 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1786 LEU Chi-restraints excluded: chain G residue 1839 VAL Chi-restraints excluded: chain G residue 1850 VAL Chi-restraints excluded: chain G residue 1865 MET Chi-restraints excluded: chain G residue 1944 GLU Chi-restraints excluded: chain G residue 2038 LEU Chi-restraints excluded: chain G residue 2188 ASN Chi-restraints excluded: chain G residue 2252 ASP Chi-restraints excluded: chain G residue 2342 ASN Chi-restraints excluded: chain G residue 2461 VAL Chi-restraints excluded: chain G residue 2466 LEU Chi-restraints excluded: chain G residue 3717 ASP Chi-restraints excluded: chain G residue 3781 GLN Chi-restraints excluded: chain G residue 3787 LYS Chi-restraints excluded: chain G residue 3793 MET Chi-restraints excluded: chain G residue 3805 LEU Chi-restraints excluded: chain G residue 3832 ILE Chi-restraints excluded: chain G residue 3883 ASP Chi-restraints excluded: chain G residue 3903 LEU Chi-restraints excluded: chain G residue 3913 ILE Chi-restraints excluded: chain G residue 3915 ILE Chi-restraints excluded: chain G residue 3938 SER Chi-restraints excluded: chain G residue 3942 VAL Chi-restraints excluded: chain G residue 3955 MET Chi-restraints excluded: chain G residue 4000 MET Chi-restraints excluded: chain G residue 4036 VAL Chi-restraints excluded: chain G residue 4044 MET Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4181 ILE Chi-restraints excluded: chain G residue 4187 SER Chi-restraints excluded: chain G residue 4207 MET Chi-restraints excluded: chain G residue 4551 PHE Chi-restraints excluded: chain G residue 4645 CYS Chi-restraints excluded: chain G residue 4688 ILE Chi-restraints excluded: chain G residue 4690 GLU Chi-restraints excluded: chain G residue 4807 PHE Chi-restraints excluded: chain G residue 4891 VAL Chi-restraints excluded: chain G residue 4929 LEU Chi-restraints excluded: chain G residue 4950 VAL Chi-restraints excluded: chain G residue 4952 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN H 43 ASN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 ASN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN B 765 GLN B 866 HIS B3781 GLN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3960 GLN B5035 GLN ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 765 GLN ** E3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3960 GLN E5035 GLN ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 904 HIS I1972 ASN ** I3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3960 GLN I5035 GLN ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 624 ASN G 765 GLN G 866 HIS G3781 GLN ** G3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3960 GLN G5035 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.106 123052 Z= 0.546 Angle : 0.879 18.723 167776 Z= 0.438 Chirality : 0.047 0.293 19608 Planarity : 0.006 0.085 22100 Dihedral : 6.231 43.192 18084 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.13 % Favored : 85.69 % Rotamer: Outliers : 3.89 % Allowed : 14.37 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.66 % Twisted General : 0.18 % 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: -2.48 (0.07), residues: 13364 helix: -0.55 (0.07), residues: 5944 sheet: -1.14 (0.15), residues: 1224 loop : -2.92 (0.07), residues: 6196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I3661 HIS 0.014 0.002 HIS B1719 PHE 0.044 0.003 PHE G1748 TYR 0.041 0.002 TYR I1712 ARG 0.008 0.001 ARG B4673 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1308 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 402 poor density : 906 time to evaluate : 8.880 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: F 29 MET cc_start: 0.7302 (tpp) cc_final: 0.6998 (tpp) REVERT: A 29 MET cc_start: 0.7278 (tpp) cc_final: 0.7009 (tpp) REVERT: J 29 MET cc_start: 0.7312 (tpp) cc_final: 0.7009 (tpp) REVERT: B 205 ILE cc_start: 0.9562 (tp) cc_final: 0.9160 (tp) REVERT: B 345 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7902 (mm) REVERT: B 394 GLN cc_start: 0.1913 (OUTLIER) cc_final: 0.0645 (pm20) REVERT: B 403 MET cc_start: 0.8518 (mtt) cc_final: 0.8276 (ttm) REVERT: B 483 MET cc_start: 0.8604 (mmm) cc_final: 0.8269 (mmm) REVERT: B 2032 GLN cc_start: 0.8542 (tp40) cc_final: 0.7861 (tm-30) REVERT: B 3711 THR cc_start: 0.9021 (m) cc_final: 0.8746 (p) REVERT: B 3805 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9006 (pp) REVERT: B 4769 MET cc_start: 0.8358 (ppp) cc_final: 0.8157 (ppp) REVERT: E 205 ILE cc_start: 0.9560 (tp) cc_final: 0.9153 (tp) REVERT: E 345 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7876 (mm) REVERT: E 394 GLN cc_start: 0.1916 (OUTLIER) cc_final: 0.0664 (pm20) REVERT: E 403 MET cc_start: 0.8542 (mtt) cc_final: 0.8296 (ttm) REVERT: E 686 TRP cc_start: 0.7480 (m100) cc_final: 0.7277 (m100) REVERT: E 710 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7569 (p0) REVERT: E 1037 ASP cc_start: 0.7263 (t0) cc_final: 0.6929 (m-30) REVERT: E 1652 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7886 (mt-10) REVERT: E 2032 GLN cc_start: 0.8558 (tp40) cc_final: 0.7879 (tm-30) REVERT: E 2347 GLU cc_start: 0.8205 (pm20) cc_final: 0.7868 (tm-30) REVERT: E 2816 MET cc_start: 0.1645 (OUTLIER) cc_final: 0.0841 (mmm) REVERT: E 3782 MET cc_start: 0.8763 (tpp) cc_final: 0.8478 (mmm) REVERT: E 3805 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.8991 (pp) REVERT: E 4026 MET cc_start: 0.9027 (ttp) cc_final: 0.8771 (ttm) REVERT: E 4769 MET cc_start: 0.8416 (ppp) cc_final: 0.8105 (ppp) REVERT: I 205 ILE cc_start: 0.9558 (tp) cc_final: 0.9156 (tp) REVERT: I 345 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7880 (mm) REVERT: I 394 GLN cc_start: 0.1921 (OUTLIER) cc_final: 0.0663 (pm20) REVERT: I 403 MET cc_start: 0.8603 (mtt) cc_final: 0.8371 (ttm) REVERT: I 2032 GLN cc_start: 0.8550 (tp40) cc_final: 0.7865 (tm-30) REVERT: I 2347 GLU cc_start: 0.8211 (pm20) cc_final: 0.7871 (tm-30) REVERT: I 3805 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9014 (pp) REVERT: I 4026 MET cc_start: 0.9144 (ttp) cc_final: 0.8560 (ttm) REVERT: I 4769 MET cc_start: 0.8357 (ppp) cc_final: 0.8142 (ppp) REVERT: I 5013 MET cc_start: 0.8118 (mtp) cc_final: 0.7895 (mtt) REVERT: G 205 ILE cc_start: 0.9562 (tp) cc_final: 0.9153 (tp) REVERT: G 345 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7891 (mm) REVERT: G 394 GLN cc_start: 0.1913 (OUTLIER) cc_final: 0.0654 (pm20) REVERT: G 403 MET cc_start: 0.8599 (mtt) cc_final: 0.8367 (ttm) REVERT: G 686 TRP cc_start: 0.7406 (m100) cc_final: 0.7180 (m100) REVERT: G 1691 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8545 (tm-30) REVERT: G 1786 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6474 (pp) REVERT: G 2347 GLU cc_start: 0.8191 (pm20) cc_final: 0.7983 (pm20) REVERT: G 3805 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9012 (pp) REVERT: G 4026 MET cc_start: 0.9142 (ttp) cc_final: 0.8549 (ttm) REVERT: G 4769 MET cc_start: 0.8411 (ppp) cc_final: 0.8066 (ppp) REVERT: G 5013 MET cc_start: 0.8112 (mtp) cc_final: 0.7887 (mtt) outliers start: 402 outliers final: 298 residues processed: 1231 average time/residue: 0.9254 time to fit residues: 2062.5051 Evaluate side-chains 1174 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 860 time to evaluate : 8.