Starting phenix.real_space_refine on Thu Mar 14 11:06:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5taw_8387/03_2024/5taw_8387.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5taw_8387/03_2024/5taw_8387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5taw_8387/03_2024/5taw_8387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5taw_8387/03_2024/5taw_8387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5taw_8387/03_2024/5taw_8387.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5taw_8387/03_2024/5taw_8387.pdb" } resolution = 4.4 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= 0.006 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 76808 2.51 5 N 21488 2.21 5 O 22328 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 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 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 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 ARG 4824": "NH1" <-> "NH2" Residue "B ARG 4860": "NH1" <-> "NH2" Residue "B ARG 4892": "NH1" <-> "NH2" Residue "B ARG 4913": "NH1" <-> "NH2" Residue "B PHE 4959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 5017": "NH1" <-> "NH2" Residue "B 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 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 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 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 ARG 4824": "NH1" <-> "NH2" Residue "G ARG 4860": "NH1" <-> "NH2" Residue "G ARG 4892": "NH1" <-> "NH2" Residue "G ARG 4913": "NH1" <-> "NH2" Residue "G ARG 5017": "NH1" <-> "NH2" Residue "G 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 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 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 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 ARG 4824": "NH1" <-> "NH2" Residue "I ARG 4860": "NH1" <-> "NH2" Residue "I ARG 4892": "NH1" <-> "NH2" Residue "I ARG 4913": "NH1" <-> "NH2" Residue "I ARG 5017": "NH1" <-> "NH2" Residue "I 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 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 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 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 ARG 4824": "NH1" <-> "NH2" Residue "E ARG 4860": "NH1" <-> "NH2" Residue "E ARG 4892": "NH1" <-> "NH2" Residue "E ARG 4913": "NH1" <-> "NH2" Residue "E ARG 5017": "NH1" <-> "NH2" Residue "E ARG 5029": "NH1" <-> "NH2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 121276 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: 29499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4194, 29499 Classifications: {'peptide': 4194} Incomplete info: {'truncation_to_alanine': 1272} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4036} Chain breaks: 26 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3079 Unresolved non-hydrogen angles: 4307 Unresolved non-hydrogen dihedrals: 1905 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 926, '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: 1786 Chain: "G" Number of atoms: 29499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4194, 29499 Classifications: {'peptide': 4194} Incomplete info: {'truncation_to_alanine': 1272} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4036} Chain breaks: 26 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3079 Unresolved non-hydrogen angles: 4307 Unresolved non-hydrogen dihedrals: 1905 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 926, '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: 1786 Chain: "I" Number of atoms: 29499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4194, 29499 Classifications: {'peptide': 4194} Incomplete info: {'truncation_to_alanine': 1272} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4036} Chain breaks: 26 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3079 Unresolved non-hydrogen angles: 4307 Unresolved non-hydrogen dihedrals: 1905 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 926, '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: 1786 Chain: "E" Number of atoms: 29499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4194, 29499 Classifications: {'peptide': 4194} Incomplete info: {'truncation_to_alanine': 1272} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4036} Chain breaks: 26 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3079 Unresolved non-hydrogen angles: 4307 Unresolved non-hydrogen dihedrals: 1905 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 926, '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: 1786 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: "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} 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: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 32100 SG CYS B4958 179.452 206.009 88.463 1.00131.45 S ATOM 61599 SG CYS G4958 210.471 183.983 87.733 1.00130.05 S ATOM 61624 SG CYS G4961 209.773 183.335 89.871 1.00121.69 S ATOM 91098 SG CYS I4958 183.959 178.523 87.706 1.00129.51 S ATOM 91123 SG CYS I4961 183.312 179.219 89.846 1.00119.39 S ATOM A0FW5 SG CYS E4958 205.066 210.540 87.732 1.00128.43 S ATOM A0FWU SG CYS E4961 205.712 209.844 89.872 1.00118.77 S Time building chain proxies: 45.31, per 1000 atoms: 0.37 Number of scatterers: 121276 At special positions: 0 Unit cell: (390.305, 390.305, 207.075, 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 22328 8.00 N 21488 7.00 C 76808 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: 31.57 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=" SG CYS B4958 " pdb=" ZN E5101 " pdb="ZN ZN E5101 " - pdb=" NE2 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=" NE2 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=" NE2 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 : 6 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 32568 Finding SS restraints... Secondary structure from input PDB file: 686 helices and 96 sheets defined 60.9% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.85 Creating SS restraints... Processing helix chain 'F' and resid 38 through 43 removed outlier: 4.277A pdb=" N ARG F 42 " --> pdb=" O SER F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 65 removed outlier: 3.623A pdb=" N GLN F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 82 removed outlier: 3.946A pdb=" N ALA F 81 " --> pdb=" O THR F 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.276A pdb=" N ARG A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 65 removed outlier: 3.623A pdb=" N GLN A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.944A pdb=" N ALA A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 43 removed outlier: 4.277A pdb=" N ARG H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 65 removed outlier: 3.624A pdb=" N GLN H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 removed outlier: 3.945A pdb=" N ALA H 81 " --> pdb=" O THR H 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 43 removed outlier: 4.276A pdb=" N ARG J 42 " --> pdb=" O SER J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 65 removed outlier: 3.623A pdb=" N GLN J 65 " --> pdb=" O GLU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 82 removed outlier: 3.946A pdb=" N ALA J 81 " --> pdb=" O THR J 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 82 removed outlier: 3.505A pdb=" N GLN B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.794A pdb=" N THR B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.698A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 421 removed outlier: 3.932A pdb=" N GLN B 399 " --> pdb=" O GLN B 395 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLN B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 450 removed outlier: 3.651A pdb=" N GLY B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 477 removed outlier: 3.781A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 514 through 529 removed outlier: 3.574A pdb=" N ILE B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.704A pdb=" N PHE B 540 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER B 541 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.701A pdb=" N VAL B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 568 removed outlier: 3.629A pdb=" N TYR B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.507A pdb=" N ILE B 577 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE B 578 " --> pdb=" O LEU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 593 removed outlier: 3.606A pdb=" N LYS B 584 " --> pdb=" O GLU B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 608 removed outlier: 3.556A pdb=" N LEU B 603 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 removed outlier: 4.120A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 622 " --> pdb=" O GLN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 889 removed outlier: 3.671A pdb=" N ILE B 870 " --> pdb=" O HIS B 866 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 886 " --> pdb=" O TRP B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 934 removed outlier: 4.066A pdb=" N ASN B 919 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR B 920 " --> pdb=" O PRO B 916 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 927 " --> pdb=" O GLN B 923 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 928 " --> pdb=" O MET B 924 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.059A pdb=" N LEU B 984 " --> pdb=" O ALA B 980 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP B 986 " --> pdb=" O THR B 982 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 991 " --> pdb=" O ARG B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1039 removed outlier: 3.691A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1049 removed outlier: 3.904A 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 1623 through 1627 Processing helix chain 'B' and resid 1652 through 1657 removed outlier: 3.500A pdb=" N LEU B1657 " --> pdb=" O LEU B1653 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1674 removed outlier: 3.642A pdb=" N HIS B1665 " --> pdb=" O ARG B1661 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B1670 " --> pdb=" O THR B1666 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG B1671 " --> pdb=" O LEU B1667 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1686 removed outlier: 3.777A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS B1686 " --> pdb=" O ALA B1682 " (cutoff:3.500A) Processing helix chain 'B' and resid 1692 through 1700 removed outlier: 4.129A pdb=" N LEU B1698 " --> pdb=" O LEU B1694 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) Processing helix chain 'B' and resid 1710 through 1712 No H-bonds generated for 'chain 'B' and resid 1710 through 1712' Processing helix chain 'B' and resid 1713 through 1720 Processing helix chain 'B' and resid 1720 through 1730 removed outlier: 4.389A pdb=" N SER B1726 " --> pdb=" O SER B1722 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET B1730 " --> pdb=" O SER B1726 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1744 Processing helix chain 'B' and resid 1803 through 1823 removed outlier: 3.631A pdb=" N MET B1814 " --> pdb=" O LYS B1810 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B1815 " --> pdb=" O ALA B1811 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B1817 " --> pdb=" O ARG B1813 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1838 Processing helix chain 'B' and resid 1840 through 1851 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 1979 removed outlier: 4.109A pdb=" N LEU B1937 " --> pdb=" O GLU B1933 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B1945 " --> pdb=" O ASN B1941 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B1946 " --> pdb=" O LEU B1942 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B1948 " --> pdb=" O GLU B1944 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU B1963 " --> pdb=" O ALA B1959 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG B1964 " --> pdb=" O ALA B1960 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B1966 " --> pdb=" O ALA B1962 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B1968 " --> pdb=" O ARG B1964 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B1978 " --> pdb=" O ARG B1974 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B1979 " --> pdb=" O SER B1975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1994 through 1999 removed outlier: 4.264A pdb=" N PHE B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) Processing helix chain 'B' and resid 2001 through 2014 removed outlier: 3.736A pdb=" N ILE B2006 " --> pdb=" O PRO B2002 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B2007 " --> pdb=" O GLN B2003 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS B2011 " --> pdb=" O ASN B2007 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE B2012 " --> pdb=" O MET B2008 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS B2013 " --> pdb=" O LEU B2009 " (cutoff:3.500A) Processing helix chain 'B' and resid 2028 through 2042 removed outlier: 3.711A pdb=" N LEU B2039 " --> pdb=" O HIS B2035 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2108 removed outlier: 3.934A pdb=" N VAL B2103 " --> pdb=" O SER B2099 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B2106 " --> pdb=" O VAL B2102 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2126 removed outlier: 3.875A pdb=" N VAL B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B2126 " --> pdb=" O SER B2122 " (cutoff:3.500A) Processing helix chain 'B' and resid 2129 through 2138 Processing helix chain 'B' and resid 2148 through 2165 removed outlier: 3.762A pdb=" N SER B2154 " --> pdb=" O GLU B2150 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS B2158 " --> pdb=" O SER B2154 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B2160 " --> pdb=" O LEU B2156 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B2161 " --> pdb=" O GLU B2157 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2186 removed outlier: 3.604A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) Processing helix chain 'B' and resid 2194 through 2201 removed outlier: 4.049A pdb=" N MET B2198 " --> pdb=" O HIS B2194 " (cutoff:3.500A) Processing helix chain 'B' and resid 2202 through 2216 removed outlier: 3.613A pdb=" N VAL B2207 " --> pdb=" O MET B2203 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B2213 " --> pdb=" O GLU B2209 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B2214 " --> pdb=" O VAL B2210 " (cutoff:3.500A) Processing helix chain 'B' and resid 2228 through 2242 removed outlier: 3.558A pdb=" N CYS B2237 " --> pdb=" O CYS B2233 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR B2238 " --> pdb=" O ARG B2234 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B2239 " --> pdb=" O PHE B2235 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2252 removed outlier: 3.732A pdb=" N ASP B2252 " --> pdb=" O ARG B2248 " (cutoff:3.500A) Processing helix chain 'B' and resid 2253 through 2262 removed outlier: 4.276A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY B2262 " --> pdb=" O LEU B2258 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2279 removed outlier: 3.514A pdb=" N SER B2279 " --> pdb=" O VAL B2275 " (cutoff:3.500A) Processing helix chain 'B' and resid 2294 through 2304 removed outlier: 3.677A pdb=" N VAL B2299 " --> pdb=" O LEU B2295 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B2300 " --> pdb=" O GLU B2296 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2315 removed outlier: 3.951A 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 2335 through 2339 removed outlier: 3.748A pdb=" N ALA B2338 " --> pdb=" O LEU B2335 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2358 removed outlier: 5.098A pdb=" N VAL B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL B2353 " --> pdb=" O ASN B2349 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B2356 " --> pdb=" O VAL B2352 " (cutoff:3.500A) Processing helix chain 'B' and resid 2359 through 2364 removed outlier: 6.565A pdb=" N GLU B2362 " --> pdb=" O ARG B2359 " (cutoff:3.500A) Processing helix chain 'B' and resid 2375 through 2389 removed outlier: 3.731A pdb=" N ILE B2380 " --> pdb=" O LEU B2376 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B2385 " --> pdb=" O GLU B2381 " (cutoff:3.500A) Processing helix chain 'B' and resid 2390 through 2393 Processing helix chain 'B' and resid 2417 through 2436 removed outlier: 4.407A pdb=" N ALA B2421 " --> pdb=" O HIS B2417 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET B2423 " --> pdb=" O GLY B2419 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B2433 " --> pdb=" O LEU B2429 " (cutoff:3.500A) Processing helix chain 'B' and resid 2448 through 2461 removed outlier: 3.563A pdb=" N ARG B2452 " --> pdb=" O GLY B2448 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE B2453 " --> pdb=" O GLU B2449 " (cutoff:3.500A) Processing helix chain 'B' and resid 2466 through 2471 Processing helix chain 'B' and resid 2502 through 2507 removed outlier: 4.004A pdb=" N UNK B2506 " --> pdb=" O UNK B2502 " (cutoff:3.500A) Processing helix chain 'B' and resid 2516 through 2530 removed outlier: 4.539A pdb=" N UNK B2523 " --> pdb=" O UNK B2519 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N UNK B2526 " --> pdb=" O UNK B2522 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N UNK B2527 " --> pdb=" O UNK B2523 " (cutoff:3.500A) Processing helix chain 'B' and resid 2543 through 2548 Processing helix chain 'B' and resid 2551 through 2557 removed outlier: 3.648A pdb=" N UNK B2555 " --> pdb=" O UNK B2551 " (cutoff:3.500A) Processing helix chain 'B' and resid 2566 through 2581 removed outlier: 4.188A pdb=" N UNK B2570 " --> pdb=" O UNK B2566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2587 through 2600 removed outlier: 3.518A pdb=" N UNK B2597 " --> pdb=" O UNK B2593 " (cutoff:3.500A) Processing helix chain 'B' and resid 2601 through 2604 removed outlier: 3.933A pdb=" N UNK B2604 " --> pdb=" O UNK B2601 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2601 through 2604' Processing helix chain 'B' and resid 2610 through 2618 removed