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 772 ASN Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 1095 VAL Chi-restraints excluded: chain B residue 1217 CYS Chi-restraints excluded: chain B residue 1234 VAL Chi-restraints excluded: chain B residue 1595 LEU Chi-restraints excluded: chain B residue 1641 ILE Chi-restraints excluded: chain B residue 1657 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1702 HIS Chi-restraints excluded: chain B residue 1703 LEU Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1736 VAL Chi-restraints excluded: chain B residue 1839 VAL Chi-restraints excluded: chain B residue 1850 VAL Chi-restraints excluded: chain B residue 1929 MET Chi-restraints excluded: chain B residue 1944 GLU Chi-restraints excluded: chain B residue 1966 VAL Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2131 LEU Chi-restraints excluded: chain B residue 2188 ASN Chi-restraints excluded: chain B residue 2223 ILE Chi-restraints excluded: chain B residue 2461 VAL Chi-restraints excluded: chain B residue 3723 MET Chi-restraints excluded: chain B residue 3781 GLN Chi-restraints excluded: chain B residue 3787 LYS Chi-restraints excluded: chain B residue 3793 MET Chi-restraints excluded: chain B residue 3805 LEU Chi-restraints excluded: chain B residue 3883 ASP Chi-restraints excluded: chain B residue 3903 LEU Chi-restraints excluded: chain B residue 3913 ILE Chi-restraints excluded: chain B residue 3915 ILE Chi-restraints excluded: chain B residue 3938 SER Chi-restraints excluded: chain B residue 3942 VAL Chi-restraints excluded: chain B residue 3955 MET Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4044 MET Chi-restraints excluded: chain B residue 4081 VAL Chi-restraints excluded: chain B residue 4104 THR Chi-restraints excluded: chain B residue 4181 ILE Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4551 PHE Chi-restraints excluded: chain B residue 4645 CYS Chi-restraints excluded: chain B residue 4688 ILE Chi-restraints excluded: chain B residue 4690 GLU Chi-restraints excluded: chain B residue 4807 PHE Chi-restraints excluded: chain B residue 4814 LEU Chi-restraints excluded: chain B residue 4891 VAL Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4950 VAL Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 5026 ASP Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 394 GLN Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 635 THR Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 664 PHE Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 671 VAL Chi-restraints excluded: chain E residue 688 LEU Chi-restraints excluded: chain E residue 710 ASP Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain E residue 750 LEU Chi-restraints excluded: chain E residue 772 ASN Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 826 ILE Chi-restraints excluded: chain E residue 920 TYR Chi-restraints excluded: chain E residue 1095 VAL Chi-restraints excluded: chain E residue 1217 CYS Chi-restraints excluded: chain E residue 1234 VAL Chi-restraints excluded: chain E residue 1595 LEU Chi-restraints excluded: chain E residue 1641 ILE Chi-restraints excluded: chain E residue 1657 LEU Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1676 LEU Chi-restraints excluded: chain E residue 1702 HIS Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1736 VAL Chi-restraints excluded: chain E residue 1839 VAL Chi-restraints excluded: chain E residue 1850 VAL Chi-restraints excluded: chain E residue 1929 MET Chi-restraints excluded: chain E residue 1944 GLU Chi-restraints excluded: chain E residue 1966 VAL Chi-restraints excluded: chain E residue 2031 LEU Chi-restraints excluded: chain E residue 2038 LEU Chi-restraints excluded: chain E residue 2188 ASN Chi-restraints excluded: chain E residue 2223 ILE Chi-restraints excluded: chain E residue 2461 VAL Chi-restraints excluded: chain E residue 2466 LEU Chi-restraints excluded: chain E residue 2816 MET Chi-restraints excluded: chain E residue 2874 MET Chi-restraints excluded: chain E residue 3679 LYS Chi-restraints excluded: chain E residue 3717 ASP Chi-restraints excluded: chain E residue 3723 MET Chi-restraints excluded: chain E residue 3781 GLN Chi-restraints excluded: chain E residue 3787 LYS Chi-restraints excluded: chain E residue 3805 LEU Chi-restraints excluded: chain E residue 3883 ASP Chi-restraints excluded: chain E residue 3903 LEU Chi-restraints excluded: chain E residue 3913 ILE Chi-restraints excluded: chain E residue 3915 ILE Chi-restraints excluded: chain E residue 3938 SER Chi-restraints excluded: chain E residue 3942 VAL Chi-restraints excluded: chain E residue 3955 MET Chi-restraints excluded: chain E residue 4036 VAL Chi-restraints excluded: chain E residue 4044 MET Chi-restraints excluded: chain E residue 4081 VAL Chi-restraints excluded: chain E residue 4104 THR Chi-restraints excluded: chain E residue 4138 ASP Chi-restraints excluded: chain E residue 4181 ILE Chi-restraints excluded: chain E residue 4187 SER Chi-restraints excluded: chain E residue 4207 MET Chi-restraints excluded: chain E residue 4247 ILE Chi-restraints excluded: chain E residue 4645 CYS Chi-restraints excluded: chain E residue 4688 ILE Chi-restraints excluded: chain E residue 4690 GLU Chi-restraints excluded: chain E residue 4807 PHE Chi-restraints excluded: chain E residue 4891 VAL Chi-restraints excluded: chain E residue 4929 LEU Chi-restraints excluded: chain E residue 4950 VAL Chi-restraints excluded: chain E residue 4952 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 65 CYS Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 394 GLN Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 589 LEU Chi-restraints excluded: chain I residue 608 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 647 ASN Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain I residue 671 VAL Chi-restraints excluded: chain I residue 674 PHE Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 772 ASN Chi-restraints excluded: chain I residue 791 PHE Chi-restraints excluded: chain I residue 826 ILE Chi-restraints excluded: chain I residue 920 TYR Chi-restraints excluded: chain I residue 1095 VAL Chi-restraints excluded: chain I residue 1217 CYS Chi-restraints excluded: chain I residue 1234 VAL Chi-restraints excluded: chain I residue 1595 LEU Chi-restraints excluded: chain I residue 1641 ILE Chi-restraints excluded: chain I residue 1657 LEU Chi-restraints excluded: chain I residue 1667 LEU Chi-restraints excluded: chain I residue 1676 LEU Chi-restraints excluded: chain I residue 1702 HIS Chi-restraints excluded: chain I residue 1703 LEU Chi-restraints excluded: chain I residue 1717 SER Chi-restraints excluded: chain I residue 1736 VAL Chi-restraints excluded: chain I residue 1839 VAL Chi-restraints excluded: chain I residue 1850 VAL Chi-restraints excluded: chain I residue 1865 MET Chi-restraints excluded: chain I residue 1929 MET Chi-restraints excluded: chain I residue 1944 GLU Chi-restraints excluded: chain I residue 1966 VAL Chi-restraints excluded: chain I residue 2038 LEU Chi-restraints excluded: chain I residue 2188 ASN Chi-restraints excluded: chain I residue 2223 ILE Chi-restraints excluded: chain I residue 2461 VAL Chi-restraints excluded: chain I residue 2466 LEU Chi-restraints excluded: chain I residue 3723 MET Chi-restraints excluded: chain I residue 3781 GLN Chi-restraints excluded: chain I residue 3787 LYS Chi-restraints excluded: chain I residue 3793 MET Chi-restraints excluded: chain I residue 3805 LEU Chi-restraints excluded: chain I residue 3883 ASP Chi-restraints excluded: chain I residue 3903 LEU Chi-restraints excluded: chain I residue 3913 ILE Chi-restraints excluded: chain I residue 3915 ILE Chi-restraints excluded: chain I residue 3938 SER Chi-restraints excluded: chain I residue 3942 VAL Chi-restraints excluded: chain I residue 3955 MET Chi-restraints excluded: chain I residue 4036 VAL Chi-restraints excluded: chain I residue 4044 MET Chi-restraints excluded: chain I residue 4081 VAL Chi-restraints excluded: chain I residue 4104 THR Chi-restraints excluded: chain I residue 4181 ILE Chi-restraints excluded: chain I residue 4207 MET Chi-restraints excluded: chain I residue 4245 MET Chi-restraints excluded: chain I residue 4247 ILE Chi-restraints excluded: chain I residue 4551 PHE Chi-restraints excluded: chain I residue 4645 CYS Chi-restraints excluded: chain I residue 4688 ILE Chi-restraints excluded: chain I residue 4690 GLU Chi-restraints excluded: chain I residue 4807 PHE Chi-restraints excluded: chain I residue 4874 MET Chi-restraints excluded: chain I residue 4891 VAL Chi-restraints excluded: chain I residue 4929 LEU Chi-restraints excluded: chain I residue 4950 VAL Chi-restraints excluded: chain I residue 4952 GLU Chi-restraints excluded: chain I residue 5026 ASP Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 65 CYS Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 394 GLN Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 529 LEU Chi-restraints excluded: chain G residue 575 LEU Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 635 THR Chi-restraints excluded: chain G residue 647 ASN Chi-restraints excluded: chain G residue 664 PHE Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 671 VAL Chi-restraints excluded: chain G residue 749 ASP Chi-restraints excluded: chain G residue 772 ASN Chi-restraints excluded: chain G residue 791 PHE Chi-restraints excluded: chain G residue 826 ILE Chi-restraints excluded: chain G residue 866 HIS Chi-restraints excluded: chain G residue 920 TYR Chi-restraints excluded: chain G residue 1095 VAL Chi-restraints excluded: chain G residue 1217 CYS Chi-restraints excluded: chain G residue 1234 VAL Chi-restraints excluded: chain G residue 1595 LEU Chi-restraints excluded: chain G residue 1641 ILE Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1676 LEU Chi-restraints excluded: chain G residue 1691 GLN Chi-restraints excluded: chain G residue 1702 HIS Chi-restraints excluded: chain G residue 1703 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1786 LEU Chi-restraints excluded: chain G residue 1839 VAL Chi-restraints excluded: chain G residue 1850 VAL Chi-restraints excluded: chain G residue 1929 MET Chi-restraints excluded: chain G residue 1944 GLU Chi-restraints excluded: chain G residue 1966 VAL Chi-restraints excluded: chain G residue 2031 LEU Chi-restraints excluded: chain G residue 2038 LEU Chi-restraints excluded: chain G residue 2131 LEU Chi-restraints excluded: chain G residue 2188 ASN Chi-restraints excluded: chain G residue 2461 VAL Chi-restraints excluded: chain G residue 3679 LYS Chi-restraints excluded: chain G residue 3723 MET Chi-restraints excluded: chain G residue 3781 GLN Chi-restraints excluded: chain G residue 3787 LYS Chi-restraints excluded: chain G residue 3793 MET Chi-restraints excluded: chain G residue 3805 LEU Chi-restraints excluded: chain G residue 3883 ASP Chi-restraints excluded: chain G residue 3903 LEU Chi-restraints excluded: chain G residue 3913 ILE Chi-restraints excluded: chain G residue 3915 ILE Chi-restraints excluded: chain G residue 3938 SER Chi-restraints excluded: chain G residue 3942 VAL Chi-restraints excluded: chain G residue 3944 GLU Chi-restraints excluded: chain G residue 3955 MET Chi-restraints excluded: chain G residue 4036 VAL Chi-restraints excluded: chain G residue 4044 MET Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4104 THR Chi-restraints excluded: chain G residue 4181 ILE Chi-restraints excluded: chain G residue 4207 MET Chi-restraints excluded: chain G residue 4247 ILE Chi-restraints excluded: chain G residue 4551 PHE Chi-restraints excluded: chain G residue 4645 CYS Chi-restraints excluded: chain G residue 4688 ILE Chi-restraints excluded: chain G residue 4690 GLU Chi-restraints excluded: chain G residue 4807 PHE Chi-restraints excluded: chain G residue 4891 VAL Chi-restraints excluded: chain G residue 4929 LEU Chi-restraints excluded: chain G residue 4950 VAL Chi-restraints excluded: chain G residue 4952 GLU Chi-restraints excluded: chain G residue 5026 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 GLN B 866 HIS B1972 ASN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3976 ASN ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 GLN ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 765 GLN E 866 HIS E1972 ASN ** E3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3976 ASN ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 460 GLN ** I 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 765 GLN I1972 ASN ** I3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3896 ASN I3897 ASN ** I3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3976 ASN G 395 GLN G 460 GLN ** G 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 765 GLN G 866 HIS G1972 ASN ** G3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3896 ASN G3897 ASN ** G3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3976 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 123052 Z= 0.225 Angle : 0.692 17.155 167776 Z= 0.343 Chirality : 0.040 0.332 19608 Planarity : 0.005 0.080 22100 Dihedral : 5.733 41.562 18084 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.90 % Favored : 88.92 % Rotamer: Outliers : 2.96 % Allowed : 15.66 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.66 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.07), residues: 13364 helix: -0.16 (0.07), residues: 5928 sheet: -0.91 (0.16), residues: 1140 loop : -2.69 (0.08), residues: 6296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP I 891 HIS 0.010 0.001 HIS G 866 PHE 0.016 0.001 PHE E 389 TYR 0.036 0.001 TYR B1712 ARG 0.007 0.000 ARG G1964 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 950 time to evaluate : 9.039 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: F 29 MET cc_start: 0.7207 (tpp) cc_final: 0.6769 (tpp) REVERT: A 29 MET cc_start: 0.7181 (tpp) cc_final: 0.6958 (tpp) REVERT: J 29 MET cc_start: 0.7210 (tpp) cc_final: 0.6781 (tpp) REVERT: B 29 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6218 (mm) REVERT: B 205 ILE cc_start: 0.9492 (tp) cc_final: 0.9094 (tp) REVERT: B 345 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7918 (mm) REVERT: B 394 GLN cc_start: 0.1387 (OUTLIER) cc_final: 0.0276 (pp30) REVERT: B 483 MET cc_start: 0.8514 (mmm) cc_final: 0.8221 (mmm) REVERT: B 1730 MET cc_start: 0.8509 (mpp) cc_final: 0.8003 (mpp) REVERT: B 2032 GLN cc_start: 0.8592 (tp40) cc_final: 0.7954 (tm-30) REVERT: B 2816 MET cc_start: 0.2927 (tpp) cc_final: 0.2716 (tmm) REVERT: B 3652 MET cc_start: 0.8535 (tpp) cc_final: 0.8099 (tpt) REVERT: B 3711 THR cc_start: 0.8792 (m) cc_final: 0.8512 (p) REVERT: B 3805 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.8967 (pp) REVERT: B 3873 LYS cc_start: 0.7178 (mmtm) cc_final: 0.6977 (mmtm) REVERT: B 4216 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8614 (tm-30) REVERT: B 4232 GLU cc_start: 0.8426 (tp30) cc_final: 0.7913 (tp30) REVERT: E 205 ILE cc_start: 0.9483 (tp) cc_final: 0.9088 (tp) REVERT: E 345 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7952 (mm) REVERT: E 394 GLN cc_start: 0.1895 (OUTLIER) cc_final: 0.0664 (pp30) REVERT: E 1037 ASP cc_start: 0.7224 (t0) cc_final: 0.6933 (m-30) REVERT: E 1652 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7811 (mt-10) REVERT: E 1730 MET cc_start: 0.8522 (mpp) cc_final: 0.8004 (mpp) REVERT: E 2032 GLN cc_start: 0.8598 (tp40) cc_final: 0.7934 (tm-30) REVERT: E 2816 MET cc_start: 0.1285 (OUTLIER) cc_final: 0.0484 (tpp) REVERT: E 3652 MET cc_start: 0.8526 (tpp) cc_final: 0.8086 (tpt) REVERT: E 3782 MET cc_start: 0.8670 (tpp) cc_final: 0.8457 (mmm) REVERT: E 3805 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8966 (pp) REVERT: E 3873 LYS cc_start: 0.7236 (mmtm) cc_final: 0.7002 (mmtm) REVERT: E 4216 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8629 (tm-30) REVERT: E 4232 GLU cc_start: 0.8445 (tp30) cc_final: 0.7927 (tp30) REVERT: E 4769 MET cc_start: 0.8296 (ppp) cc_final: 0.7943 (ppp) REVERT: E 4795 TYR cc_start: 0.8680 (t80) cc_final: 0.8430 (t80) REVERT: E 4922 PHE cc_start: 0.7928 (t80) cc_final: 0.7722 (t80) REVERT: I 205 ILE cc_start: 0.9485 (tp) cc_final: 0.9096 (tp) REVERT: I 345 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7910 (mm) REVERT: I 394 GLN cc_start: 0.1679 (OUTLIER) cc_final: 0.0478 (pp30) REVERT: I 1730 MET cc_start: 0.8513 (mpp) cc_final: 0.7997 (mpp) REVERT: I 2032 GLN cc_start: 0.8601 (tp40) cc_final: 0.7930 (tm-30) REVERT: I 2816 MET cc_start: 0.3368 (tpp) cc_final: 0.2987 (tmm) REVERT: I 3652 MET cc_start: 0.8530 (tpp) cc_final: 0.8089 (tpt) REVERT: I 3805 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8973 (pp) REVERT: I 4216 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8647 (tm-30) REVERT: I 4232 GLU cc_start: 0.8434 (tp30) cc_final: 0.7917 (tp30) REVERT: I 4769 MET cc_start: 0.8289 (ppp) cc_final: 0.8054 (ppp) REVERT: I 5013 MET cc_start: 0.8048 (mtp) cc_final: 0.7771 (mtt) REVERT: G 205 ILE cc_start: 0.9492 (tp) cc_final: 0.9095 (tp) REVERT: G 345 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7964 (mm) REVERT: G 394 GLN cc_start: 0.1686 (OUTLIER) cc_final: 0.0485 (pp30) REVERT: G 961 MET cc_start: 0.4045 (mmp) cc_final: 0.3644 (mmp) REVERT: G 1730 MET cc_start: 0.8516 (mpp) cc_final: 0.8004 (mpp) REVERT: G 2347 GLU cc_start: 0.8066 (pm20) cc_final: 0.7672 (tm-30) REVERT: G 2816 MET cc_start: 0.3068 (tpp) cc_final: 0.2814 (tmm) REVERT: G 3652 MET cc_start: 0.8539 (tpp) cc_final: 0.8098 (tpt) REVERT: G 3711 THR cc_start: 0.8821 (m) cc_final: 0.8536 (p) REVERT: G 3805 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8972 (pp) REVERT: G 4216 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8611 (tm-30) REVERT: G 4232 GLU cc_start: 0.8441 (tp30) cc_final: 0.7907 (tp30) REVERT: G 4769 MET cc_start: 0.8279 (ppp) cc_final: 0.7927 (ppp) REVERT: G 4922 PHE cc_start: 0.7915 (t80) cc_final: 0.7699 (t80) REVERT: G 5013 MET cc_start: 0.8045 (mtp) cc_final: 0.7761 (mtt) outliers start: 306 outliers final: 250 residues processed: 1183 average time/residue: 0.9182 time to fit residues: 1972.3391 Evaluate side-chains 1174 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 910 time to evaluate : 8.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 772 ASN Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 1095 VAL Chi-restraints excluded: chain B residue 1217 CYS Chi-restraints excluded: chain B residue 1641 ILE Chi-restraints excluded: chain B residue 1657 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1702 HIS Chi-restraints excluded: chain B residue 1703 LEU Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1736 VAL Chi-restraints excluded: chain B residue 1850 VAL Chi-restraints excluded: chain B residue 1944 GLU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2131 LEU Chi-restraints excluded: chain B residue 2188 ASN Chi-restraints excluded: chain B residue 2461 VAL Chi-restraints excluded: chain B residue 3723 MET Chi-restraints excluded: chain B residue 3781 GLN Chi-restraints excluded: chain B residue 3787 LYS Chi-restraints excluded: chain B residue 3805 LEU Chi-restraints excluded: chain B residue 3832 ILE Chi-restraints excluded: chain B residue 3883 ASP Chi-restraints excluded: chain B residue 3903 LEU Chi-restraints excluded: chain B residue 3913 ILE Chi-restraints excluded: chain B residue 3915 ILE Chi-restraints excluded: chain B residue 3942 VAL Chi-restraints excluded: chain B residue 3955 MET Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4044 MET Chi-restraints excluded: chain B residue 4081 VAL Chi-restraints excluded: chain B residue 4104 THR Chi-restraints excluded: chain B residue 4181 ILE Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4645 CYS Chi-restraints excluded: chain B residue 4688 ILE Chi-restraints excluded: chain B residue 4690 GLU Chi-restraints excluded: chain B residue 4807 PHE Chi-restraints excluded: chain B residue 4891 VAL Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4950 VAL Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 5026 ASP Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 394 GLN Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 635 THR Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 664 PHE Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 671 VAL Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain E residue 750 LEU Chi-restraints excluded: chain E residue 772 ASN Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 866 HIS Chi-restraints excluded: chain E residue 1095 VAL Chi-restraints excluded: chain E residue 1217 CYS Chi-restraints excluded: chain E residue 1234 VAL Chi-restraints excluded: chain E residue 1641 ILE Chi-restraints excluded: chain E residue 1657 LEU Chi-restraints excluded: chain E residue 1676 LEU Chi-restraints excluded: chain E residue 1702 HIS Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1736 VAL Chi-restraints excluded: chain E residue 1839 VAL Chi-restraints excluded: chain E residue 1850 VAL Chi-restraints excluded: chain E residue 1865 MET Chi-restraints excluded: chain E residue 1944 GLU Chi-restraints excluded: chain E residue 2038 LEU Chi-restraints excluded: chain E residue 2131 LEU Chi-restraints excluded: chain E residue 2188 ASN Chi-restraints excluded: chain E residue 2461 VAL Chi-restraints excluded: chain E residue 2466 LEU Chi-restraints excluded: chain E residue 2816 MET Chi-restraints excluded: chain E residue 2874 MET Chi-restraints excluded: chain E residue 3717 ASP Chi-restraints excluded: chain E residue 3781 GLN Chi-restraints excluded: chain E residue 3787 LYS Chi-restraints excluded: chain E residue 3805 LEU Chi-restraints excluded: chain E residue 3832 ILE Chi-restraints excluded: chain E residue 3883 ASP Chi-restraints excluded: chain E residue 3903 LEU Chi-restraints excluded: chain E residue 3913 ILE Chi-restraints excluded: chain E residue 3915 ILE Chi-restraints excluded: chain E residue 3938 SER Chi-restraints excluded: chain E residue 3942 VAL Chi-restraints excluded: chain E residue 3955 MET Chi-restraints excluded: chain E residue 4036 VAL Chi-restraints excluded: chain E residue 4044 MET Chi-restraints excluded: chain E residue 4081 VAL Chi-restraints excluded: chain E residue 4104 THR Chi-restraints excluded: chain E residue 4138 ASP Chi-restraints excluded: chain E residue 4181 ILE Chi-restraints excluded: chain E residue 4187 SER Chi-restraints excluded: chain E residue 4207 MET Chi-restraints excluded: chain E residue 4247 ILE Chi-restraints excluded: chain E residue 4645 CYS Chi-restraints excluded: chain E residue 4688 ILE Chi-restraints excluded: chain E residue 4690 GLU Chi-restraints excluded: chain E residue 4807 PHE Chi-restraints excluded: chain E residue 4891 VAL Chi-restraints excluded: chain E residue 4950 VAL Chi-restraints excluded: chain E residue 4952 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 65 CYS Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 394 GLN Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 589 LEU Chi-restraints excluded: chain I residue 608 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 647 ASN Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain I residue 671 VAL Chi-restraints excluded: chain I residue 674 PHE Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 772 ASN Chi-restraints excluded: chain I residue 920 TYR Chi-restraints excluded: chain I residue 1095 VAL Chi-restraints excluded: chain I residue 1217 CYS Chi-restraints excluded: chain I residue 1641 ILE Chi-restraints excluded: chain I residue 1657 LEU Chi-restraints excluded: chain I residue 1676 LEU Chi-restraints excluded: chain I residue 1702 HIS Chi-restraints excluded: chain I residue 1703 LEU Chi-restraints excluded: chain I residue 1717 SER Chi-restraints excluded: chain I residue 1736 VAL Chi-restraints excluded: chain I residue 1850 VAL Chi-restraints excluded: chain I residue 1865 MET Chi-restraints excluded: chain I residue 1944 GLU Chi-restraints excluded: chain I residue 2038 LEU Chi-restraints excluded: chain I residue 2131 LEU Chi-restraints excluded: chain I residue 2188 ASN Chi-restraints excluded: chain I residue 2461 VAL Chi-restraints excluded: chain I residue 2466 LEU Chi-restraints excluded: chain I residue 3717 ASP Chi-restraints excluded: chain I residue 3781 GLN Chi-restraints excluded: chain I residue 3787 LYS Chi-restraints excluded: chain I residue 3793 MET Chi-restraints excluded: chain I residue 3805 LEU Chi-restraints excluded: chain I residue 3832 ILE Chi-restraints excluded: chain I residue 3883 ASP Chi-restraints excluded: chain I residue 3903 LEU Chi-restraints excluded: chain I residue 3913 ILE Chi-restraints excluded: chain I residue 3915 ILE Chi-restraints excluded: chain I residue 3938 SER Chi-restraints excluded: chain I residue 3942 VAL Chi-restraints excluded: chain I residue 3955 MET Chi-restraints excluded: chain I residue 4036 VAL Chi-restraints excluded: chain I residue 4044 MET Chi-restraints excluded: chain I residue 4081 VAL Chi-restraints excluded: chain I residue 4104 THR Chi-restraints excluded: chain I residue 4181 ILE Chi-restraints excluded: chain I residue 4207 MET Chi-restraints excluded: chain I residue 4245 MET Chi-restraints excluded: chain I residue 4247 ILE Chi-restraints excluded: chain I residue 4645 CYS Chi-restraints excluded: chain I residue 4688 ILE Chi-restraints excluded: chain I residue 4690 GLU Chi-restraints excluded: chain I residue 4807 PHE Chi-restraints excluded: chain I residue 4891 VAL Chi-restraints excluded: chain I residue 4929 LEU Chi-restraints excluded: chain I residue 4950 VAL Chi-restraints excluded: chain I residue 4952 GLU Chi-restraints excluded: chain I residue 5026 ASP Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 65 CYS Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 394 GLN Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 623 GLU Chi-restraints excluded: chain G residue 635 THR Chi-restraints excluded: chain G residue 647 ASN Chi-restraints excluded: chain G residue 664 PHE Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 671 VAL Chi-restraints excluded: chain G residue 749 ASP Chi-restraints excluded: chain G residue 772 ASN Chi-restraints excluded: chain G residue 791 PHE Chi-restraints excluded: chain G residue 866 HIS Chi-restraints excluded: chain G residue 920 TYR Chi-restraints excluded: chain G residue 1095 VAL Chi-restraints excluded: chain G residue 1217 CYS Chi-restraints excluded: chain G residue 1234 VAL Chi-restraints excluded: chain G residue 1641 ILE Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1676 LEU Chi-restraints excluded: chain G residue 1702 HIS Chi-restraints excluded: chain G residue 1703 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1850 VAL Chi-restraints excluded: chain G residue 1944 GLU Chi-restraints