outlier: 3.749A pdb=" N UNK B2617 " --> pdb=" O UNK B2613 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N UNK B2618 " --> pdb=" O UNK B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2628 through 2641 removed outlier: 3.519A pdb=" N UNK B2634 " --> pdb=" O UNK B2630 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N UNK B2635 " --> pdb=" O UNK B2631 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N UNK B2637 " --> pdb=" O UNK B2633 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N UNK B2639 " --> pdb=" O UNK B2635 " (cutoff:3.500A) Processing helix chain 'B' and resid 2651 through 2666 Processing helix chain 'B' and resid 2675 through 2680 removed outlier: 3.610A pdb=" N UNK B2680 " --> pdb=" O UNK B2676 " (cutoff:3.500A) Processing helix chain 'B' and resid 2683 through 2687 removed outlier: 3.998A pdb=" N UNK B2686 " --> pdb=" O UNK B2683 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N UNK B2687 " --> pdb=" O UNK B2684 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2683 through 2687' Processing helix chain 'B' and resid 2741 through 2745 removed outlier: 3.806A pdb=" N ASN B2744 " --> pdb=" O GLU B2741 " (cutoff:3.500A) Processing helix chain 'B' and resid 2748 through 2773 removed outlier: 4.241A pdb=" N SER B2753 " --> pdb=" O GLU B2749 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE B2754 " --> pdb=" O LYS B2750 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE B2768 " --> pdb=" O GLU B2764 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP B2769 " --> pdb=" O LYS B2765 " (cutoff:3.500A) Processing helix chain 'B' and resid 2793 through 2797 removed outlier: 3.941A pdb=" N THR B2796 " --> pdb=" O PRO B2793 " (cutoff:3.500A) Processing helix chain 'B' and resid 2800 through 2805 removed outlier: 4.173A pdb=" N ILE B2804 " --> pdb=" O LYS B2800 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR B2805 " --> pdb=" O ASP B2801 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2800 through 2805' Processing helix chain 'B' and resid 2809 through 2820 removed outlier: 3.723A pdb=" N ALA B2815 " --> pdb=" O GLU B2811 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2895 removed outlier: 4.366A pdb=" N MET B2874 " --> pdb=" O GLU B2870 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B2875 " --> pdb=" O LEU B2871 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B2880 " --> pdb=" O GLU B2876 " (cutoff:3.500A) removed outlier: 4.040A 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 2918 through 2932 removed outlier: 3.703A pdb=" N LEU B2926 " --> pdb=" O LYS B2922 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B2927 " --> pdb=" O ALA B2923 " (cutoff:3.500A) Processing helix chain 'B' and resid 2950 through 2976 removed outlier: 3.890A pdb=" N UNK B2956 " --> pdb=" O UNK B2952 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N UNK B2968 " --> pdb=" O UNK B2964 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N UNK B2969 " --> pdb=" O UNK B2965 " (cutoff:3.500A) Processing helix chain 'B' and resid 2999 through 3015 removed outlier: 3.665A pdb=" N UNK B3004 " --> pdb=" O UNK B3000 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N UNK B3006 " --> pdb=" O UNK B3002 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N UNK B3007 " --> pdb=" O UNK B3003 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N UNK B3009 " --> pdb=" O UNK B3005 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N UNK B3010 " --> pdb=" O UNK B3006 " (cutoff:3.500A) Processing helix chain 'B' and resid 3017 through 3022 Processing helix chain 'B' and resid 3025 through 3040 removed outlier: 4.026A pdb=" N UNK B3032 " --> pdb=" O UNK B3028 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N UNK B3040 " --> pdb=" O UNK B3036 " (cutoff:3.500A) Processing helix chain 'B' and resid 3050 through 3063 removed outlier: 4.038A pdb=" N UNK B3056 " --> pdb=" O UNK B3052 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N UNK B3060 " --> pdb=" O UNK B3056 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N UNK B3061 " --> pdb=" O UNK B3057 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N UNK B3062 " --> pdb=" O UNK B3058 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N UNK B3063 " --> pdb=" O UNK B3059 " (cutoff:3.500A) Processing helix chain 'B' and resid 3141 through 3146 Processing helix chain 'B' and resid 3146 through 3162 removed outlier: 3.812A pdb=" N UNK B3154 " --> pdb=" O UNK B3150 " (cutoff:3.500A) Processing helix chain 'B' and resid 3175 through 3187 Processing helix chain 'B' and resid 3198 through 3212 removed outlier: 3.689A pdb=" N UNK B3205 " --> pdb=" O UNK B3201 " (cutoff:3.500A) Processing helix chain 'B' and resid 3224 through 3230 removed outlier: 3.845A pdb=" N UNK B3228 " --> pdb=" O UNK B3224 " (cutoff:3.500A) Processing helix chain 'B' and resid 3244 through 3247 removed outlier: 3.737A pdb=" N UNK B3247 " --> pdb=" O UNK B3244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3244 through 3247' Processing helix chain 'B' and resid 3248 through 3254 removed outlier: 3.554A pdb=" N UNK B3252 " --> pdb=" O UNK B3248 " (cutoff:3.500A) Processing helix chain 'B' and resid 3271 through 3285 removed outlier: 3.946A pdb=" N UNK B3282 " --> pdb=" O UNK B3278 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N UNK B3284 " --> pdb=" O UNK B3280 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N UNK B3285 " --> pdb=" O UNK B3281 " (cutoff:3.500A) Processing helix chain 'B' and resid 3301 through 3304 Processing helix chain 'B' and resid 3305 through 3310 Processing helix chain 'B' and resid 3315 through 3331 removed outlier: 3.602A pdb=" N UNK B3319 " --> pdb=" O UNK B3315 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N UNK B3322 " --> pdb=" O UNK B3318 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N UNK B3323 " --> pdb=" O UNK B3319 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N UNK B3324 " --> pdb=" O UNK B3320 " (cutoff:3.500A) Processing helix chain 'B' and resid 3344 through 3349 removed outlier: 3.691A pdb=" N UNK B3348 " --> pdb=" O UNK B3344 " (cutoff:3.500A) Processing helix chain 'B' and resid 3350 through 3354 Processing helix chain 'B' and resid 3361 through 3388 Processing helix chain 'B' and resid 3400 through 3407 Processing helix chain 'B' and resid 3407 through 3413 removed outlier: 3.780A pdb=" N UNK B3413 " --> pdb=" O UNK B3409 " (cutoff:3.500A) Processing helix chain 'B' and resid 3414 through 3425 removed outlier: 4.292A pdb=" N UNK B3420 " --> pdb=" O UNK B3416 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N UNK B3421 " --> pdb=" O UNK B3417 " (cutoff:3.500A) Processing helix chain 'B' and resid 3425 through 3431 removed outlier: 3.578A pdb=" N UNK B3429 " --> pdb=" O UNK B3425 " (cutoff:3.500A) Processing helix chain 'B' and resid 3437 through 3443 Processing helix chain 'B' and resid 3445 through 3450 Processing helix chain 'B' and resid 3461 through 3468 Processing helix chain 'B' and resid 3522 through 3527 Processing helix chain 'B' and resid 3541 through 3546 Processing helix chain 'B' and resid 3551 through 3560 Processing helix chain 'B' and resid 3574 through 3583 removed outlier: 4.104A pdb=" N UNK B3580 " --> pdb=" O UNK B3576 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N UNK B3583 " --> pdb=" O UNK B3579 " (cutoff:3.500A) Processing helix chain 'B' and resid 3588 through 3608 removed outlier: 3.795A pdb=" N UNK B3592 " --> pdb=" O UNK B3588 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N UNK B3596 " --> pdb=" O UNK B3592 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N UNK B3598 " --> pdb=" O UNK B3594 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N UNK B3600 " --> pdb=" O UNK B3596 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N UNK B3601 " --> pdb=" O UNK B3597 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3656 Processing helix chain 'B' and resid 3671 through 3680 removed outlier: 3.573A pdb=" N ASP B3676 " --> pdb=" O ARG B3672 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU B3677 " --> pdb=" O MET B3673 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B3678 " --> pdb=" O ILE B3674 " (cutoff:3.500A) Processing helix chain 'B' and resid 3681 through 3687 removed outlier: 6.695A pdb=" N GLU B3684 " --> pdb=" O GLY B3681 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU B3685 " --> pdb=" O GLU B3682 " (cutoff:3.500A) Processing helix chain 'B' and resid 3696 through 3711 removed outlier: 3.551A pdb=" N LEU B3701 " --> pdb=" O PRO B3697 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B3711 " --> pdb=" O ARG B3707 " (cutoff:3.500A) Processing helix chain 'B' and resid 3719 through 3738 removed outlier: 3.612A pdb=" N TYR B3725 " --> pdb=" O LEU B3721 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS B3733 " --> pdb=" O MET B3729 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B3734 " --> pdb=" O ALA B3730 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU B3736 " --> pdb=" O SER B3732 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B3737 " --> pdb=" O CYS B3733 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3771 removed outlier: 3.871A pdb=" N LYS B3760 " --> pdb=" O LYS B3756 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B3765 " --> pdb=" O GLN B3761 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B3766 " --> pdb=" O ARG B3762 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLN B3767 " --> pdb=" O LEU B3763 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER B3768 " --> pdb=" O LEU B3764 " (cutoff:3.500A) Processing helix chain 'B' and resid 3774 through 3782 removed outlier: 4.030A pdb=" N MET B3778 " --> pdb=" O GLY B3774 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU B3780 " --> pdb=" O ALA B3776 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B3781 " --> pdb=" O GLU B3777 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3805 removed outlier: 3.839A pdb=" N LYS B3799 " --> pdb=" O SER B3795 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B3800 " --> pdb=" O SER B3796 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B3803 " --> pdb=" O LYS B3799 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B3805 " --> pdb=" O GLY B3801 " (cutoff:3.500A) Processing helix chain 'B' and resid 3809 through 3824 removed outlier: 3.550A pdb=" N LYS B3815 " --> pdb=" O GLU B3811 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B3824 " --> pdb=" O LEU B3820 " (cutoff:3.500A) Processing helix chain 'B' and resid 3829 through 3838 Processing helix chain 'B' and resid 3843 through 3854 removed outlier: 3.553A 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 3892 removed outlier: 3.543A pdb=" N PHE B3885 " --> pdb=" O THR B3881 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS B3892 " --> pdb=" O LEU B3888 " (cutoff:3.500A) Processing helix chain 'B' and resid 3898 through 3905 Processing helix chain 'B' and resid 3914 through 3937 removed outlier: 3.644A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B3933 " --> pdb=" O SER B3929 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR B3934 " --> pdb=" O ILE B3930 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP B3935 " --> pdb=" O SER B3931 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR B3936 " --> pdb=" O ASP B3932 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3967 removed outlier: 3.642A pdb=" N LYS B3953 " --> pdb=" O ARG B3949 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA B3954 " --> pdb=" O ASN B3950 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B3960 " --> pdb=" O SER B3956 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B3963 " --> pdb=" O LYS B3959 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3983 removed outlier: 3.617A pdb=" N HIS B3982 " --> pdb=" O GLN B3978 " (cutoff:3.500A) Processing helix chain 'B' and resid 3984 through 3996 removed outlier: 3.577A pdb=" N VAL B3990 " --> pdb=" O TRP B3986 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY B3991 " --> pdb=" O ASP B3987 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE B3992 " --> pdb=" O ALA B3988 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B3993 " --> pdb=" O VAL B3989 " (cutoff:3.500A) Processing helix chain 'B' and resid 3998 through 4003 Processing helix chain 'B' and resid 4009 through 4032 removed outlier: 3.521A pdb=" N ASP B4018 " --> pdb=" O LYS B4014 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET B4026 " --> pdb=" O ASP B4022 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU B4032 " --> pdb=" O LEU B4028 " (cutoff:3.500A) Processing helix chain 'B' and resid 4040 through 4051 Processing helix chain 'B' and resid 4051 through 4072 removed outlier: 4.058A pdb=" N PHE B4065 " --> pdb=" O PHE B4061 " (cutoff:3.500A) removed outlier: 3.565A 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) removed outlier: 3.619A pdb=" N VAL B4072 " --> pdb=" O LEU B4068 " (cutoff:3.500A) Processing helix chain 'B' and resid 4074 through 4081 removed outlier: 3.593A pdb=" N GLN B4078 " --> pdb=" O SER B4074 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR B4080 " --> pdb=" O ALA B4076 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL B4081 " --> pdb=" O PHE B4077 " (cutoff:3.500A) Processing helix chain 'B' and resid 4090 through 4100 removed outlier: 4.179A pdb=" N ASP B4098 " --> pdb=" O GLN B4094 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4115 Processing helix chain 'B' and resid 4124 through 4132 removed outlier: 4.098A pdb=" N PHE B4132 " --> pdb=" O PHE B4128 " (cutoff:3.500A) Processing helix chain 'B' and resid 4132 through 4154 removed outlier: 3.628A pdb=" N ALA B4136 " --> pdb=" O PHE B4132 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE B4139 " --> pdb=" O PRO B4135 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE B4141 " --> pdb=" O ARG B4137 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN B4142 " --> pdb=" O ASP B4138 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B4143 " --> pdb=" O ILE B4139 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B4145 " --> pdb=" O PHE B4141 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B4146 " --> pdb=" O ASN B4142 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B4151 " --> pdb=" O LEU B4147 " (cutoff:3.500A) Processing helix chain 'B' and resid 4157 through 4167 Processing helix chain 'B' and resid 4168 through 4175 removed outlier: 3.522A pdb=" N PHE B4174 " --> pdb=" O ILE B4170 " (cutoff:3.500A) Processing helix chain 'B' and resid 4199 through 4206 removed outlier: 3.614A pdb=" N ALA B4203 " --> pdb=" O GLU B4199 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B4204 " --> pdb=" O THR B4200 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B4206 " --> pdb=" O ARG B4202 " (cutoff:3.500A) Processing helix chain 'B' and resid 4207 through 4224 removed outlier: 3.972A pdb=" N SER B4213 " --> pdb=" O GLN B4209 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B4222 " --> pdb=" O ILE B4218 " (cutoff:3.500A) Processing helix chain 'B' and resid 4228 through 4252 removed outlier: 3.550A pdb=" N PHE B4234 " --> pdb=" O LYS B4230 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE B4243 " --> pdb=" O GLU B4239 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B4249 " --> pdb=" O MET B4245 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN B4250 " --> pdb=" O GLN B4246 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B4251 " --> pdb=" O ILE B4247 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B4252 " --> pdb=" O ALA B4248 " (cutoff:3.500A) Processing helix chain 'B' and resid 4321 through 4337 removed outlier: 3.625A pdb=" N UNK B4327 " --> pdb=" O UNK B4323 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N UNK B4332 " --> pdb=" O UNK B4328 " (cutoff:3.500A) Processing helix chain 'B' and resid 4542 through 4556 removed outlier: 3.550A pdb=" N VAL B4546 " --> pdb=" O GLY B4542 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR B4554 " --> pdb=" O LYS B4550 " (cutoff:3.500A) Processing helix chain 'B' and resid 4558 through 4576 removed outlier: 3.544A pdb=" N ALA B4566 " --> pdb=" O LEU B4562 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE B4571 " --> pdb=" O LEU B4567 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA B4572 " --> pdb=" O PHE B4568 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B4573 " --> pdb=" O LEU B4569 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B4574 " --> pdb=" O ALA B4570 " (cutoff:3.500A) Processing helix chain 'B' and resid 4577 through 4580 removed outlier: 3.873A pdb=" N TYR B4580 " --> pdb=" O LEU B4577 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4577 through 4580' Processing helix chain 'B' and resid 4643 through 4663 removed outlier: 3.690A pdb=" N LEU B4648 " --> pdb=" O TRP B4644 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B4649 " --> pdb=" O CYS B4645 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS B4657 " --> pdb=" O VAL B4653 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE B4658 " --> pdb=" O ALA B4654 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE B4659 " --> pdb=" O PHE B4655 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B4660 " --> pdb=" O LEU B4656 " (cutoff:3.500A) Processing helix chain 'B' and resid 4665 through 4683 removed outlier: 3.688A pdb=" N ALA B4678 " --> pdb=" O GLU B4674 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B4683 " --> pdb=" O ARG B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4696 through 4702 removed outlier: 3.981A pdb=" N GLN B4700 " --> pdb=" O ASP B4696 " (cutoff:3.500A) Processing helix chain 'B' and resid 4710 through 4714 removed outlier: 3.654A pdb=" N SER B4713 " --> pdb=" O SER B4710 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASN B4714 " --> pdb=" O PHE B4711 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4710 through 4714' Processing helix chain 'B' and resid 4719 through 4728 removed outlier: 3.579A pdb=" N LYS B4723 " --> pdb=" O PHE B4719 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B4725 " --> pdb=" O LYS B4721 