excluded: chain G residue 2038 LEU Chi-restraints excluded: chain G residue 2131 LEU Chi-restraints excluded: chain G residue 2188 ASN Chi-restraints excluded: chain G residue 2461 VAL Chi-restraints excluded: chain G residue 3781 GLN Chi-restraints excluded: chain G residue 3787 LYS Chi-restraints excluded: chain G residue 3793 MET Chi-restraints excluded: chain G residue 3805 LEU Chi-restraints excluded: chain G residue 3832 ILE Chi-restraints excluded: chain G residue 3883 ASP Chi-restraints excluded: chain G residue 3903 LEU Chi-restraints excluded: chain G residue 3913 ILE Chi-restraints excluded: chain G residue 3915 ILE Chi-restraints excluded: chain G residue 3938 SER Chi-restraints excluded: chain G residue 3942 VAL Chi-restraints excluded: chain G residue 3955 MET Chi-restraints excluded: chain G residue 4000 MET Chi-restraints excluded: chain G residue 4036 VAL Chi-restraints excluded: chain G residue 4044 MET Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4104 THR Chi-restraints excluded: chain G residue 4181 ILE Chi-restraints excluded: chain G residue 4207 MET Chi-restraints excluded: chain G residue 4247 ILE Chi-restraints excluded: chain G residue 4645 CYS Chi-restraints excluded: chain G residue 4688 ILE Chi-restraints excluded: chain G residue 4690 GLU Chi-restraints excluded: chain G residue 4807 PHE Chi-restraints excluded: chain G residue 4891 VAL Chi-restraints excluded: chain G residue 4929 LEU Chi-restraints excluded: chain G residue 4950 VAL Chi-restraints excluded: chain G residue 4952 GLU Chi-restraints excluded: chain G residue 5026 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS B 866 HIS B1972 ASN B3781 GLN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3897 ASN ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3976 ASN E 395 GLN ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 HIS E 866 HIS E1972 ASN ** E3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3897 ASN ** E3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3976 ASN I 395 GLN ** I 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 765 GLN I 866 HIS I1972 ASN ** I3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3896 ASN ** I3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3976 ASN G 395 GLN ** G 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 597 HIS G 866 HIS G1972 ASN G3781 GLN ** G3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3896 ASN ** G3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3976 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 123052 Z= 0.280 Angle : 0.711 18.190 167776 Z= 0.351 Chirality : 0.041 0.321 19608 Planarity : 0.005 0.083 22100 Dihedral : 5.657 41.570 18084 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.37 % Favored : 87.45 % Rotamer: Outliers : 2.80 % Allowed : 15.92 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.66 % Twisted General : 0.11 % 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: -2.00 (0.07), residues: 13364 helix: -0.07 (0.07), residues: 5892 sheet: -1.00 (0.15), residues: 1240 loop : -2.71 (0.08), residues: 6232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP I 891 HIS 0.015 0.001 HIS E 866 PHE 0.049 0.002 PHE E1748 TYR 0.033 0.002 TYR B1712 ARG 0.008 0.000 ARG G1964 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26728 Ramachandran restraints generated. 13364 Oldfield, 0 Emsley, 13364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 911 time to evaluate : 8.896 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: F 29 MET cc_start: 0.7245 (tpp) cc_final: 0.6825 (tpp) REVERT: A 29 MET cc_start: 0.7168 (tpp) cc_final: 0.6957 (tpp) REVERT: J 29 MET cc_start: 0.7240 (tpp) cc_final: 0.6827 (tpp) REVERT: B 205 ILE cc_start: 0.9490 (tp) cc_final: 0.9089 (tp) REVERT: B 345 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7854 (mm) REVERT: B 394 GLN cc_start: 0.1634 (OUTLIER) cc_final: 0.0471 (pp30) REVERT: B 483 MET cc_start: 0.8533 (mmm) cc_final: 0.8266 (mmm) REVERT: B 1730 MET cc_start: 0.8450 (mpp) cc_final: 0.7976 (mpp) REVERT: B 2032 GLN cc_start: 0.8608 (tp40) cc_final: 0.7941 (tm-30) REVERT: B 2816 MET cc_start: 0.3000 (tpp) cc_final: 0.2784 (tmm) REVERT: B 3652 MET cc_start: 0.8624 (tpp) cc_final: 0.8176 (tpt) REVERT: B 3711 THR cc_start: 0.8857 (m) cc_final: 0.8569 (p) REVERT: B 3805 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9001 (pp) REVERT: B 4188 ARG cc_start: 0.8222 (mmp80) cc_final: 0.7892 (mmp80) REVERT: B 4216 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8613 (tm-30) REVERT: E 205 ILE cc_start: 0.9484 (tp) cc_final: 0.9080 (tp) REVERT: E 345 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7888 (mm) REVERT: E 394 GLN cc_start: 0.1577 (OUTLIER) cc_final: 0.0434 (pp30) REVERT: E 686 TRP cc_start: 0.7409 (m100) cc_final: 0.7198 (m100) REVERT: E 1037 ASP cc_start: 0.7361 (t0) cc_final: 0.7069 (m-30) REVERT: E 1652 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7840 (mt-10) REVERT: E 1730 MET cc_start: 0.8465 (mpp) cc_final: 0.7968 (mpp) REVERT: E 2032 GLN cc_start: 0.8592 (tp40) cc_final: 0.7890 (tm-30) REVERT: E 2816 MET cc_start: 0.1385 (OUTLIER) cc_final: 0.0611 (mmm) REVERT: E 3652 MET cc_start: 0.8593 (tpp) cc_final: 0.8138 (tpt) REVERT: E 3782 MET cc_start: 0.8698 (tpp) cc_final: 0.8472 (mmm) REVERT: E 3805 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.8991 (pp) REVERT: E 4026 MET cc_start: 0.8931 (ttp) cc_final: 0.8657 (ttm) REVERT: E 4216 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8627 (tm-30) REVERT: E 4769 MET cc_start: 0.8322 (ppp) cc_final: 0.7873 (ppp) REVERT: E 4795 TYR cc_start: 0.8687 (t80) cc_final: 0.8423 (t80) REVERT: E 4922 PHE cc_start: 0.7934 (t80) cc_final: 0.7734 (t80) REVERT: I 205 ILE cc_start: 0.9485 (tp) cc_final: 0.9085 (tp) REVERT: I 345 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7895 (mm) REVERT: I 394 GLN cc_start: 0.1799 (OUTLIER) cc_final: 0.0542 (pp30) REVERT: I 1730 MET cc_start: 0.8456 (mpp) cc_final: 0.7961 (mpp) REVERT: I 2032 GLN cc_start: 0.8616 (tp40) cc_final: 0.7942 (tm-30) REVERT: I 2816 MET cc_start: 0.3189 (tpp) cc_final: 0.2763 (tmm) REVERT: I 3652 MET cc_start: 0.8594 (tpp) cc_final: 0.8141 (tpt) REVERT: I 3805 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9004 (pp) REVERT: I 4026 MET cc_start: 0.8913 (ttp) cc_final: 0.8596 (ttm) REVERT: I 5013 MET cc_start: 0.8057 (mtp) cc_final: 0.7789 (mtt) REVERT: G 19 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: G 205 ILE cc_start: 0.9495 (tp) cc_final: 0.9088 (tp) REVERT: G 345 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7904 (mm) REVERT: G 394 GLN cc_start: 0.1629 (OUTLIER) cc_final: 0.0350 (pp30) REVERT: G 397 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8224 (mt-10) REVERT: G 686 TRP cc_start: 0.7521 (m100) cc_final: 0.7195 (m100) REVERT: G 961 MET cc_start: 0.4416 (mmp) cc_final: 0.3987 (mmp) REVERT: G 1730 MET cc_start: 0.8457 (mpp) cc_final: 0.7969 (mpp) REVERT: G 2347 GLU cc_start: 0.8067 (pm20) cc_final: 0.7698 (tm-30) REVERT: G 3711 THR cc_start: 0.8966 (m) cc_final: 0.8667 (p) REVERT: G 3805 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9003 (pp) REVERT: G 4216 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8605 (tm-30) REVERT: G 4769 MET cc_start: 0.8282 (ppp) cc_final: 0.7842 (ppp) REVERT: G 4922 PHE cc_start: 0.7929 (t80) cc_final: 0.7721 (t80) REVERT: G 5013 MET cc_start: 0.8051 (mtp) cc_final: 0.7778 (mtt) outliers start: 289 outliers final: 259 residues processed: 1132 average time/residue: 0.9112 time to fit residues: 1875.1543 Evaluate side-chains 1169 residues out of total 11712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 896 time to evaluate : 8.