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4741 Processing helix chain 'B' and resid 4751 through 4755 removed outlier: 4.083A pdb=" N GLU B4755 " --> pdb=" O ALA B4752 " (cutoff:3.500A) Processing helix chain 'B' and resid 4772 through 4785 Processing helix chain 'B' and resid 4786 through 4802 Processing helix chain 'B' and resid 4810 through 4813 Processing helix chain 'B' and resid 4814 through 4820 removed outlier: 3.600A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B4820 " --> pdb=" O ILE B4816 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.577A pdb=" N ILE B4826 " --> pdb=" O THR B4822 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B4831 " --> pdb=" O LEU B4827 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4858 removed outlier: 4.197A pdb=" N MET B4839 " --> pdb=" O LYS B4835 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B4840 " --> pdb=" O GLN B4836 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B4848 " --> pdb=" O LEU B4844 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B4854 " --> pdb=" O LEU B4850 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA B4855 " --> pdb=" O TYR B4851 " (cutoff:3.500A) Processing helix chain 'B' and resid 4859 through 4863 removed outlier: 4.059A pdb=" N TYR B4863 " --> pdb=" O ARG B4860 " (cutoff:3.500A) Processing helix chain 'B' and resid 4878 through 4890 removed outlier: 3.598A pdb=" N MET B4887 " --> pdb=" O TYR B4883 " (cutoff:3.500A) Processing helix chain 'B' and resid 4909 through 4925 removed outlier: 3.574A pdb=" N ARG B4913 " --> pdb=" O TYR B4909 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B4914 " --> pdb=" O GLU B4910 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B4918 " --> pdb=" O VAL B4914 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B4923 " --> pdb=" O THR B4919 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B4924 " --> pdb=" O PHE B4920 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B4925 " --> pdb=" O PHE B4921 " (cutoff:3.500A) Processing helix chain 'B' and resid 4927 through 4955 removed outlier: 3.668A pdb=" N ILE B4936 " --> pdb=" O ILE B4932 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B4948 " --> pdb=" O ARG B4944 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B4951 " --> pdb=" O GLN B4947 " (cutoff:3.500A) Processing helix chain 'B' and resid 4965 through 4971 removed outlier: 4.342A pdb=" N THR B4971 " --> pdb=" O TYR B4967 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4979 Processing helix chain 'B' and resid 4986 through 4997 removed outlier: 3.781A pdb=" N PHE B4990 " --> pdb=" O ALA B4986 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN B4997 " --> pdb=" O MET B4993 " (cutoff:3.500A) Processing helix chain 'B' and resid 5006 through 5017 Processing helix chain 'G' and resid 74 through 82 removed outlier: 3.505A pdb=" N GLN G 79 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 255 removed outlier: 3.794A pdb=" N THR G 254 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 369 removed outlier: 3.698A pdb=" N LEU G 369 " --> pdb=" O LYS G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 421 removed outlier: 3.932A pdb=" N GLN G 399 " --> pdb=" O GLN G 395 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG G 402 " --> pdb=" O SER G 398 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN G 413 " --> pdb=" O GLY G 409 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE G 414 " --> pdb=" O LEU G 410 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS G 416 " --> pdb=" O ASN G 412 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY G 417 " --> pdb=" O GLN G 413 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER G 420 " --> pdb=" O LYS G 416 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE G 421 " --> pdb=" O GLY G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 450 removed outlier: 3.651A pdb=" N GLY G 450 " --> pdb=" O GLN G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 477 removed outlier: 3.780A pdb=" N SER G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG G 474 " --> pdb=" O SER G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 494 Processing helix chain 'G' and resid 514 through 529 removed outlier: 3.573A pdb=" N ILE G 518 " --> pdb=" O SER G 514 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR G 523 " --> pdb=" O VAL G 519 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU G 529 " --> pdb=" O LEU G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 541 removed outlier: 3.705A pdb=" N PHE G 540 " --> pdb=" O CYS G 537 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER G 541 " --> pdb=" O ALA G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 543 through 551 removed outlier: 3.700A pdb=" N VAL G 548 " --> pdb=" O LEU G 544 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER G 549 " --> pdb=" O ASP G 545 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS G 550 " --> pdb=" O TRP G 546 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU G 551 " --> pdb=" O VAL G 547 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 568 removed outlier: 3.629A pdb=" N TYR G 565 " --> pdb=" O LEU G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 578 removed outlier: 3.507A pdb=" N ILE G 577 " --> pdb=" O VAL G 574 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE G 578 " --> pdb=" O LEU G 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 593 removed outlier: 3.606A pdb=" N LYS G 584 " --> pdb=" O GLU G 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 597 through 608 removed outlier: 3.555A pdb=" N LEU G 603 " --> pdb=" O VAL G 599 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS G 607 " --> pdb=" O LEU G 603 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL G 608 " --> pdb=" O CYS G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 625 removed outlier: 4.122A pdb=" N GLN G 618 " --> pdb=" O VAL G 614 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP G 619 " --> pdb=" O ARG G 615 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR G 622 " --> pdb=" O GLN G 618 " (cutoff:3.500A) Processing helix chain 'G' and resid 864 through 889 removed outlier: 3.672A pdb=" N ILE G 870 " --> pdb=" O HIS G 866 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU G 872 " --> pdb=" O GLU G 868 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS G 873 " --> pdb=" O ARG G 869 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG G 886 " --> pdb=" O TRP G 882 " (cutoff:3.500A) Processing helix chain 'G' and resid 914 through 934 removed outlier: 4.067A pdb=" N ASN G 919 " --> pdb=" O GLU G 915 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR G 920 " --> pdb=" O PRO G 916 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU G 927 " --> pdb=" O GLN G 923 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR G 928 " --> pdb=" O MET G 924 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA G 934 " --> pdb=" O LYS G 930 " (cutoff:3.500A) Processing helix chain 'G' and resid 980 through 1001 removed outlier: 4.057A pdb=" N LEU G 984 " --> pdb=" O ALA G 980 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP G 986 " --> pdb=" O THR G 982 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN G 991 " --> pdb=" O ARG G 987 " (cutoff:3.500A) Processing helix chain 'G' and resid 1028 through 1039 removed outlier: 3.691A pdb=" N LEU G1039 " --> pdb=" O ASN G1035 " (cutoff:3.500A) Processing helix chain 'G' and resid 1042 through 1049 removed outlier: 3.903A 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 1623 through 1627 Processing helix chain 'G' and resid 1652 through 1657 removed outlier: 3.500A pdb=" N LEU G1657 " --> pdb=" O LEU G1653 " (cutoff:3.500A) Processing helix chain 'G' and resid 1658 through 1674 removed outlier: 3.641A pdb=" N HIS G1665 " --> pdb=" O ARG G1661 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR G1670 " --> pdb=" O THR G1666 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG G1671 " --> pdb=" O LEU G1667 " (cutoff:3.500A) Processing helix chain 'G' and resid 1678 through 1686 removed outlier: 3.777A pdb=" N ALA G1684 " --> pdb=" O ARG G1680 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS G1686 " --> pdb=" O ALA G1682 " (cutoff:3.500A) Processing helix chain 'G' and resid 1692 through 1700 removed outlier: 4.128A pdb=" N LEU G1698 " --> pdb=" O LEU G1694 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU G1699 " --> pdb=" O LEU G1695 " (cutoff:3.500A) Processing helix chain 'G' and resid 1710 through 1712 No H-bonds generated for 'chain 'G' and resid 1710 through 1712' Processing helix chain 'G' and resid 1713 through 1720 Processing helix chain 'G' and resid 1720 through 1730 removed outlier: 4.390A pdb=" N SER G1726 " --> pdb=" O SER G1722 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET G1730 " --> pdb=" O SER G1726 " (cutoff:3.500A) Processing helix chain 'G' and resid 1739 through 1744 Processing helix chain 'G' and resid 1803 through 1823 removed outlier: 3.632A pdb=" N MET G1814 " --> pdb=" O LYS G1810 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G1815 " --> pdb=" O ALA G1811 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU G1817 " --> pdb=" O ARG G1813 " (cutoff:3.500A) Processing helix chain 'G' and resid 1833 through 1838 Processing helix chain 'G' and resid 1840 through 1851 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 1979 removed outlier: 4.108A pdb=" N LEU G1937 " --> pdb=" O GLU G1933 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN G1938 " --> pdb=" O SER G1934 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR G1945 " --> pdb=" O ASN G1941 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE G1946 " --> pdb=" O LEU G1942 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP G1948 " --> pdb=" O GLU G1944 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU G1963 " --> pdb=" O ALA G1959 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG G1964 " --> pdb=" O ALA G1960 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL G1966 " --> pdb=" O ALA G1962 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS G1968 " --> pdb=" O ARG G1964 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G1978 " --> pdb=" O ARG G1974 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU G1979 " --> pdb=" O SER G1975 " (cutoff:3.500A) Processing helix chain 'G' and resid 1994 through 1999 removed outlier: 4.264A pdb=" N PHE G1998 " --> pdb=" O ARG G1994 " (cutoff:3.500A) Processing helix chain 'G' and resid 2001 through 2014 removed outlier: 3.737A pdb=" N ILE G2006 " --> pdb=" O PRO G2002 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN G2007 " --> pdb=" O GLN G2003 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS G2011 " --> pdb=" O ASN G2007 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE G2012 " --> pdb=" O MET G2008 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS G2013 " --> pdb=" O LEU G2009 " (cutoff:3.500A) Processing helix chain 'G' and resid 2028 through 2042 removed outlier: 3.710A pdb=" N LEU G2039 " --> pdb=" O HIS G2035 " (cutoff:3.500A) Processing helix chain 'G' and resid 2093 through 2108 removed outlier: 3.934A pdb=" N VAL G2103 " --> pdb=" O SER G2099 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA G2106 " --> pdb=" O VAL G2102 " (cutoff:3.500A) Processing helix chain 'G' and resid 2113 through 2126 removed outlier: 3.875A pdb=" N VAL G2117 " --> pdb=" O SER G2113 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG G2126 " --> pdb=" O SER G2122 " (cutoff:3.500A) Processing helix chain 'G' and resid 2129 through 2138 Processing helix chain 'G' and resid 2148 through 2165 removed outlier: 3.762A pdb=" N SER G2154 " --> pdb=" O GLU G2150 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS G2158 " --> pdb=" O SER G2154 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY G2160 " --> pdb=" O LEU G2156 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN G2161 " --> pdb=" O GLU G2157 " (cutoff:3.500A) Processing helix chain 'G' and resid 2171 through 2186 removed outlier: 3.604A pdb=" N LEU G2177 " --> pdb=" O GLN G2173 " (cutoff:3.500A) Processing helix chain 'G' and resid 2194 through 2201 removed outlier: 4.049A pdb=" N MET G2198 " --> pdb=" O HIS G2194 " (cutoff:3.500A) Processing helix chain 'G' and resid 2202 through 2216 removed outlier: 3.613A pdb=" N VAL G2207 " --> pdb=" O MET G2203 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN G2213 " --> pdb=" O GLU G2209 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL G2214 " --> pdb=" O VAL G2210 " (cutoff:3.500A) Processing helix chain 'G' and resid 2228 through 2242 removed outlier: 3.557A pdb=" N CYS G2237 " --> pdb=" O CYS G2233 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR G2238 " --> pdb=" O ARG G2234 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE G2239 " --> pdb=" O PHE G2235 " (cutoff:3.500A) Processing helix chain 'G' and resid 2245 through 2252 removed outlier: 3.731A pdb=" N ASP G2252 " --> pdb=" O ARG G2248 " (cutoff:3.500A) Processing helix chain 'G' and resid 2253 through 2262 removed outlier: 4.276A pdb=" N ASN G2260 " --> pdb=" O TYR G2256 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY G2262 " --> pdb=" O LEU G2258 " (cutoff:3.500A) Processing helix chain 'G' and resid 2271 through 2279 removed outlier: 3.513A pdb=" N SER G2279 " --> pdb=" O VAL G2275 " (cutoff:3.500A) Processing helix chain 'G' and resid 2294 through 2304 removed outlier: 3.677A pdb=" N VAL G2299 " --> pdb=" O LEU G2295 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER G2300 " --> pdb=" O GLU G2296 " (cutoff:3.500A) Processing helix chain 'G' and resid 2310 through 2315 removed outlier: 3.951A 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 2335 through 2339 removed outlier: 3.748A pdb=" N ALA G2338 " --> pdb=" O LEU G2335 " (cutoff:3.500A) Processing helix chain 'G' and resid 2346 through 2358 removed outlier: 5.097A pdb=" N VAL G2352 " --> pdb=" O GLU G2348 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL G2353 " --> pdb=" O ASN G2349 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU G2356 " --> pdb=" O VAL G2352 " (cutoff:3.500A) Processing helix chain 'G' and resid 2359 through 2364 removed outlier: 6.565A pdb=" N GLU G2362 " --> pdb=" O ARG G2359 " (cutoff:3.500A) Processing helix chain 'G' and resid 2375 through 2389 removed outlier: 3.731A pdb=" N ILE G2380 " --> pdb=" O LEU G2376 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG G2385 " --> pdb=" O GLU G2381 " (cutoff:3.500A) Processing helix chain 'G' and resid 2390 through 2393 Processing helix chain 'G' and resid 2417 through 2436 removed outlier: 4.408A pdb=" N ALA G2421 " --> pdb=" O HIS G2417 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET G2423 " --> pdb=" O GLY G2419 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU G2433 " --> pdb=" O LEU G2429 " (cutoff:3.500A) Processing helix chain 'G' and resid 2448 through 2461 removed outlier: 3.563A pdb=" N ARG G2452 " --> pdb=" O GLY G2448 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE G2453 " --> pdb=" O GLU G2449 " (cutoff:3.500A) Processing helix chain 'G' and resid 2466 through 2471 Processing helix chain 'G' and resid 2502 through 2507 removed outlier: 4.019A pdb=" N UNK G2506 " --> pdb=" O UNK G2502 " (cutoff:3.500A) Processing helix chain 'G' and resid 2516 through 2530 removed outlier: 4.579A pdb=" N UNK G2523 " --> pdb=" O UNK G2519 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N UNK G2526 " --> pdb=" O UNK G2522 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N UNK G2527 " --> pdb=" O UNK G2523 " (cutoff:3.500A) Processing helix chain 'G' and resid 2543 through 2548 Processing helix chain 'G' and resid 2551 through 2557 removed outlier: 3.647A 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: 3.514A pdb=" N UNK G2597 " --> pdb=" O UNK G2593 " (cutoff:3.500A) Processing helix chain 'G' and resid 2601 through 2604 removed outlier: 3.935A pdb=" N UNK G2604 " --> pdb=" O UNK G2601 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2601 through 2604' Processing helix chain 'G' and resid 2610 through 2618 removed outlier: 3.742A pdb=" N UNK G2617 " --> pdb=" O UNK G2613 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N UNK G2618 " --> pdb=" O UNK G2614 " (cutoff:3.500A) Processing helix chain 'G' and resid 2628 through 2641 removed outlier: 3.514A pdb=" N UNK G2634 " --> pdb=" O UNK G2630 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N UNK G2635 " --> pdb=" O UNK G2631 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N UNK G2637 " --> pdb=" O UNK G2633 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N UNK G2639 " --> pdb=" O UNK G2635 " (cutoff:3.500A) Processing helix chain 'G' and resid 2651 through 2666 Processing helix chain 'G' and resid 2675 through 2680 removed outlier: 3.612A pdb=" N UNK G2680 " --> pdb=" O UNK G2676 " (cutoff:3.500A) Processing helix chain 'G' and resid 2741 through 2745 removed outlier: 3.806A pdb=" N ASN G2744 " --> pdb=" O GLU G2741 " (cutoff:3.500A) Processing helix chain 'G' and resid 2748 through 2773 removed outlier: 4.242A pdb=" N SER G2753 " --> pdb=" O GLU G2749 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE G2754 " --> pdb=" O LYS G2750 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE G2768 " --> pdb=" O GLU G2764 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP G2769 " --> pdb=" O LYS G2765 " (cutoff:3.500A) Processing helix chain 'G' and resid 2793 through 2797 removed outlier: 3.941A pdb=" N THR G2796 " --> pdb=" O PRO G2793 " (cutoff:3.500A) Processing helix chain 'G' and resid 2800 through 2805 removed outlier: 4.173A pdb=" N ILE G2804 " --> pdb=" O LYS G2800 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR G2805 " --> pdb=" O ASP G2801 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2800 through 2805' Processing helix chain 'G' and resid 2809 through 2820 removed outlier: 3.722A pdb=" N ALA G2815 " --> pdb=" O GLU G2811 " (cutoff:3.500A) Processing helix chain 'G' and resid 2868 through 2895 removed outlier: 4.366A pdb=" N MET G2874 " --> pdb=" O GLU G2870 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA G2875 " --> pdb=" O LEU G2871 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU G2880 " --> pdb=" O GLU G2876 " (cutoff:3.500A) removed outlier: 4.041A 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 2918 through 2932 removed outlier: 3.702A pdb=" N LEU G2926 " --> pdb=" O LYS G2922 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G2927 " --> pdb=" O ALA G2923 " (cutoff:3.500A) Processing helix chain 'G' and resid 2950 through 2976 removed outlier: 3.895A pdb=" N UNK G2956 " --> pdb=" O UNK G2952 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N UNK G2968 " --> pdb=" O UNK G2964 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N UNK G2969 " --> pdb=" O UNK G2965 " (cutoff:3.500A) Processing helix chain 'G' and resid 2999 through 3015 removed outlier: 3.671A pdb=" N UNK G3004 " --> pdb=" O UNK G3000 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N UNK G3006 " --> pdb=" O UNK G3002 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N UNK G3007 " --> pdb=" O UNK G3003 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N UNK G3009 " --> pdb=" O UNK G3005 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N UNK G3010 " --> pdb=" O UNK G3006 " (cutoff:3.500A) Processing helix chain 'G' and resid 3017 through 3022 Processing helix chain 'G' and resid 3025 through 3040 removed outlier: 4.024A pdb=" N UNK G3032 " --> pdb=" O UNK G3028 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N UNK G3040 " --> pdb=" O UNK G3036 " (cutoff:3.500A) Processing helix chain 'G' and resid 3050 through 3063 removed outlier: 4.030A pdb=" N UNK G3056 " --> pdb=" O UNK G3052 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N UNK G3060 " --> pdb=" O UNK G3056 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N UNK G3061 " --> pdb=" O UNK G3057 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N UNK G3062 " --> pdb=" O UNK G3058 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N UNK G3063 " --> pdb=" O UNK G3059 " (cutoff:3.500A) Processing helix chain 'G' and resid 3141 through 3146 Processing helix chain 'G' and resid 3146 through 3162 removed outlier: 3.813A pdb=" N UNK G3154 " --> pdb=" O UNK G3150 " (cutoff:3.500A) Processing helix chain 'G' and resid 3175 through 3187 Processing helix chain 'G' and resid 3198 through 3212 removed outlier: 3.686A pdb=" N UNK G3205 " --> pdb=" O UNK G3201 " (cutoff:3.500A) Processing helix chain 'G' and resid 3224 through 3230 removed outlier: 3.845A pdb=" N UNK G3228 " --> pdb=" O UNK G3224 " (cutoff:3.500A) Processing helix chain 'G' and resid 3248 through 3254 removed outlier: 3.556A pdb=" N UNK G3252 " --> pdb=" O UNK G3248 " (cutoff:3.500A) Processing helix chain 'G' and resid 3271 through 3285 removed outlier: 3.948A pdb=" N UNK G3282 " --> pdb=" O UNK G3278 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N UNK G3284 " --> pdb=" O UNK G3280 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N UNK G3285 " --> pdb=" O UNK G3281 " (cutoff:3.500A) Processing helix chain 'G' and resid 3301 through 3304 Processing helix chain 'G' and resid 3305 through 3310 Processing helix chain 'G' and resid 3315 through 3331 removed outlier: 3.602A pdb=" N UNK G3319 " --> pdb=" O UNK G3315 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N UNK G3322 " --> pdb=" O UNK G3318 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N UNK G3323 " --> pdb=" O UNK G3319 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N UNK G3324 " --> pdb=" O UNK G3320 " (cutoff:3.500A) Processing helix chain 'G' and resid 3344 through 3349 removed outlier: 3.700A pdb=" N UNK G3348 " --> pdb=" O UNK G3344 " (cutoff:3.500A) Processing helix chain 'G' and resid 3350 through 3354 Processing helix chain 'G' and resid 3361 through 3388 Processing helix chain 'G' and resid 3400 through 3407 Processing helix chain 'G' and resid 3407 through 3425 removed outlier: 3.772A pdb=" N UNK G3413 " --> pdb=" O UNK G3409 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N UNK G3416 " --> pdb=" O UNK G3412 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N UNK G3417 " --> pdb=" O UNK G3413 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N UNK G3420 " --> pdb=" O UNK G3416 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N UNK G3421 " --> pdb=" O UNK G3417 " (cutoff:3.500A) Processing helix chain 'G' and resid 3425 through 3431 removed outlier: 3.578A pdb=" N UNK G3429 " --> pdb=" O UNK G3425 " (cutoff:3.500A) Processing helix chain 'G' and resid 3437 through 3443 Processing helix chain 'G' and resid 3445 through 3450 Processing helix chain 'G' and resid 3461 through 3468 Processing helix chain 'G' and resid 3522 through 3527 Processing helix chain 'G' and resid 3541 through 3546 Processing helix chain 'G' and resid 3551 through 3560 Processing helix chain 'G' and resid 3574 through 3583 removed outlier: 4.095A pdb=" N UNK G3580 " --> pdb=" O UNK G3576 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N UNK G3583 " --> pdb=" O UNK G3579 " (cutoff:3.500A) Processing helix chain 'G' and resid 3588 through 3608 removed outlier: 3.799A pdb=" N UNK G3592 " --> pdb=" O UNK G3588 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N UNK G3596 " --> pdb=" O UNK G3592 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N UNK G3598 " --> pdb=" O UNK G3594 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N UNK G3600 " --> pdb=" O UNK G3596 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N UNK G3601 " --> pdb=" O UNK G3597 " (cutoff:3.500A) Processing helix chain 'G' and resid 3645 through 3656 Processing helix chain 'G' and resid 3671 through 3680 removed outlier: 3.573A pdb=" N ASP G3676 " --> pdb=" O ARG G3672 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU G3677 " --> pdb=" O MET G3673 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER G3678 " --> pdb=" O ILE G3674 " (cutoff:3.500A) Processing helix chain 'G' and resid 3681 through 3687 removed outlier: 6.694A pdb=" N GLU G3684 " --> pdb=" O GLY G3681 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU G3685 " --> pdb=" O GLU G3682 " (cutoff:3.500A) Processing helix chain 'G' and resid 3696 through 3711 removed outlier: 3.551A pdb=" N LEU G3701 " --> pdb=" O PRO G3697 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR G3711 " --> pdb=" O ARG G3707 " (cutoff:3.500A) Processing helix chain 'G' and resid 3719 through 3738 removed outlier: 3.611A pdb=" N TYR G3725 " --> pdb=" O LEU G3721 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS G3733 " --> pdb=" O MET G3729 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS G3734 " --> pdb=" O ALA G3730 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU G3736 " --> pdb=" O SER G3732 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU G3737 " --> pdb=" O CYS G3733 " (cutoff:3.500A) Processing helix chain 'G' and resid 3752 through 3771 removed outlier: 3.870A pdb=" N LYS G3760 " --> pdb=" O LYS G3756 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR G3765 " --> pdb=" O GLN G3761 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN G3766 " --> pdb=" O ARG G3762 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLN G3767 " --> pdb=" O LEU G3763 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER G3768 " --> pdb=" O LEU G3764 " (cutoff:3.500A) Processing helix chain 'G' and resid 3774 through 3782 removed outlier: 4.030A pdb=" N MET G3778 " --> pdb=" O GLY G3774 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU G3780 " --> pdb=" O ALA G3776 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN G3781 " --> pdb=" O GLU G3777 " (cutoff:3.500A) Processing helix chain 'G' and resid 3791 through 3805 removed outlier: 3.839A pdb=" N LYS G3799 " --> pdb=" O SER G3795 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU G3800 " --> pdb=" O SER G3796 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER G3803 " --> pdb=" O LYS G3799 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU G3805 " --> pdb=" O GLY G3801 " (cutoff:3.500A) Processing helix chain 'G' and resid 3809 through 3824 removed outlier: 3.550A pdb=" N LYS G3815 " --> pdb=" O GLU G3811 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS G3824 " --> pdb=" O LEU G3820 " (cutoff:3.500A) Processing helix chain 'G' and resid 3829 through 3838 Processing helix chain 'G' and resid 3843 through 3854 removed outlier: 3.554A 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 3892 removed outlier: 3.542A pdb=" N PHE G3885 " --> pdb=" O THR G3881 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS G3892 " --> pdb=" O LEU G3888 " (cutoff:3.500A) Processing helix chain 'G' and resid 3898 through 3905 Processing helix chain 'G' and resid 3914 through 3937 removed outlier: 3.644A pdb=" N CYS G3918 " --> pdb=" O ASN G3914 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE G3933 " --> pdb=" O SER G3929 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR G3934 " --> pdb=" O ILE G3930 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP G3935 " --> pdb=" O SER G3931 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR G3936 " --> pdb=" O ASP G3932 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR G3937 " --> pdb=" O PHE G3933 " (cutoff:3.500A) Processing helix chain 'G' and resid 3944 through 3967 removed outlier: 3.642A pdb=" N LYS G3953 " --> pdb=" O ARG G3949 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA G3954 " --> pdb=" O ASN G3950 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN G3960 " --> pdb=" O SER G3956 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN G3963 " --> pdb=" O LYS G3959 " (cutoff:3.500A) Processing helix chain 'G' and resid 3973 through 3983 removed outlier: 3.618A pdb=" N HIS G3982 " --> pdb=" O GLN G3978 " (cutoff:3.500A) Processing helix chain 'G' and resid 3984 through 3996 removed outlier: 3.577A pdb=" N VAL G3990 " --> pdb=" O TRP G3986 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY G3991 " --> pdb=" O ASP G3987 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N PHE G3992 " --> pdb=" O ALA G3988 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU G3993 " --> pdb=" O VAL G3989 " (cutoff:3.500A) Processing helix chain 'G' and resid 3998 through 4003 Processing helix chain 'G' and resid 4009 through 4032 removed outlier: 3.520A pdb=" N ASP G4018 " --> pdb=" O LYS G4014 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET G4026 " --> pdb=" O ASP G4022 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU G4031 " --> pdb=" O LEU G4027 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU G4032 " --> pdb=" O LEU G4028 " (cutoff:3.500A) Processing helix chain 'G' and resid 4040 through 4051 Processing helix chain 'G' and resid 4051 through 4072 removed outlier: 4.058A pdb=" N PHE G4065 " --> pdb=" O PHE G4061 " (cutoff:3.500A) removed outlier: 3.564A 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) removed outlier: 3.619A pdb=" N VAL G4072 " --> pdb=" O LEU G4068 " (cutoff:3.500A) Processing helix chain 'G' and resid 4074 through 4081 removed outlier: 3.592A pdb=" N GLN G4078 " --> pdb=" O SER G4074 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR G4080 " --> pdb=" O ALA G4076 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL G4081 " --> pdb=" O PHE G4077 " (cutoff:3.500A) Processing helix chain 'G' and resid 4090 through 4100 removed outlier: 4.179A pdb=" N ASP G4098 " --> pdb=" O GLN G4094 " (cutoff:3.500A) Processing helix chain 'G' and resid 4104 through 4115 Processing helix chain 'G' and resid 4124 through 4132 removed outlier: 4.098A pdb=" N PHE G4132 " --> pdb=" O PHE G4128 " (cutoff:3.500A) Processing helix chain 'G' and resid 4132 through 4154 removed outlier: 3.628A pdb=" N ALA G4136 " --> pdb=" O PHE G4132 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP G4138 " --> pdb=" O GLU G4134 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE G4139 " --> pdb=" O PRO G4135 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE G4141 " --> pdb=" O ARG G4137 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN G4142 " --> pdb=" O ASP G4138 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL G4143 " --> pdb=" O ILE G4139 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL G4145 " --> pdb=" O PHE G4141 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU G4146 " --> pdb=" O ASN G4142 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER G4151 " --> pdb=" O LEU G4147 " (cutoff:3.500A) Processing helix chain 'G' and resid 4157 through 4167 Processing helix chain 'G' and resid 4168 through 4175 removed outlier: 3.521A pdb=" N PHE G4174 " --> pdb=" O ILE G4170 " (cutoff:3.500A) Processing helix chain 'G' and resid 4199 through 4206 removed outlier: 3.614A pdb=" N ALA G4203 " --> pdb=" O GLU G4199 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN G4204 " --> pdb=" O THR G4200 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU G4206 " --> pdb=" O ARG G4202 " (cutoff:3.500A) Processing helix chain 'G' and resid 4207 through 4224 removed outlier: 3.972A pdb=" N SER G4213 " --> pdb=" O GLN G4209 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL G4222 " --> pdb=" O ILE G4218 " (cutoff:3.500A) Processing helix chain 'G' and resid 4228 through 4252 removed outlier: 3.549A pdb=" N PHE G4234 " --> pdb=" O LYS G4230 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE G4243 " --> pdb=" O GLU G4239 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA G4249 " --> pdb=" O MET G4245 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN G4250 " --> pdb=" O GLN G4246 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE G4251 " --> pdb=" O ILE G4247 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER G4252 " --> pdb=" O ALA G4248 " (cutoff:3.500A) Processing helix chain 'G' and resid 4321 through 4337 removed outlier: 3.622A pdb=" N UNK G4327 " --> pdb=" O UNK G4323 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N UNK G4332 " --> pdb=" O UNK G4328 " (cutoff:3.500A) Processing helix chain 'G' and resid 4542 through 4556 removed outlier: 3.549A pdb=" N VAL G4546 " --> pdb=" O GLY G4542 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR G4554 " --> pdb=" O LYS G4550 " (cutoff:3.500A) Processing helix chain 'G' and resid 4558 through 4576 removed outlier: 3.543A pdb=" N ALA G4566 " --> pdb=" O LEU G4562 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE G4571 " --> pdb=" O LEU G4567 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA G4572 " --> pdb=" O PHE G4568 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE G4573 " --> pdb=" O LEU G4569 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN G4574 " --> pdb=" O ALA G4570 " (cutoff:3.500A) Processing helix chain 'G' and resid 4577 through 4580 removed outlier: 3.874A pdb=" N TYR G4580 " --> pdb=" O LEU G4577 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4577 through 4580' Processing helix chain 'G' and resid 4643 through 4663 removed outlier: 3.690A pdb=" N LEU G4648 " --> pdb=" O TRP G4644 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU G4649 " --> pdb=" O CYS G4645 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS G4657 " --> pdb=" O VAL G4653 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE G4658 " --> pdb=" O ALA G4654 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE G4659 " --> pdb=" O PHE G4655 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY G4660 " --> pdb=" O LEU G4656 " (cutoff:3.500A) Processing helix chain 'G' and resid 4665 through 4683 removed outlier: 3.688A pdb=" N ALA G4678 " --> pdb=" O GLU G4674 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE G4683 " --> pdb=" O ARG G4679 " (cutoff:3.500A) Processing helix chain 'G' and resid 4696 through 4702 removed outlier: 3.981A pdb=" N GLN G4700 " --> pdb=" O ASP G4696 " (cutoff:3.500A) Processing helix chain 'G' and resid 4710 through 4714 removed outlier: 3.654A pdb=" N SER G4713 " --> pdb=" O SER G4710 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN G4714 " --> pdb=" O PHE G4711 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4710 through 4714' Processing helix chain 'G' and resid 4719 through 4728 removed outlier: 3.580A pdb=" N LYS G4723 " --> pdb=" O PHE G4719 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU G4725 " --> pdb=" O LYS G4721 " (cutoff:3.500A) Processing helix chain 'G' and resid 4733 through 4741 Processing helix chain 'G' and resid 4751 through 4755 removed outlier: 4.083A pdb=" N GLU G4755 " --> pdb=" O ALA G4752 " (cutoff:3.500A) Processing helix chain 'G' and resid 4772 through 4785 Processing helix chain 'G' and resid 4786 through 4802 Processing helix chain 'G' and resid 4810 through 4813 Processing helix chain 'G' and resid 4814 through 4820 removed outlier: 3.600A pdb=" N MET G4818 " --> pdb=" O LEU G4814 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL G4820 " --> pdb=" O ILE G4816 " (cutoff:3.500A) Processing helix chain 'G' and resid 4820 through 4833 removed outlier: 3.578A pdb=" N ILE G4826 " --> pdb=" O THR G4822 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR G4831 " --> pdb=" O LEU G4827 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN G4833 " --> pdb=" O SER G4829 " (cutoff:3.500A) Processing helix chain 'G' and resid 4833 through 4858 removed outlier: 4.197A pdb=" N MET G4839 " --> pdb=" O LYS G4835 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR G4840 " --> pdb=" O GLN G4836 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL G4848 " --> pdb=" O LEU G4844 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL G4854 " --> pdb=" O LEU G4850 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA G4855 " --> pdb=" O TYR G4851 " (cutoff:3.500A) Processing helix chain 'G' and resid 4859 through 4863 removed outlier: 4.059A pdb=" N TYR G4863 " --> pdb=" O ARG G4860 " (cutoff:3.500A) Processing helix chain 'G' and resid 4878 through 4890 removed outlier: 3.597A pdb=" N MET G4887 " --> pdb=" O TYR G4883 " (cutoff:3.500A) Processing helix chain 'G' and resid 4909 through 4925 removed outlier: 3.575A pdb=" N ARG G4913 " --> pdb=" O TYR G4909 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL G4914 " --> pdb=" O GLU