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 772 ASN Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 1095 VAL Chi-restraints excluded: chain B residue 1217 CYS Chi-restraints excluded: chain B residue 1234 VAL Chi-restraints excluded: chain B residue 1641 ILE Chi-restraints excluded: chain B residue 1657 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1702 HIS Chi-restraints excluded: chain B residue 1703 LEU Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1736 VAL Chi-restraints excluded: chain B residue 1850 VAL Chi-restraints excluded: chain B residue 1944 GLU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2131 LEU Chi-restraints excluded: chain B residue 2188 ASN Chi-restraints excluded: chain B residue 2461 VAL Chi-restraints excluded: chain B residue 3781 GLN Chi-restraints excluded: chain B residue 3787 LYS Chi-restraints excluded: chain B residue 3805 LEU Chi-restraints excluded: chain B residue 3832 ILE Chi-restraints excluded: chain B residue 3883 ASP Chi-restraints excluded: chain B residue 3897 ASN Chi-restraints excluded: chain B residue 3903 LEU Chi-restraints excluded: chain B residue 3913 ILE Chi-restraints excluded: chain B residue 3915 ILE Chi-restraints excluded: chain B residue 3938 SER Chi-restraints excluded: chain B residue 3942 VAL Chi-restraints excluded: chain B residue 3955 MET Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4044 MET Chi-restraints excluded: chain B residue 4081 VAL Chi-restraints excluded: chain B residue 4104 THR Chi-restraints excluded: chain B residue 4181 ILE Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4645 CYS Chi-restraints excluded: chain B residue 4688 ILE Chi-restraints excluded: chain B residue 4690 GLU Chi-restraints excluded: chain B residue 4807 PHE Chi-restraints excluded: chain B residue 4891 VAL Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4950 VAL Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 5026 ASP Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 394 GLN Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 635 THR Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 664 PHE Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 671 VAL Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain E residue 772 ASN Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 826 ILE Chi-restraints excluded: chain E residue 866 HIS Chi-restraints excluded: chain E residue 948 ASP Chi-restraints excluded: chain E residue 1095 VAL Chi-restraints excluded: chain E residue 1217 CYS Chi-restraints excluded: chain E residue 1234 VAL Chi-restraints excluded: chain E residue 1641 ILE Chi-restraints excluded: chain E residue 1657 LEU Chi-restraints excluded: chain E residue 1676 LEU Chi-restraints excluded: chain E residue 1702 HIS Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1736 VAL Chi-restraints excluded: chain E residue 1839 VAL Chi-restraints excluded: chain E residue 1850 VAL Chi-restraints excluded: chain E residue 1865 MET Chi-restraints excluded: chain E residue 1939 MET Chi-restraints excluded: chain E residue 1944 GLU Chi-restraints excluded: chain E residue 2038 LEU Chi-restraints excluded: chain E residue 2188 ASN Chi-restraints excluded: chain E residue 2461 VAL Chi-restraints excluded: chain E residue 2466 LEU Chi-restraints excluded: chain E residue 2816 MET Chi-restraints excluded: chain E residue 2874 MET Chi-restraints excluded: chain E residue 3717 ASP Chi-restraints excluded: chain E residue 3781 GLN Chi-restraints excluded: chain E residue 3787 LYS Chi-restraints excluded: chain E residue 3805 LEU Chi-restraints excluded: chain E residue 3832 ILE Chi-restraints excluded: chain E residue 3883 ASP Chi-restraints excluded: chain E residue 3897 ASN Chi-restraints excluded: chain E residue 3903 LEU Chi-restraints excluded: chain E residue 3913 ILE Chi-restraints excluded: chain E residue 3915 ILE Chi-restraints excluded: chain E residue 3938 SER Chi-restraints excluded: chain E residue 3942 VAL Chi-restraints excluded: chain E residue 3955 MET Chi-restraints excluded: chain E residue 4036 VAL Chi-restraints excluded: chain E residue 4044 MET Chi-restraints excluded: chain E residue 4081 VAL Chi-restraints excluded: chain E residue 4104 THR Chi-restraints excluded: chain E residue 4138 ASP Chi-restraints excluded: chain E residue 4181 ILE Chi-restraints excluded: chain E residue 4207 MET Chi-restraints excluded: chain E residue 4247 ILE Chi-restraints excluded: chain E residue 4645 CYS Chi-restraints excluded: chain E residue 4688 ILE Chi-restraints excluded: chain E residue 4690 GLU Chi-restraints excluded: chain E residue 4807 PHE Chi-restraints excluded: chain E residue 4874 MET Chi-restraints excluded: chain E residue 4891 VAL Chi-restraints excluded: chain E residue 4950 VAL Chi-restraints excluded: chain E residue 4952 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 65 CYS Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 394 GLN Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 589 LEU Chi-restraints excluded: chain I residue 608 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 647 ASN Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain I residue 671 VAL Chi-restraints excluded: chain I residue 674 PHE Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 772 ASN Chi-restraints excluded: chain I residue 866 HIS Chi-restraints excluded: chain I residue 920 TYR Chi-restraints excluded: chain I residue 1095 VAL Chi-restraints excluded: chain I residue 1217 CYS Chi-restraints excluded: chain I residue 1234 VAL Chi-restraints excluded: chain I residue 1641 ILE Chi-restraints excluded: chain I residue 1657 LEU Chi-restraints excluded: chain I residue 1676 LEU Chi-restraints excluded: chain I residue 1702 HIS Chi-restraints excluded: chain I residue 1703 LEU Chi-restraints excluded: chain I residue 1717 SER Chi-restraints excluded: chain I residue 1736 VAL Chi-restraints excluded: chain I residue 1850 VAL Chi-restraints excluded: chain I residue 1939 MET Chi-restraints excluded: chain I residue 1944 GLU Chi-restraints excluded: chain I residue 2031 LEU Chi-restraints excluded: chain I residue 2038 LEU Chi-restraints excluded: chain I residue 2131 LEU Chi-restraints excluded: chain I residue 2188 ASN Chi-restraints excluded: chain I residue 2461 VAL Chi-restraints excluded: chain I residue 2466 LEU Chi-restraints excluded: chain I residue 3781 GLN Chi-restraints excluded: chain I residue 3787 LYS Chi-restraints excluded: chain I residue 3793 MET Chi-restraints excluded: chain I residue 3805 LEU Chi-restraints excluded: chain I residue 3832 ILE Chi-restraints excluded: chain I residue 3883 ASP Chi-restraints excluded: chain I residue 3903 LEU Chi-restraints excluded: chain I residue 3913 ILE Chi-restraints excluded: chain I residue 3915 ILE Chi-restraints excluded: chain I residue 3938 SER Chi-restraints excluded: chain I residue 3942 VAL Chi-restraints excluded: chain I residue 3955 MET Chi-restraints excluded: chain I residue 4036 VAL Chi-restraints excluded: chain I residue 4044 MET Chi-restraints excluded: chain I residue 4081 VAL Chi-restraints excluded: chain I residue 4104 THR Chi-restraints excluded: chain I residue 4181 ILE Chi-restraints excluded: chain I residue 4207 MET Chi-restraints excluded: chain I residue 4247 ILE Chi-restraints excluded: chain I residue 4645 CYS Chi-restraints excluded: chain I residue 4688 ILE Chi-restraints excluded: chain I residue 4690 GLU Chi-restraints excluded: chain I residue 4807 PHE Chi-restraints excluded: chain I residue 4891 VAL Chi-restraints excluded: chain I residue 4929 LEU Chi-restraints excluded: chain I residue 4950 VAL Chi-restraints excluded: chain I residue 4952 GLU Chi-restraints excluded: chain I residue 5026 ASP Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 65 CYS Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 394 GLN Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 550 LYS Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 635 THR Chi-restraints excluded: chain G residue 647 ASN Chi-restraints excluded: chain G residue 664 PHE Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 671 VAL Chi-restraints excluded: chain G residue 749 ASP Chi-restraints excluded: chain G residue 772 ASN Chi-restraints excluded: chain G residue 791 PHE Chi-restraints excluded: chain G residue 826 ILE Chi-restraints excluded: chain G residue 866 HIS Chi-restraints excluded: chain G residue 920 TYR Chi-restraints excluded: chain G residue 1095 VAL Chi-restraints excluded: chain G residue 1217 CYS Chi-restraints excluded: chain G residue 1234 VAL Chi-restraints excluded: chain G residue 1641 ILE Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1676 LEU Chi-restraints excluded: chain G residue 1702 HIS Chi-restraints excluded: chain G residue 1703 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1850 VAL Chi-restraints excluded: chain G residue 1944 GLU Chi-restraints excluded: chain G residue 2038 LEU Chi-restraints excluded: chain G residue 2131 LEU Chi-restraints excluded: chain G residue 2188 ASN Chi-restraints excluded: chain G residue 2461 VAL Chi-restraints excluded: chain G residue 3679 LYS Chi-restraints excluded: chain G residue 3781 GLN Chi-restraints excluded: chain G residue 3787 LYS Chi-restraints excluded: chain G residue 3793 MET Chi-restraints excluded: chain G residue 3805 LEU Chi-restraints excluded: chain G residue 3832 ILE Chi-restraints excluded: chain G residue 3883 ASP Chi-restraints excluded: chain G residue 3903 LEU Chi-restraints excluded: chain G residue 3913 ILE Chi-restraints excluded: chain G residue 3915 ILE Chi-restraints excluded: chain G residue 3938 SER Chi-restraints excluded: chain G residue 3942 VAL Chi-restraints excluded: chain G residue 3955 MET Chi-restraints excluded: chain G residue 4000 MET Chi-restraints excluded: chain G residue 4036 VAL Chi-restraints excluded: chain G residue 4044 MET Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4104 THR Chi-restraints excluded: chain G residue 4181 ILE Chi-restraints excluded: chain G residue 4207 MET Chi-restraints excluded: chain G residue 4247 ILE Chi-restraints excluded: chain G residue 4645 CYS Chi-restraints excluded: chain G residue 4688 ILE Chi-restraints excluded: chain G residue 4690 GLU Chi-restraints excluded: chain G residue 4807 PHE Chi-restraints excluded: chain G residue 4891 VAL Chi-restraints excluded: chain G residue 4929 LEU Chi-restraints excluded: chain G residue 4950 VAL Chi-restraints excluded: chain G residue 4952 GLU Chi-restraints excluded: chain G residue 5026 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 39 optimal weight: 0.0010 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 HIS B1972 ASN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3897 ASN ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3976 ASN ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 866 HIS E1972 ASN ** E3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3897 ASN ** E3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3976 ASN ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 395 GLN ** I 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 866 HIS I 877 ASN I1972 ASN I2884 ASN ** I3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3896 ASN I3897 ASN ** I3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3976 ASN ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 866 HIS G1972 ASN G2881 ASN G3781 GLN ** G3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3896 ASN ** G3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3976 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.104527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.084947 restraints weight = 447918.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.083862 restraints weight = 273251.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.084620 restraints weight = 290144.222| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 123052 Z= 0.151 Angle : 0.652 18.061 167776 Z= 0.320 Chirality : 0.038 0.345 19608 Planarity : 0.005 0.084 22100 Dihedral : 5.310 39.473 18084 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.74 % Favored : 90.09 % Rotamer: Outliers : 2.07 % Allowed : 16.75 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.66 % Twisted General : 0.10 % 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: -1.69 (0.07), residues: 13364 helix: 0.22 (0.07), residues: 5872 sheet: -0.93 (0.15), residues: 1212 loop : -2.55 (0.08), residues: 6280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP I 891 HIS 0.016 0.001 HIS I 866 PHE 0.019 0.001 PHE E 389 TYR 0.027 0.001 TYR B1712 ARG 0.014 0.000 ARG I 869 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30905.25 seconds wall clock time: 509 minutes 43.65 seconds (30583.65 seconds total)