G4910 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE G4918 " --> pdb=" O VAL G4914 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE G4923 " --> pdb=" O THR G4919 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL G4924 " --> pdb=" O PHE G4920 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE G4925 " --> pdb=" O PHE G4921 " (cutoff:3.500A) Processing helix chain 'G' and resid 4927 through 4955 removed outlier: 3.669A pdb=" N ILE G4936 " --> pdb=" O ILE G4932 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU G4948 " --> pdb=" O ARG G4944 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS G4951 " --> pdb=" O GLN G4947 " (cutoff:3.500A) Processing helix chain 'G' and resid 4965 through 4971 removed outlier: 4.342A pdb=" N THR G4971 " --> pdb=" O TYR G4967 " (cutoff:3.500A) Processing helix chain 'G' and resid 4973 through 4979 Processing helix chain 'G' and resid 4986 through 4997 removed outlier: 3.781A pdb=" N PHE G4990 " --> pdb=" O ALA G4986 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN G4997 " --> pdb=" O MET G4993 " (cutoff:3.500A) Processing helix chain 'G' and resid 5006 through 5017 Processing helix chain 'I' and resid 74 through 82 removed outlier: 3.505A pdb=" N GLN I 79 " --> pdb=" O VAL I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 255 removed outlier: 3.794A pdb=" N THR I 254 " --> pdb=" O ALA I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 369 removed outlier: 3.698A pdb=" N LEU I 369 " --> pdb=" O LYS I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 421 removed outlier: 3.932A pdb=" N GLN I 399 " --> pdb=" O GLN I 395 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG I 402 " --> pdb=" O SER I 398 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLN I 413 " --> pdb=" O GLY I 409 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE I 414 " --> pdb=" O LEU I 410 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS I 416 " --> pdb=" O ASN I 412 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY I 417 " --> pdb=" O GLN I 413 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER I 420 " --> pdb=" O LYS I 416 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE I 421 " --> pdb=" O GLY I 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 450 removed outlier: 3.651A pdb=" N GLY I 450 " --> pdb=" O GLN I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 460 through 477 removed outlier: 3.780A pdb=" N SER I 466 " --> pdb=" O GLU I 462 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG I 474 " --> pdb=" O SER I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 494 Processing helix chain 'I' and resid 514 through 529 removed outlier: 3.573A pdb=" N ILE I 518 " --> pdb=" O SER I 514 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR I 523 " --> pdb=" O VAL I 519 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU I 529 " --> pdb=" O LEU I 525 " (cutoff:3.500A) Processing helix chain 'I' and resid 536 through 541 removed outlier: 3.705A pdb=" N PHE I 540 " --> pdb=" O CYS I 537 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER I 541 " --> pdb=" O ALA I 538 " (cutoff:3.500A) Processing helix chain 'I' and resid 543 through 551 removed outlier: 3.701A pdb=" N VAL I 548 " --> pdb=" O LEU I 544 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER I 549 " --> pdb=" O ASP I 545 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS I 550 " --> pdb=" O TRP I 546 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU I 551 " --> pdb=" O VAL I 547 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 568 removed outlier: 3.628A pdb=" N TYR I 565 " --> pdb=" O LEU I 561 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 578 removed outlier: 3.507A pdb=" N ILE I 577 " --> pdb=" O VAL I 574 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE I 578 " --> pdb=" O LEU I 575 " (cutoff:3.500A) Processing helix chain 'I' and resid 580 through 593 removed outlier: 3.605A pdb=" N LYS I 584 " --> pdb=" O GLU I 580 " (cutoff:3.500A) Processing helix chain 'I' and resid 597 through 608 removed outlier: 3.555A pdb=" N LEU I 603 " --> pdb=" O VAL I 599 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS I 607 " --> pdb=" O LEU I 603 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL I 608 " --> pdb=" O CYS I 604 " (cutoff:3.500A) Processing helix chain 'I' and resid 614 through 625 removed outlier: 4.122A pdb=" N GLN I 618 " --> pdb=" O VAL I 614 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP I 619 " --> pdb=" O ARG I 615 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR I 622 " --> pdb=" O GLN I 618 " (cutoff:3.500A) Processing helix chain 'I' and resid 864 through 889 removed outlier: 3.671A pdb=" N ILE I 870 " --> pdb=" O HIS I 866 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU I 872 " --> pdb=" O GLU I 868 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS I 873 " --> pdb=" O ARG I 869 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG I 886 " --> pdb=" O TRP I 882 " (cutoff:3.500A) Processing helix chain 'I' and resid 914 through 934 removed outlier: 4.067A pdb=" N ASN I 919 " --> pdb=" O GLU I 915 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR I 920 " --> pdb=" O PRO I 916 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU I 927 " --> pdb=" O GLN I 923 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR I 928 " --> pdb=" O MET I 924 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA I 934 " --> pdb=" O LYS I 930 " (cutoff:3.500A) Processing helix chain 'I' and resid 980 through 1001 removed outlier: 4.058A pdb=" N LEU I 984 " --> pdb=" O ALA I 980 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP I 986 " --> pdb=" O THR I 982 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN I 991 " --> pdb=" O ARG I 987 " (cutoff:3.500A) Processing helix chain 'I' and resid 1028 through 1039 removed outlier: 3.692A pdb=" N LEU I1039 " --> pdb=" O ASN I1035 " (cutoff:3.500A) Processing helix chain 'I' and resid 1042 through 1049 removed outlier: 3.903A 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 1623 through 1627 Processing helix chain 'I' and resid 1652 through 1657 removed outlier: 3.501A pdb=" N LEU I1657 " --> pdb=" O LEU I1653 " (cutoff:3.500A) Processing helix chain 'I' and resid 1658 through 1674 removed outlier: 3.642A pdb=" N HIS I1665 " --> pdb=" O ARG I1661 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR I1670 " --> pdb=" O THR I1666 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG I1671 " --> pdb=" O LEU I1667 " (cutoff:3.500A) Processing helix chain 'I' and resid 1678 through 1686 removed outlier: 3.778A pdb=" N ALA I1684 " --> pdb=" O ARG I1680 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS I1686 " --> pdb=" O ALA I1682 " (cutoff:3.500A) Processing helix chain 'I' and resid 1692 through 1700 removed outlier: 4.128A pdb=" N LEU I1698 " --> pdb=" O LEU I1694 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU I1699 " --> pdb=" O LEU I1695 " (cutoff:3.500A) Processing helix chain 'I' and resid 1710 through 1712 No H-bonds generated for 'chain 'I' and resid 1710 through 1712' Processing helix chain 'I' and resid 1713 through 1720 Processing helix chain 'I' and resid 1720 through 1730 removed outlier: 4.389A pdb=" N SER I1726 " --> pdb=" O SER I1722 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET I1730 " --> pdb=" O SER I1726 " (cutoff:3.500A) Processing helix chain 'I' and resid 1739 through 1744 Processing helix chain 'I' and resid 1803 through 1823 removed outlier: 3.632A pdb=" N MET I1814 " --> pdb=" O LYS I1810 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU I1815 " --> pdb=" O ALA I1811 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU I1817 " --> pdb=" O ARG I1813 " (cutoff:3.500A) Processing helix chain 'I' and resid 1833 through 1838 Processing helix chain 'I' and resid 1840 through 1851 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 1979 removed outlier: 4.108A pdb=" N LEU I1937 " --> pdb=" O GLU I1933 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN I1938 " --> pdb=" O SER I1934 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR I1945 " --> pdb=" O ASN I1941 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE I1946 " --> pdb=" O LEU I1942 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP I1948 " --> pdb=" O GLU I1944 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU I1963 " --> pdb=" O ALA I1959 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG I1964 " --> pdb=" O ALA I1960 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL I1966 " --> pdb=" O ALA I1962 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS I1968 " --> pdb=" O ARG I1964 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA I1978 " --> pdb=" O ARG I1974 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU I1979 " --> pdb=" O SER I1975 " (cutoff:3.500A) Processing helix chain 'I' and resid 1994 through 1999 removed outlier: 4.264A pdb=" N PHE I1998 " --> pdb=" O ARG I1994 " (cutoff:3.500A) Processing helix chain 'I' and resid 2001 through 2014 removed outlier: 3.736A pdb=" N ILE I2006 " --> pdb=" O PRO I2002 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN I2007 " --> pdb=" O GLN I2003 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS I2011 " --> pdb=" O ASN I2007 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE I2012 " --> pdb=" O MET I2008 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS I2013 " --> pdb=" O LEU I2009 " (cutoff:3.500A) Processing helix chain 'I' and resid 2028 through 2042 removed outlier: 3.710A pdb=" N LEU I2039 " --> pdb=" O HIS I2035 " (cutoff:3.500A) Processing helix chain 'I' and resid 2093 through 2108 removed outlier: 3.934A pdb=" N VAL I2103 " --> pdb=" O SER I2099 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA I2106 " --> pdb=" O VAL I2102 " (cutoff:3.500A) Processing helix chain 'I' and resid 2113 through 2126 removed outlier: 3.875A pdb=" N VAL I2117 " --> pdb=" O SER I2113 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG I2126 " --> pdb=" O SER I2122 " (cutoff:3.500A) Processing helix chain 'I' and resid 2129 through 2138 Processing helix chain 'I' and resid 2148 through 2165 removed outlier: 3.762A pdb=" N SER I2154 " --> pdb=" O GLU I2150 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS I2158 " --> pdb=" O SER I2154 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY I2160 " --> pdb=" O LEU I2156 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN I2161 " --> pdb=" O GLU I2157 " (cutoff:3.500A) Processing helix chain 'I' and resid 2171 through 2186 removed outlier: 3.604A pdb=" N LEU I2177 " --> pdb=" O GLN I2173 " (cutoff:3.500A) Processing helix chain 'I' and resid 2194 through 2201 removed outlier: 4.049A pdb=" N MET I2198 " --> pdb=" O HIS I2194 " (cutoff:3.500A) Processing helix chain 'I' and resid 2202 through 2216 removed outlier: 3.613A pdb=" N VAL I2207 " --> pdb=" O MET I2203 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN I2213 " --> pdb=" O GLU I2209 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL I2214 " --> pdb=" O VAL I2210 " (cutoff:3.500A) Processing helix chain 'I' and resid 2228 through 2242 removed outlier: 3.558A pdb=" N CYS I2237 " --> pdb=" O CYS I2233 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR I2238 " --> pdb=" O ARG I2234 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE I2239 " --> pdb=" O PHE I2235 " (cutoff:3.500A) Processing helix chain 'I' and resid 2245 through 2252 removed outlier: 3.732A pdb=" N ASP I2252 " --> pdb=" O ARG I2248 " (cutoff:3.500A) Processing helix chain 'I' and resid 2253 through 2262 removed outlier: 4.276A pdb=" N ASN I2260 " --> pdb=" O TYR I2256 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY I2262 " --> pdb=" O LEU I2258 " (cutoff:3.500A) Processing helix chain 'I' and resid 2271 through 2279 removed outlier: 3.513A pdb=" N SER I2279 " --> pdb=" O VAL I2275 " (cutoff:3.500A) Processing helix chain 'I' and resid 2294 through 2304 removed outlier: 3.677A pdb=" N VAL I2299 " --> pdb=" O LEU I2295 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER I2300 " --> pdb=" O GLU I2296 " (cutoff:3.500A) Processing helix chain 'I' and resid 2310 through 2315 removed outlier: 3.951A 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 2335 through 2339 removed outlier: 3.748A pdb=" N ALA I2338 " --> pdb=" O LEU I2335 " (cutoff:3.500A) Processing helix chain 'I' and resid 2346 through 2358 removed outlier: 5.097A pdb=" N VAL I2352 " --> pdb=" O GLU I2348 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL I2353 " --> pdb=" O ASN I2349 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU I2356 " --> pdb=" O VAL I2352 " (cutoff:3.500A) Processing helix chain 'I' and resid 2359 through 2364 removed outlier: 6.563A pdb=" N GLU I2362 " --> pdb=" O ARG I2359 " (cutoff:3.500A) Processing helix chain 'I' and resid 2375 through 2389 removed outlier: 3.731A pdb=" N ILE I2380 " --> pdb=" O LEU I2376 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG I2385 " --> pdb=" O GLU I2381 " (cutoff:3.500A) Processing helix chain 'I' and resid 2390 through 2393 Processing helix chain 'I' and resid 2417 through 2436 removed outlier: 4.407A pdb=" N ALA I2421 " --> pdb=" O HIS I2417 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET I2423 " --> pdb=" O GLY I2419 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU I2433 " --> pdb=" O LEU I2429 " (cutoff:3.500A) Processing helix chain 'I' and resid 2448 through 2461 removed outlier: 3.563A pdb=" N ARG I2452 " --> pdb=" O GLY I2448 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE I2453 " --> pdb=" O GLU I2449 " (cutoff:3.500A) Processing helix chain 'I' and resid 2466 through 2471 Processing helix chain 'I' and resid 2502 through 2507 removed outlier: 3.985A pdb=" N UNK I2506 " --> pdb=" O UNK I2502 " (cutoff:3.500A) Processing helix chain 'I' and resid 2516 through 2530 removed outlier: 4.499A pdb=" N UNK I2523 " --> pdb=" O UNK I2519 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N UNK I2526 " --> pdb=" O UNK I2522 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N UNK I2527 " --> pdb=" O UNK I2523 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N UNK I2528 " --> pdb=" O UNK I2524 " (cutoff:3.500A) Processing helix chain 'I' and resid 2543 through 2548 Processing helix chain 'I' and resid 2551 through 2557 removed outlier: 3.652A pdb=" N UNK I2555 " --> pdb=" O UNK I2551 " (cutoff:3.500A) Processing helix chain 'I' and resid 2566 through 2581 removed outlier: 4.183A pdb=" N UNK I2570 " --> pdb=" O UNK I2566 " (cutoff:3.500A) Processing helix chain 'I' and resid 2587 through 2600 removed outlier: 3.519A pdb=" N UNK I2597 " --> pdb=" O UNK I2593 " (cutoff:3.500A) Processing helix chain 'I' and resid 2601 through 2604 removed outlier: 3.930A pdb=" N UNK I2604 " --> pdb=" O UNK I2601 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2601 through 2604' Processing helix chain 'I' and resid 2610 through 2618 removed outlier: 3.755A pdb=" N UNK I2617 " --> pdb=" O UNK I2613 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N UNK I2618 " --> pdb=" O UNK I2614 " (cutoff:3.500A) Processing helix chain 'I' and resid 2628 through 2640 removed outlier: 3.524A pdb=" N UNK I2634 " --> pdb=" O UNK I2630 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N UNK I2635 " --> pdb=" O UNK I2631 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N UNK I2637 " --> pdb=" O UNK I2633 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N UNK I2639 " --> pdb=" O UNK I2635 " (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 2651 through 2666 Processing helix chain 'I' and resid 2675 through 2680 removed outlier: 3.611A pdb=" N UNK I2680 " --> pdb=" O UNK I2676 " (cutoff:3.500A) Processing helix chain 'I' and resid 2683 through 2687 removed outlier: 3.986A pdb=" N UNK I2686 " --> pdb=" O UNK I2683 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N UNK I2687 " --> pdb=" O UNK I2684 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2683 through 2687' Processing helix chain 'I' and resid 2741 through 2745 removed outlier: 3.807A pdb=" N ASN I2744 " --> pdb=" O GLU I2741 " (cutoff:3.500A) Processing helix chain 'I' and resid 2748 through 2773 removed outlier: 4.241A pdb=" N SER I2753 " --> pdb=" O GLU I2749 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE I2754 " --> pdb=" O LYS I2750 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE I2768 " --> pdb=" O GLU I2764 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP I2769 " --> pdb=" O LYS I2765 " (cutoff:3.500A) Processing helix chain 'I' and resid 2793 through 2797 removed outlier: 3.941A pdb=" N THR I2796 " --> pdb=" O PRO I2793 " (cutoff:3.500A) Processing helix chain 'I' and resid 2800 through 2805 removed outlier: 4.172A pdb=" N ILE I2804 " --> pdb=" O LYS I2800 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR I2805 " --> pdb=" O ASP I2801 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2800 through 2805' Processing helix chain 'I' and resid 2809 through 2820 removed outlier: 3.723A pdb=" N ALA I2815 " --> pdb=" O GLU I2811 " (cutoff:3.500A) Processing helix chain 'I' and resid 2868 through 2895 removed outlier: 4.367A pdb=" N MET I2874 " --> pdb=" O GLU I2870 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA I2875 " --> pdb=" O LEU I2871 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU I2880 " --> pdb=" O GLU I2876 " (cutoff:3.500A) removed outlier: 4.040A 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 2918 through 2932 removed outlier: 3.703A pdb=" N LEU I2926 " --> pdb=" O LYS I2922 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU I2927 " --> pdb=" O ALA I2923 " (cutoff:3.500A) Processing helix chain 'I' and resid 2950 through 2976 removed outlier: 3.886A pdb=" N UNK I2956 " --> pdb=" O UNK I2952 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N UNK I2968 " --> pdb=" O UNK I2964 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N UNK I2969 " --> pdb=" O UNK I2965 " (cutoff:3.500A) Processing helix chain 'I' and resid 2999 through 3015 removed outlier: 3.659A pdb=" N UNK I3004 " --> pdb=" O UNK I3000 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N UNK I3006 " --> pdb=" O UNK I3002 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N UNK I3007 " --> pdb=" O UNK I3003 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N UNK I3009 " --> pdb=" O UNK I3005 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N UNK I3010 " --> pdb=" O UNK I3006 " (cutoff:3.500A) Processing helix chain 'I' and resid 3017 through 3022 Processing helix chain 'I' and resid 3025 through 3040 removed outlier: 4.026A pdb=" N UNK I3032 " --> pdb=" O UNK I3028 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N UNK I3040 " --> pdb=" O UNK I3036 " (cutoff:3.500A) Processing helix chain 'I' and resid 3050 through 3063 removed outlier: 4.044A pdb=" N UNK I3056 " --> pdb=" O UNK I3052 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N UNK I3060 " --> pdb=" O UNK I3056 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N UNK I3061 " --> pdb=" O UNK I3057 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N UNK I3062 " --> pdb=" O UNK I3058 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N UNK I3063 " --> pdb=" O UNK I3059 " (cutoff:3.500A) Processing helix chain 'I' and resid 3141 through 3146 Processing helix chain 'I' and resid 3146 through 3162 removed outlier: 3.813A pdb=" N UNK I3154 " --> pdb=" O UNK I3150 " (cutoff:3.500A) Processing helix chain 'I' and resid 3175 through 3187 Processing helix chain 'I' and resid 3198 through 3212 removed outlier: 3.691A pdb=" N UNK I3205 " --> pdb=" O UNK I3201 " (cutoff:3.500A) Processing helix chain 'I' and resid 3224 through 3230 removed outlier: 3.844A pdb=" N UNK I3228 " --> pdb=" O UNK I3224 " (cutoff:3.500A) Processing helix chain 'I' and resid 3244 through 3247 removed outlier: 3.732A pdb=" N UNK I3247 " --> pdb=" O UNK I3244 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3244 through 3247' Processing helix chain 'I' and resid 3248 through 3254 removed outlier: 3.555A pdb=" N UNK I3252 " --> pdb=" O UNK I3248 " (cutoff:3.500A) Processing helix chain 'I' and resid 3271 through 3285 removed outlier: 3.946A pdb=" N UNK I3282 " --> pdb=" O UNK I3278 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N UNK I3284 " --> pdb=" O UNK I3280 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N UNK I3285 " --> pdb=" O UNK I3281 " (cutoff:3.500A) Processing helix chain 'I' and resid 3301 through 3304 Processing helix chain 'I' and resid 3305 through 3310 Processing helix chain 'I' and resid 3315 through 3331 removed outlier: 3.603A pdb=" N UNK I3319 " --> pdb=" O UNK I3315 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N UNK I3322 " --> pdb=" O UNK I3318 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N UNK I3323 " --> pdb=" O UNK I3319 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N UNK I3324 " --> pdb=" O UNK I3320 " (cutoff:3.500A) Processing helix chain 'I' and resid 3344 through 3349 removed outlier: 3.681A pdb=" N UNK I3348 " --> pdb=" O UNK I3344 " (cutoff:3.500A) Processing helix chain 'I' and resid 3350 through 3354 Processing helix chain 'I' and resid 3361 through 3388 Processing helix chain 'I' and resid 3400 through 3407 Processing helix chain 'I' and resid 3407 through 3413 removed outlier: 3.788A pdb=" N UNK I3413 " --> pdb=" O UNK I3409 " (cutoff:3.500A) Processing helix chain 'I' and resid 3414 through 3425 removed outlier: 4.293A pdb=" N UNK I3420 " --> pdb=" O UNK I3416 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N UNK I3421 " --> pdb=" O UNK I3417 " (cutoff:3.500A) Processing helix chain 'I' and resid 3425 through 3431 removed outlier: 3.577A pdb=" N UNK I3429 " --> pdb=" O UNK I3425 " (cutoff:3.500A) Processing helix chain 'I' and resid 3437 through 3443 Processing helix chain 'I' and resid 3445 through 3450 Processing helix chain 'I' and resid 3461 through 3468 Processing helix chain 'I' and resid 3522 through 3527 Processing helix chain 'I' and resid 3541 through 3546 Processing helix chain 'I' and resid 3551 through 3560 Processing helix chain 'I' and resid 3574 through 3583 removed outlier: 4.109A pdb=" N UNK I3580 " --> pdb=" O UNK I3576 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N UNK I3583 " --> pdb=" O UNK I3579 " (cutoff:3.500A) Processing helix chain 'I' and resid 3588 through 3608 removed outlier: 3.791A pdb=" N UNK I3592 " --> pdb=" O UNK I3588 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N UNK I3596 " --> pdb=" O UNK I3592 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N UNK I3598 " --> pdb=" O UNK I3594 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N UNK I3600 " --> pdb=" O UNK I3596 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N UNK I3601 " --> pdb=" O UNK I3597 " (cutoff:3.500A) Processing helix chain 'I' and resid 3645 through 3656 Processing helix chain 'I' and resid 3671 through 3680 removed outlier: 3.573A pdb=" N ASP I3676 " --> pdb=" O ARG I3672 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU I3677 " --> pdb=" O MET I3673 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER I3678 " --> pdb=" O ILE I3674 " (cutoff:3.500A) Processing helix chain 'I' and resid 3681 through 3687 removed outlier: 6.695A pdb=" N GLU I3684 " --> pdb=" O GLY I3681 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU I3685 " --> pdb=" O GLU I3682 " (cutoff:3.500A) Processing helix chain 'I' and resid 3696 through 3711 removed outlier: 3.550A pdb=" N LEU I3701 " --> pdb=" O PRO I3697 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR I3711 " --> pdb=" O ARG I3707 " (cutoff:3.500A) Processing helix chain 'I' and resid 3719 through 3738 removed outlier: 3.611A pdb=" N TYR I3725 " --> pdb=" O LEU I3721 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS I3733 " --> pdb=" O MET I3729 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS I3734 " --> pdb=" O ALA I3730 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU I3736 " --> pdb=" O SER I3732 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU I3737 " --> pdb=" O CYS I3733 " (cutoff:3.500A) Processing helix chain 'I' and resid 3752 through 3771 removed outlier: 3.871A pdb=" N LYS I3760 " --> pdb=" O LYS I3756 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR I3765 " --> pdb=" O GLN I3761 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN I3766 " --> pdb=" O ARG I3762 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN I3767 " --> pdb=" O LEU I3763 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER I3768 " --> pdb=" O LEU I3764 " (cutoff:3.500A) Processing helix chain 'I' and resid 3774 through 3782 removed outlier: 4.030A pdb=" N MET I3778 " --> pdb=" O GLY I3774 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU I3780 " --> pdb=" O ALA I3776 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN I3781 " --> pdb=" O GLU I3777 " (cutoff:3.500A) Processing helix chain 'I' and resid 3791 through 3805 removed outlier: 3.840A pdb=" N LYS I3799 " --> pdb=" O SER I3795 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU I3800 " --> pdb=" O SER I3796 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER I3803 " --> pdb=" O LYS I3799 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU I3805 " --> pdb=" O GLY I3801 " (cutoff:3.500A) Processing helix chain 'I' and resid 3809 through 3824 removed outlier: 3.550A pdb=" N LYS I3815 " --> pdb=" O GLU I3811 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS I3824 " --> pdb=" O LEU I3820 " (cutoff:3.500A) Processing helix chain 'I' and resid 3829 through 3838 Processing helix chain 'I' and resid 3843 through 3854 removed outlier: 3.554A 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 3892 removed outlier: 3.543A pdb=" N PHE I3885 " --> pdb=" O THR I3881 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS I3892 " --> pdb=" O LEU I3888 " (cutoff:3.500A) Processing helix chain 'I' and resid 3898 through 3905 Processing helix chain 'I' and resid 3914 through 3937 removed outlier: 3.644A pdb=" N CYS I3918 " --> pdb=" O ASN I3914 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE I3933 " --> pdb=" O SER I3929 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR I3934 " --> pdb=" O ILE I3930 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP I3935 " --> pdb=" O SER I3931 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR I3936 " --> pdb=" O ASP I3932 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR I3937 " --> pdb=" O PHE I3933 " (cutoff:3.500A) Processing helix chain 'I' and resid 3944 through 3967 removed outlier: 3.642A pdb=" N LYS I3953 " --> pdb=" O ARG I3949 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA I3954 " --> pdb=" O ASN I3950 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN I3960 " --> pdb=" O SER I3956 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN I3963 " --> pdb=" O LYS I3959 " (cutoff:3.500A) Processing helix chain 'I' and resid 3973 through 3983 removed outlier: 3.618A pdb=" N HIS I3982 " --> pdb=" O GLN I3978 " (cutoff:3.500A) Processing helix chain 'I' and resid 3984 through 3996 removed outlier: 3.578A pdb=" N VAL I3990 " --> pdb=" O TRP I3986 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY I3991 " --> pdb=" O ASP I3987 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE I3992 " --> pdb=" O ALA I3988 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU I3993 " --> pdb=" O VAL I3989 " (cutoff:3.500A) Processing helix chain 'I' and resid 3998 through 4003 Processing helix chain 'I' and resid 4009 through 4032 removed outlier: 3.520A pdb=" N ASP I4018 " --> pdb=" O LYS I4014 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET I4026 " --> pdb=" O ASP I4022 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU I4031 " --> pdb=" O LEU I4027 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU I4032 " --> pdb=" O LEU I4028 " (cutoff:3.500A) Processing helix chain 'I' and resid 4040 through 4051 Processing helix chain 'I' and resid 4051 through 4072 removed outlier: 4.058A pdb=" N PHE I4065 " --> pdb=" O PHE I4061 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS I4069 " --> pdb=" O PHE I4065 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP I4070 " --> pdb=" O LEU I4066 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL I4072 " --> pdb=" O LEU I4068 " (cutoff:3.500A) Processing helix chain 'I' and resid 4074 through 4081 removed outlier: 3.593A pdb=" N GLN I4078 " --> pdb=" O SER I4074 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR I4080 " --> pdb=" O ALA I4076 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL I4081 " --> pdb=" O PHE I4077 " (cutoff:3.500A) Processing helix chain 'I' and resid 4090 through 4100 removed outlier: 4.179A pdb=" N ASP I4098 " --> pdb=" O GLN I4094 " (cutoff:3.500A) Processing helix chain 'I' and resid 4104 through 4115 Processing helix chain 'I' and resid 4124 through 4132 removed outlier: 4.098A pdb=" N PHE I4132 " --> pdb=" O PHE I4128 " (cutoff:3.500A) Processing helix chain 'I' and resid 4132 through 4154 removed outlier: 3.628A pdb=" N ALA I4136 " --> pdb=" O PHE I4132 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP I4138 " --> pdb=" O GLU I4134 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE I4139 " --> pdb=" O PRO I4135 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE I4141 " --> pdb=" O ARG I4137 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN I4142 " --> pdb=" O ASP I4138 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL I4143 " --> pdb=" O ILE I4139 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL I4145 " --> pdb=" O PHE I4141 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU I4146 " --> pdb=" O ASN I4142 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I4151 " --> pdb=" O LEU I4147 " (cutoff:3.500A) Processing helix chain 'I' and resid 4157 through 4167 Processing helix chain 'I' and resid 4168 through 4175 removed outlier: 3.521A pdb=" N PHE I4174 " --> pdb=" O ILE I4170 " (cutoff:3.500A) Processing helix chain 'I' and resid 4199 through 4206 removed outlier: 3.613A pdb=" N ALA I4203 " --> pdb=" O GLU I4199 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN I4204 " --> pdb=" O THR I4200 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU I4206 " --> pdb=" O ARG I4202 " (cutoff:3.500A) Processing helix chain 'I' and resid 4207 through 4224 removed outlier: 3.972A pdb=" N SER I4213 " --> pdb=" O GLN I4209 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL I4222 " --> pdb=" O ILE I4218 " (cutoff:3.500A) Processing helix chain 'I' and resid 4228 through 4252 removed outlier: 3.550A pdb=" N PHE I4234 " --> pdb=" O LYS I4230 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE I4243 " --> pdb=" O GLU I4239 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA I4249 " --> pdb=" O MET I4245 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN I4250 " --> pdb=" O GLN I4246 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE I4251 " --> pdb=" O ILE I4247 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER I4252 " --> pdb=" O ALA I4248 " (cutoff:3.500A) Processing helix chain 'I' and resid 4321 through 4337 removed outlier: 3.625A pdb=" N UNK I4327 " --> pdb=" O UNK I4323 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N UNK I4332 " --> pdb=" O UNK I4328 " (cutoff:3.500A) Processing helix chain 'I' and resid 4542 through 4556 removed outlier: 3.550A pdb=" N VAL I4546 " --> pdb=" O GLY I4542 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR I4554 " --> pdb=" O LYS I4550 " (cutoff:3.500A) Processing helix chain 'I' and resid 4558 through 4576 removed outlier: 3.543A pdb=" N ALA I4566 " --> pdb=" O LEU I4562 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE I4571 " --> pdb=" O LEU I4567 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA I4572 " --> pdb=" O PHE I4568 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE I4573 " --> pdb=" O LEU I4569 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN I4574 " --> pdb=" O ALA I4570 " (cutoff:3.500A) Processing helix chain 'I' and resid 4577 through 4580 removed outlier: 3.874A pdb=" N TYR I4580 " --> pdb=" O LEU I4577 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4577 through 4580' Processing helix chain 'I' and resid 4643 through 4663 removed outlier: 3.691A pdb=" N LEU I4648 " --> pdb=" O TRP I4644 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU I4649 " --> pdb=" O CYS I4645 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS I4657 " --> pdb=" O VAL I4653 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE I4658 " --> pdb=" O ALA I4654 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE I4659 " --> pdb=" O PHE I4655 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY I4660 " --> pdb=" O LEU I4656 " (cutoff:3.500A) Processing helix chain 'I' and resid 4665 through 4683 removed outlier: 3.688A pdb=" N ALA I4678 " --> pdb=" O GLU I4674 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE I4683 " --> pdb=" O ARG I4679 " (cutoff:3.500A) Processing helix chain 'I' and resid 4696 through 4702 removed outlier: 3.981A pdb=" N GLN I4700 " --> pdb=" O ASP I4696 " (cutoff:3.500A) Processing helix chain 'I' and resid 4710 through 4714 removed outlier: 3.654A pdb=" N SER I4713 " --> pdb=" O SER I4710 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN I4714 " --> pdb=" O PHE I4711 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4710 through 4714' Processing helix chain 'I' and resid 4719 through 4728 removed outlier: 3.578A pdb=" N LYS I4723 " --> pdb=" O PHE I4719 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU I4725 " --> pdb=" O LYS I4721 " (cutoff:3.500A) Processing helix chain 'I' and resid 4733 through 4741 Processing helix chain 'I' and resid 4751 through 4755 removed outlier: 4.082A pdb=" N GLU I4755 " --> pdb=" O ALA I4752 " (cutoff:3.500A) Processing helix chain 'I' and resid 4772 through 4785 Processing helix chain 'I' and resid 4786 through 4802 Processing helix chain 'I' and resid 4810 through 4813 Processing helix chain 'I' and resid 4814 through 4820 removed outlier: 3.600A pdb=" N MET I4818 " --> pdb=" O LEU I4814 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL I4820 " --> pdb=" O ILE I4816 " (cutoff:3.500A) Processing helix chain 'I' and resid 4820 through 4833 removed outlier: 3.577A pdb=" N ILE I4826 " --> pdb=" O THR I4822 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR I4831 " --> pdb=" O LEU I4827 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN I4833 " --> pdb=" O SER I4829 " (cutoff:3.500A) Processing helix chain 'I' and resid 4833 through 4858 removed outlier: 4.197A pdb=" N MET I4839 " --> pdb=" O LYS I4835 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR I4840 " --> pdb=" O GLN I4836 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL I4848 " --> pdb=" O LEU I4844 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL I4854 " --> pdb=" O LEU I4850 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA I4855 " --> pdb=" O TYR I4851 " (cutoff:3.500A) Processing helix chain 'I' and resid 4859 through 4863 removed outlier: 4.059A pdb=" N TYR I4863 " --> pdb=" O ARG I4860 " (cutoff:3.500A) Processing helix chain 'I' and resid 4878 through 4890 removed outlier: 3.598A pdb=" N MET I4887 " --> pdb=" O TYR I4883 " (cutoff:3.500A) Processing helix chain 'I' and resid 4909 through 4925 removed outlier: 3.574A pdb=" N ARG I4913 " --> pdb=" O TYR I4909 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL I4914 " --> pdb=" O GLU I4910 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE I4918 " --> pdb=" O VAL I4914 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE I4923 " --> pdb=" O THR I4919 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL I4924 " --> pdb=" O PHE I4920 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE I4925 " --> pdb=" O PHE I4921 " (cutoff:3.500A) Processing helix chain 'I' and resid 4927 through 4955 removed outlier: 3.669A pdb=" N ILE I4936 " --> pdb=" O ILE I4932 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU I4948 " --> pdb=" O ARG I4944 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS I4951 " --> pdb=" O GLN I4947 " (cutoff:3.500A) Processing helix chain 'I' and resid 4965 through 4971 removed outlier: 4.342A pdb=" N THR I4971 " --> pdb=" O TYR I4967 " (cutoff:3.500A) Processing helix chain 'I' and resid 4973 through 4979 Processing helix chain 'I' and resid 4986 through 4997 removed outlier: 3.782A pdb=" N PHE I4990 " --> pdb=" O ALA I4986 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN I4997 " --> pdb=" O MET I4993 " (cutoff:3.500A) Processing helix chain 'I' and resid 5006 through 5017 Processing helix chain 'E' and resid 74 through 82 removed outlier: 3.505A pdb=" N GLN E 79 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 255 removed outlier: 3.794A pdb=" N THR E 254 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 369 removed outlier: 3.698A pdb=" N LEU E 369 " --> pdb=" O LYS E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 421 removed outlier: 3.932A pdb=" N GLN E 399 " --> pdb=" O GLN E 395 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLN E 413 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE E 414 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS E 416 " --> pdb=" O ASN E 412 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY E 417 " --> pdb=" O GLN E 413 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER E 420 " --> pdb=" O LYS E 416 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 450 removed outlier: 3.651A pdb=" N GLY E 450 " --> pdb=" O GLN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 477 removed outlier: 3.781A pdb=" N SER E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG E 474 " --> pdb=" O SER E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 514 through 529 removed outlier: 3.574A pdb=" N ILE E 518 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR E 523 " --> pdb=" O VAL E 519 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU E 529 " --> pdb=" O LEU E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 541 removed outlier: 3.705A pdb=" N PHE E 540 " --> pdb=" O CYS E 537 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER E 541 " --> pdb=" O ALA E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 551 removed outlier: 3.700A pdb=" N VAL E 548 " --> pdb=" O LEU E 544 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS E 550 " --> pdb=" O TRP E 546 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU E 551 " --> pdb=" O VAL E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 568 removed outlier: 3.629A pdb=" N TYR E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 578 removed outlier: 3.507A pdb=" N ILE E 577 " --> pdb=" O VAL E 574 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE E 578 " --> pdb=" O LEU E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 593 removed outlier: 3.606A pdb=" N LYS E 584 " --> pdb=" O GLU E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 608 removed outlier: 3.555A pdb=" N LEU E 603 " --> pdb=" O VAL E 599 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS E 607 " --> pdb=" O LEU E 603 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL E 608 " --> pdb=" O CYS E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 625 removed outlier: 4.122A pdb=" N GLN E 618 " --> pdb=" O VAL E 614 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP E 619 " --> pdb=" O ARG E 615 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR E 622 " --> pdb=" O GLN E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 889 removed outlier: 3.671A pdb=" N ILE E 870 " --> pdb=" O HIS E 866 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU E 872 " --> pdb=" O GLU E 868 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS E 873 " --> pdb=" O ARG E 869 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG E 886 " --> pdb=" O TRP E 882 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 934 removed outlier: 4.066A pdb=" N ASN E 919 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR E 920 " --> pdb=" O PRO E 916 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU E 927 " --> pdb=" O GLN E 923 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR E 928 " --> pdb=" O MET E 924 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA E 934 " --> pdb=" O LYS E 930 " (cutoff:3.500A) Processing helix chain 'E' and resid 980 through 1001 removed outlier: 4.058A pdb=" N LEU E 984 " --> pdb=" O ALA E 980 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP E 986 " --> pdb=" O THR E 982 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN E 991 " --> pdb=" O ARG E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1039 removed outlier: 3.691A pdb=" N LEU E1039 " --> pdb=" O ASN E1035 " (cutoff:3.500A) Processing helix chain 'E' and resid 1042 through 1049 removed outlier: 3.903A 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 1623 through 1627 Processing helix chain 'E' and resid 1652 through 1657 removed outlier: 3.500A pdb=" N LEU E1657 " --> pdb=" O LEU E1653 " (cutoff:3.500A) Processing helix chain 'E' and resid 1658 through 1674 removed outlier: 3.642A pdb=" N HIS E1665 " --> pdb=" O ARG E1661 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR E1670 " --> pdb=" O THR E1666 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG E1671 " --> pdb=" O LEU E1667 " (cutoff:3.500A) Processing helix chain 'E' and resid 1678 through 1686 removed outlier: 3.777A pdb=" N ALA E1684 " --> pdb=" O ARG E1680 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS E1686 " --> pdb=" O ALA E1682 " (cutoff:3.500A) Processing helix chain 'E' and resid 1692 through 1700 removed outlier: 4.128A pdb=" N LEU E1698 " --> pdb=" O LEU E1694 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU E1699 " --> pdb=" O LEU E1695 " (cutoff:3.500A) Processing helix chain 'E' and resid 1709 through 1712 removed outlier: 3.668A pdb=" N TYR E1712 " --> pdb=" O ALA E1709 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1709 through 1712' Processing helix chain 'E' and resid 1713 through 1720 Processing helix chain 'E' and resid 1720 through 1730 removed outlier: 4.389A pdb=" N SER E1726 " --> pdb=" O SER E1722 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET E1730 " --> pdb=" O SER E1726 " (cutoff:3.500A) Processing helix chain 'E' and resid 1739 through 1744 Processing helix chain 'E' and resid 1803 through 1823 removed outlier: 3.631A pdb=" N MET E1814 " --> pdb=" O LYS E1810 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E1815 " --> pdb=" O ALA E1811 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU E1817 " --> pdb=" O ARG E1813 " (cutoff:3.500A) Processing helix chain 'E' and resid 1833 through 1838 Processing helix chain 'E' and resid 1840 through 1851 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 1979 removed outlier: 4.109A pdb=" N LEU E1937 " --> pdb=" O GLU E1933 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN E1938 " --> pdb=" O SER E1934 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR E1945 " --> pdb=" O ASN E1941 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE E1946 " --> pdb=" O LEU E1942 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP E1948 " --> pdb=" O GLU E1944 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU E1963 " --> pdb=" O ALA E1959 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG E1964 " --> pdb=" O ALA E1960 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL E1966 " --> pdb=" O ALA E1962 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS E1968 " --> pdb=" O ARG E1964 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA E1978 " --> pdb=" O ARG E1974 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU E1979 " --> pdb=" O SER E1975 " (cutoff:3.500A) Processing helix chain 'E' and resid 1994 through 1999 removed outlier: 4.264A pdb=" N PHE E1998 " --> pdb=" O ARG E1994 " (cutoff:3.500A) Processing helix chain 'E' and resid 2001 through 2014 removed outlier: 3.737A pdb=" N ILE E2006 " --> pdb=" O PRO E2002 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN E2007 " --> pdb=" O GLN E2003 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS E2011 " --> pdb=" O ASN E2007 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE E2012 " --> pdb=" O MET E2008 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS E2013 " --> pdb=" O LEU E2009 " (cutoff:3.500A) Processing helix chain 'E' and resid 2028 through 2042 removed outlier: 3.711A pdb=" N LEU E2039 " --> pdb=" O HIS E2035 " (cutoff:3.500A) Processing helix chain 'E' and resid 2093 through 2108 removed outlier: 3.934A pdb=" N VAL E2103 " --> pdb=" O SER E2099 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E2106 " --> pdb=" O VAL E2102 " (cutoff:3.500A) Processing helix chain 'E' and resid 2113 through 2126 removed outlier: 3.875A pdb=" N VAL E2117 " --> pdb=" O SER E2113 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG E2126 " --> pdb=" O SER E2122 " (cutoff:3.500A) Processing helix chain 'E' and resid 2129 through 2138 Processing helix chain 'E' and resid 2148 through 2165 removed outlier: 3.763A pdb=" N SER E2154 " --> pdb=" O GLU E2150 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS E2158 " --> pdb=" O SER E2154 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY E2160 " --> pdb=" O LEU E2156 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E2161 " --> pdb=" O GLU E2157 " (cutoff:3.500A) Processing helix chain 'E' and resid 2171 through 2186 removed outlier: 3.604A pdb=" N LEU E2177 " --> pdb=" O GLN E2173 " (cutoff:3.500A) Processing helix chain 'E' and resid 2194 through 2201 removed outlier: 4.048A pdb=" N MET E2198 " --> pdb=" O HIS E2194 " (cutoff:3.500A) Processing helix chain 'E' and resid 2202 through 2216 removed outlier: 3.613A pdb=" N VAL E2207 " --> pdb=" O MET E2203 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN E2213 " --> pdb=" O GLU E2209 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL E2214 " --> pdb=" O VAL E2210 " (cutoff:3.500A) Processing helix chain 'E' and resid 2228 through 2242 removed outlier: 3.557A pdb=" N CYS E2237 " --> pdb=" O CYS E2233 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR E2238 " --> pdb=" O ARG E2234 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE E2239 " --> pdb=" O PHE E2235 " (cutoff:3.500A) Processing helix chain 'E' and resid 2245 through 2252 removed outlier: 3.731A pdb=" N ASP E2252 " --> pdb=" O ARG E2248 " (cutoff:3.500A) Processing helix chain 'E' and resid 2253 through 2262 removed outlier: 4.275A pdb=" N ASN E2260 " --> pdb=" O TYR E2256 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY E2262 " --> pdb=" O LEU E2258 " (cutoff:3.500A) Processing helix chain 'E' and resid 2271 through 2279 removed outlier: 3.513A pdb=" N SER E2279 " --> pdb=" O VAL E2275 " (cutoff:3.500A) Processing helix chain 'E' and resid 2294 through 2304 removed outlier: 3.677A pdb=" N VAL E2299 " --> pdb=" O LEU E2295 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER E2300 " --> pdb=" O GLU E2296 " (cutoff:3.500A) Processing helix chain 'E' and resid 2310 through 2315 removed outlier: 3.950A 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 2335 through 2339 removed outlier: 3.749A pdb=" N ALA E2338 " --> pdb=" O LEU E2335 " (cutoff:3.500A) Processing helix chain 'E' and resid 2346 through 2358 removed outlier: 5.097A pdb=" N VAL E2352 " --> pdb=" O GLU E2348 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL E2353 " --> pdb=" O ASN E2349 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU E2356 " --> pdb=" O VAL E2352 " (cutoff:3.500A) Processing helix chain 'E' and resid 2359 through 2364 removed outlier: 6.565A pdb=" N GLU E2362 " --> pdb=" O ARG E2359 " (cutoff:3.500A) Processing helix chain 'E' and resid 2375 through 2389 removed outlier: 3.731A pdb=" N ILE E2380 " --> pdb=" O LEU E2376 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG E2385 " --> pdb=" O GLU E2381 " (cutoff:3.500A) Processing helix chain 'E' and resid 2390 through 2393 Processing helix chain 'E' and resid 2417 through 2436 removed outlier: 4.407A pdb=" N ALA E2421 " --> pdb=" O HIS E2417 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET E2423 " --> pdb=" O GLY E2419 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU E2433 " --> pdb=" O LEU E2429 " (cutoff:3.500A) Processing helix chain 'E' and resid 2448 through 2461 removed outlier: 3.563A pdb=" N ARG E2452 " --> pdb=" O GLY E2448 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE E2453 " --> pdb=" O GLU E2449 " (cutoff:3.500A) Processing helix chain 'E' and resid 2466 through 2471 Processing helix chain 'E' and resid 2502 through 2507 removed outlier: 3.992A pdb=" N UNK E2506 " --> pdb=" O UNK E2502 " (cutoff:3.500A) Processing helix chain 'E' and resid 2516 through 2530 removed outlier: 4.512A pdb=" N UNK E2523 " --> pdb=" O UNK E2519 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N UNK E2526 " --> pdb=" O UNK E2522 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N UNK E2527 " --> pdb=" O UNK E2523 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N UNK E2528 " --> pdb=" O UNK E2524 " (cutoff:3.500A) Processing helix chain 'E' and resid 2543 through 2548 Processing helix chain 'E' and resid 2551 through 2557 removed outlier: 3.649A pdb=" N UNK E2555 " --> pdb=" O UNK E2551 " (cutoff:3.500A) Processing helix chain 'E' and resid 2566 through 2581 removed outlier: 4.184A pdb=" N UNK E2570 " --> pdb=" O UNK E2566 " (cutoff:3.500A) Processing helix chain 'E' and resid 2587 through 2600 removed outlier: 3.517A pdb=" N UNK E2597 " --> pdb=" O UNK E2593 " (cutoff:3.500A) Processing helix chain 'E' and resid 2601 through 2604 removed outlier: 3.929A pdb=" N UNK E2604 " --> pdb=" O UNK E2601 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2601 through 2604' Processing helix chain 'E' and resid 2610 through 2618 removed outlier: 3.752A pdb=" N UNK E2617 " --> pdb=" O UNK E2613 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N UNK E2618 " --> pdb=" O UNK E2614 " (cutoff:3.500A) Processing helix chain 'E' and resid 2628 through 2641 removed outlier: 3.522A pdb=" N UNK E2634 " --> pdb=" O UNK E2630 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N UNK E2635 " --> pdb=" O UNK E2631 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N UNK E2637 " --> pdb=" O UNK E2633 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N UNK E2639 " --> pdb=" O UNK E2635 " (cutoff:3.500A) Processing helix chain 'E' and resid 2651 through 2666 Processing helix chain 'E' and resid 2675 through 2680 removed outlier: 3.611A pdb=" N UNK E2680 " --> pdb=" O UNK E2676 " (cutoff:3.500A) Processing helix chain 'E' and resid 2683 through 2687 removed outlier: 3.989A pdb=" N UNK E2686 " --> pdb=" O UNK E2683 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N UNK E2687 " --> pdb=" O UNK E2684 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2683 through 2687' Processing helix chain 'E' and resid 2741 through 2745 removed outlier: 3.806A pdb=" N ASN E2744 " --> pdb=" O GLU E2741 " (cutoff:3.500A) Processing helix chain 'E' and resid 2748 through 2773 removed outlier: 4.241A pdb=" N SER E2753 " --> pdb=" O GLU E2749 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE E2754 " --> pdb=" O LYS E2750 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE E2768 " --> pdb=" O GLU E2764 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP E2769 " --> pdb=" O LYS E2765 " (cutoff:3.500A) Processing helix chain 'E' and resid 2793 through 2797 removed outlier: 3.941A pdb=" N THR E2796 " --> pdb=" O PRO E2793 " (cutoff:3.500A) Processing helix chain 'E' and resid 2800 through 2805 removed outlier: 4.173A pdb=" N ILE E2804 " --> pdb=" O LYS E2800 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR E2805 " --> pdb=" O ASP E2801 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2800 through 2805' Processing helix chain 'E' and resid 2809 through 2820 removed outlier: 3.723A pdb=" N ALA E2815 " --> pdb=" O GLU E2811 " (cutoff:3.500A) Processing helix chain 'E' and resid 2868 through 2895 removed outlier: 4.367A pdb=" N MET E2874 " --> pdb=" O GLU E2870 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA E2875 " --> pdb=" O LEU E2871 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E2880 " --> pdb=" O GLU E2876 " (cutoff:3.500A) removed outlier: 4.040A 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 2918 through 2932 removed outlier: 3.702A pdb=" N LEU E2926 " --> pdb=" O LYS E2922 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E2927 " --> pdb=" O ALA E2923 " (cutoff:3.500A) Processing helix chain 'E' and resid 2950 through 2976 removed outlier: 3.887A pdb=" N UNK E2956 " --> pdb=" O UNK E2952 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N UNK E2968 " --> pdb=" O UNK E2964 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N UNK E2969 " --> pdb=" O UNK E2965 " (cutoff:3.500A) Processing helix chain 'E' and resid 2999 through 3015 removed outlier: 3.662A pdb=" N UNK E3004 " --> pdb=" O UNK E3000 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N UNK E3006 " --> pdb=" O UNK E3002 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N UNK E3007 " --> pdb=" O UNK E3003 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N UNK E3009 " --> pdb=" O UNK E3005 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N UNK E3010 " --> pdb=" O UNK E3006 " (cutoff:3.500A) Processing helix chain 'E' and resid 3017 through 3022 Processing helix chain 'E' and resid 3025 through 3040 removed outlier: 4.026A pdb=" N UNK E3032 " --> pdb=" O UNK E3028 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N UNK E3040 " --> pdb=" O UNK E3036 " (cutoff:3.500A) Processing helix chain 'E' and resid 3050 through 3063 removed outlier: 4.040A pdb=" N UNK E3056 " --> pdb=" O UNK E3052 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N UNK E3060 " --> pdb=" O UNK E3056 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N UNK E3061 " --> pdb=" O UNK E3057 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N UNK E3062 " --> pdb=" O UNK E3058 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N UNK E3063 " --> pdb=" O UNK E3059 " (cutoff:3.500A) Processing helix chain 'E' and resid 3141 through 3146 Processing helix chain 'E' and resid 3146 through 3162 removed outlier: 3.814A pdb=" N UNK E3154 " --> pdb=" O UNK E3150 " (cutoff:3.500A) Processing helix chain 'E' and resid 3175 through 3187 Processing helix chain 'E' and resid 3198 through 3212 removed outlier: 3.690A pdb=" N UNK E3205 " --> pdb=" O UNK E3201 " (cutoff:3.500A) Processing helix chain 'E' and resid 3224 through 3230 removed outlier: 3.844A pdb=" N UNK E3228 " --> pdb=" O UNK E3224 " (cutoff:3.500A) Processing helix chain 'E' and resid 3244 through 3247 removed outlier: 3.735A pdb=" N UNK E3247 " --> pdb=" O UNK E3244 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3244 through 3247' Processing helix chain 'E' and resid 3248 through 3254 removed outlier: 3.555A pdb=" N UNK E3252 " --> pdb=" O UNK E3248 " (cutoff:3.500A) Processing helix chain 'E' and resid 3271 through 3285 removed outlier: 3.945A pdb=" N UNK E3282 " --> pdb=" O UNK E3278 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N UNK E3284 " --> pdb=" O UNK E3280 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N UNK E3285 " --> pdb=" O UNK E3281 " (cutoff:3.500A) Processing helix chain 'E' and resid 3301 through 3304 Processing helix chain 'E' and resid 3305 through 3310 Processing helix chain 'E' and resid 3315 through 3331 removed outlier: 3.602A pdb=" N UNK E3319 " --> pdb=" O UNK E3315 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N UNK E3322 " --> pdb=" O UNK E3318 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N UNK E3323 " --> pdb=" O UNK E3319 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N UNK E3324 " --> pdb=" O UNK E3320 " (cutoff:3.500A) Processing helix chain 'E' and resid 3344 through 3349 removed outlier: 3.687A pdb=" N UNK E3348 " --> pdb=" O UNK E3344 " (cutoff:3.500A) Processing helix chain 'E' and resid 3350 through 3354 Processing helix chain 'E' and resid 3361 through 3388 Processing helix chain 'E' and resid 3400 through 3407 Processing helix chain 'E' and resid 3407 through 3413 removed outlier: 3.785A pdb=" N UNK E3413 " --> pdb=" O UNK E3409 " (cutoff:3.500A) Processing helix chain 'E' and resid 3414 through 3425 removed outlier: 4.293A pdb=" N UNK E3420 " --> pdb=" O UNK E3416 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N UNK E3421 " --> pdb=" O UNK E3417 " (cutoff:3.500A) Processing helix chain 'E' and resid 3425 through 3431 removed outlier: 3.579A pdb=" N UNK E3429 " --> pdb=" O UNK E3425 " (cutoff:3.500A) Processing helix chain 'E' and resid 3437 through 3443 Processing helix chain 'E' and resid 3445 through 3450 Processing helix chain 'E' and resid 3461 through 3468 Processing helix chain 'E' and resid 3522 through 3527 Processing helix chain 'E' and resid 3541 through 3546 Processing helix chain 'E' and resid 3551 through 3560 Processing helix chain 'E' and resid 3574 through 3583 removed outlier: 4.106A pdb=" N UNK E3580 " --> pdb=" O UNK E3576 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N UNK E3583 " --> pdb=" O UNK E3579 " (cutoff:3.500A) Processing helix chain 'E' and resid 3588 through 3608 removed outlier: 3.793A pdb=" N UNK E3592 " --> pdb=" O UNK E3588 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N UNK E3596 " --> pdb=" O UNK E3592 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N UNK E3598 " --> pdb=" O UNK E3594 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N UNK E3600 " --> pdb=" O UNK E3596 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N UNK E3601 " --> pdb=" O UNK E3597 " (cutoff:3.500A) Processing helix chain 'E' and resid 3645 through 3656 Processing helix chain 'E' and resid 3671 through 3680 removed outlier: 3.572A pdb=" N ASP E3676 " --> pdb=" O ARG E3672 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU E3677 " --> pdb=" O MET E3673 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER E3678 " --> pdb=" O ILE E3674 " (cutoff:3.500A) Processing helix chain 'E' and resid 3681 through 3687 removed outlier: 6.695A pdb=" N GLU E3684 " --> pdb=" O GLY E3681 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU E3685 " --> pdb=" O GLU E3682 " (cutoff:3.500A) Processing helix chain 'E' and resid 3696 through 3711 removed outlier: 3.551A pdb=" N LEU E3701 " --> pdb=" O PRO E3697 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR E3711 " --> pdb=" O ARG E3707 " (cutoff:3.500A) Processing helix chain 'E' and resid 3719 through 3738 removed outlier: 3.612A pdb=" N TYR E3725 " --> pdb=" O LEU E3721 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS E3733 " --> pdb=" O MET E3729 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS E3734 " --> pdb=" O ALA E3730 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU E3736 " --> pdb=" O SER E3732 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU E3737 " --> pdb=" O CYS E3733 " (cutoff:3.500A) Processing helix chain 'E' and resid 3752 through 3771 removed outlier: 3.870A pdb=" N LYS E3760 " --> pdb=" O LYS E3756 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR E3765 " --> pdb=" O GLN E3761 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN E3766 " --> pdb=" O ARG E3762 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN E3767 " --> pdb=" O LEU E3763 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER E3768 " --> pdb=" O LEU E3764 " (cutoff:3.500A) Processing helix chain 'E' and resid 3774 through 3782 removed outlier: 4.030A pdb=" N MET E3778 " --> pdb=" O GLY E3774 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU E3780 " --> pdb=" O ALA E3776 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN E3781 " --> pdb=" O GLU E3777 " (cutoff:3.500A) Processing helix chain 'E' and resid 3791 through 3805 removed outlier: 3.840A pdb=" N LYS E3799 " --> pdb=" O SER E3795 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU E3800 " --> pdb=" O SER E3796 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER E3803 " --> pdb=" O LYS E3799 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU E3805 " --> pdb=" O GLY E3801 " (cutoff:3.500A) Processing helix chain 'E' and resid 3809 through 3824 removed outlier: 3.550A pdb=" N LYS E3815 " --> pdb=" O GLU E3811 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS E3824 " --> pdb=" O LEU E3820 " (cutoff:3.500A) Processing helix chain 'E' and resid 3829 through 3838 Processing helix chain 'E' and resid 3843 through 3854 removed outlier: 3.554A 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 3892 removed outlier: 3.543A pdb=" N PHE E3885 " --> pdb=" O THR E3881 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS E3892 " --> pdb=" O LEU E3888 " (cutoff:3.500A) Processing helix chain 'E' and resid 3898 through 3905 Processing helix chain 'E' and resid 3914 through 3937 removed outlier: 3.644A pdb=" N CYS E3918 " --> pdb=" O ASN E3914 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE E3933 " --> pdb=" O SER E3929 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR E3934 " --> pdb=" O ILE E3930 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP E3935 " --> pdb=" O SER E3931 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR E3936 " --> pdb=" O ASP E3932 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR E3937 " --> pdb=" O PHE E3933 " (cutoff:3.500A) Processing helix chain 'E' and resid 3944 through 3967 removed outlier: 3.642A pdb=" N LYS E3953 " --> pdb=" O ARG E3949 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA E3954 " --> pdb=" O ASN E3950 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN E3960 " --> pdb=" O SER E3956 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN E3963 " --> pdb=" O LYS E3959 " (cutoff:3.500A) Processing helix chain 'E' and resid 3973 through 3983 removed outlier: 3.618A pdb=" N HIS E3982 " --> pdb=" O GLN E3978 " (cutoff:3.500A) Processing helix chain 'E' and resid 3984 through 3996 removed outlier: 3.578A pdb=" N VAL E3990 " --> pdb=" O TRP E3986 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY E3991 " --> pdb=" O ASP E3987 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N PHE E3992 " --> pdb=" O ALA E3988 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU E3993 " --> pdb=" O VAL E3989 " (cutoff:3.500A) Processing helix chain 'E' and resid 3998 through 4003 Processing helix chain 'E' and resid 4009 through 4032 removed outlier: 3.520A pdb=" N ASP E4018 " --> pdb=" O LYS E4014 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET E4026 " --> pdb=" O ASP E4022 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU E4031 " --> pdb=" O LEU E4027 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU E4032 " --> pdb=" O LEU E4028 " (cutoff:3.500A) Processing helix chain 'E' and resid 4040 through 4051 Processing helix chain 'E' and resid 4051 through 4072 removed outlier: 4.057A pdb=" N PHE E4065 " --> pdb=" O PHE E4061 " (cutoff:3.500A) removed outlier: 3.564A 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) removed outlier: 3.619A pdb=" N VAL E4072 " --> pdb=" O LEU E4068 " (cutoff:3.500A) Processing helix chain 'E' and resid 4074 through 4081 removed outlier: 3.592A pdb=" N GLN E4078 " --> pdb=" O SER E4074 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR E4080 " --> pdb=" O ALA E4076 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL E4081 " --> pdb=" O PHE E4077 " (cutoff:3.500A) Processing helix chain 'E' and resid 4090 through 4100 removed outlier: 4.178A pdb=" N ASP E4098 " --> pdb=" O GLN E4094 " (cutoff:3.500A) Processing helix chain 'E' and resid 4104 through 4115 Processing helix chain 'E' and resid 4124 through 4132 removed outlier: 4.098A pdb=" N PHE E4132 " --> pdb=" O PHE E4128 " (cutoff:3.500A) Processing helix chain 'E' and resid 4132 through 4154 removed outlier: 3.629A pdb=" N ALA E4136 " --> pdb=" O PHE E4132 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP E4138 " --> pdb=" O GLU E4134 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE E4139 " --> pdb=" O PRO E4135 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE E4141 " --> pdb=" O ARG E4137 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN E4142 " --> pdb=" O ASP E4138 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL E4143 " --> pdb=" O ILE E4139 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E4145 " --> pdb=" O PHE E4141 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU E4146 " --> pdb=" O ASN E4142 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER E4151 " --> pdb=" O LEU E4147 " (cutoff:3.500A) Processing helix chain 'E' and resid 4157 through 4167 Processing helix chain 'E' and resid 4168 through 4175 removed outlier: 3.522A pdb=" N PHE E4174 " --> pdb=" O ILE E4170 " (cutoff:3.500A) Processing helix chain 'E' and resid 4199 through 4206 removed outlier: 3.614A pdb=" N ALA E4203 " --> pdb=" O GLU E4199 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E4204 " --> pdb=" O THR E4200 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU E4206 " --> pdb=" O ARG E4202 " (cutoff:3.500A) Processing helix chain 'E' and resid 4207 through 4224 removed outlier: 3.971A pdb=" N SER E4213 " --> pdb=" O GLN E4209 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL E4222 " --> pdb=" O ILE E4218 " (cutoff:3.500A) Processing helix chain 'E' and resid 4228 through 4252 removed outlier: 3.550A pdb=" N PHE E4234 " --> pdb=" O LYS E4230 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE E4243 " --> pdb=" O GLU E4239 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA E4249 " --> pdb=" O MET E4245 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN E4250 " --> pdb=" O GLN E4246 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE E4251 " --> pdb=" O ILE E4247 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER E4252 " --> pdb=" O ALA E4248 " (cutoff:3.500A) Processing helix chain 'E' and resid 4321 through 4337 removed outlier: 3.625A pdb=" N UNK E4327 " --> pdb=" O UNK E4323 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N UNK E4332 " --> pdb=" O UNK E4328 " (cutoff:3.500A) Processing helix chain 'E' and resid 4542 through 4556 removed outlier: 3.549A pdb=" N VAL E4546 " --> pdb=" O GLY E4542 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR E4554 " --> pdb=" O LYS E4550 " (cutoff:3.500A) Processing helix chain 'E' and resid 4558 through 4576 removed outlier: 3.543A pdb=" N ALA E4566 " --> pdb=" O LEU E4562 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE E4571 " --> pdb=" O LEU E4567 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA E4572 " --> pdb=" O PHE E4568 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E4573 " --> pdb=" O LEU E4569 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN E4574 " --> pdb=" O ALA E4570 " (cutoff:3.500A) Processing helix chain 'E' and resid 4577 through 4580 removed outlier: 3.874A pdb=" N TYR E4580 " --> pdb=" O LEU E4577 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4577 through 4580' Processing helix chain 'E' and resid 4643 through 4663 removed outlier: 3.690A pdb=" N LEU E4648 " --> pdb=" O TRP E4644 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU E4649 " --> pdb=" O CYS E4645 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS E4657 " --> pdb=" O VAL E4653 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE E4658 " --> pdb=" O ALA E4654 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE E4659 " --> pdb=" O PHE E4655 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY E4660 " --> pdb=" O LEU E4656 " (cutoff:3.500A) Processing helix chain 'E' and resid 4665 through 4683 removed outlier: 3.688A pdb=" N ALA E4678 " --> pdb=" O GLU E4674 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE E4683 " --> pdb=" O ARG E4679 " (cutoff:3.500A) Processing helix chain 'E' and resid 4696 through 4702 removed outlier: 3.981A pdb=" N GLN E4700 " --> pdb=" O ASP E4696 " (cutoff:3.500A) Processing helix chain 'E' and resid 4710 through 4714 removed outlier: 3.654A pdb=" N SER E4713 " --> pdb=" O SER E4710 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN E4714 " --> pdb=" O PHE E4711 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4710 through 4714' Processing helix chain 'E' and resid 4719 through 4728 removed outlier: 3.580A pdb=" N LYS E4723 " --> pdb=" O PHE E4719 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E4725 " --> pdb=" O LYS E4721 " (cutoff:3.500A) Processing helix chain 'E' and resid 4733 through 4741 Processing helix chain 'E' and resid 4751 through 4755 removed outlier: 4.083A pdb=" N GLU E4755 " --> pdb=" O ALA E4752 " (cutoff:3.500A) Processing helix chain 'E' and resid 4772 through 4785 Processing helix chain 'E' and resid 4786 through 4802 Processing helix chain 'E' and resid 4810 through 4813 Processing helix chain 'E' and resid 4814 through 4820 removed outlier: 3.599A pdb=" N MET E4818 " --> pdb=" O LEU E4814 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL E4820 " --> pdb=" O ILE E4816 " (cutoff:3.500A) Processing helix chain 'E' and resid 4820 through 4833 removed outlier: 3.577A pdb=" N ILE E4826 " --> pdb=" O THR E4822 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR E4831 " --> pdb=" O LEU E4827 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN E4833 " --> pdb=" O SER E4829 " (cutoff:3.500A) Processing helix chain 'E' and resid 4833 through 4858 removed outlier: 4.197A pdb=" N MET E4839 " --> pdb=" O LYS E4835 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR E4840 " --> pdb=" O GLN E4836 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E4848 " --> pdb=" O LEU E4844 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL E4854 " --> pdb=" O LEU E4850 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA E4855 " --> pdb=" O TYR E4851 " (cutoff:3.500A) Processing helix chain 'E' and resid 4859 through 4863 removed outlier: 4.060A pdb=" N TYR E4863 " --> pdb=" O ARG E4860 " (cutoff:3.500A) Processing helix chain 'E' and resid 4878 through 4890 removed outlier: 3.598A pdb=" N MET E4887 " --> pdb=" O TYR E4883 " (cutoff:3.500A) Processing helix chain 'E' and resid 4909 through 4925 removed outlier: 3.575A pdb=" N ARG E4913 " --> pdb=" O TYR E4909 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL E4914 " --> pdb=" O GLU E4910 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE E4918 " --> pdb=" O VAL E4914 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE E4923 " --> pdb=" O THR E4919 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL E4924 " --> pdb=" O PHE E4920 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE E4925 " --> pdb=" O PHE E4921 " (cutoff:3.500A) Processing helix chain 'E' and resid 4927 through 4955 removed outlier: 3.669A pdb=" N ILE E4936 " --> pdb=" O ILE E4932 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU E4948 " --> pdb=" O ARG E4944 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS E4951 " --> pdb=" O GLN E4947 " (cutoff:3.500A) Processing helix chain 'E' and resid 4965 through 4971 removed outlier: 4.342A pdb=" N THR E4971 " --> pdb=" O TYR E4967 " (cutoff:3.500A) Processing helix chain 'E' and resid 4973 through 4979 Processing helix chain 'E' and resid 4986 through 4997 removed outlier: 3.781A pdb=" N PHE E4990 " --> pdb=" O ALA E4986 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN E4997 " --> pdb=" O MET E4993 " (cutoff:3.500A) Processing helix chain 'E' and resid 5006 through 5017 Processing sheet with id=AA1, first strand: chain 'F' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'F' and resid 27 through 30 removed outlier: 3.734A pdb=" N PHE F 99 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 3.627A 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 23 Processing sheet with id=AA4, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.735A pdb=" N PHE A 99 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.627A 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 23 Processing sheet with id=AA6, first strand: chain 'H' and resid 27 through 30 removed outlier: 3.734A pdb=" N PHE H 99 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 3.626A 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 23 Processing sheet with id=AA8, first strand: chain 'J' and resid 27 through 30 removed outlier: 3.735A pdb=" N PHE J 99 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL J 101 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 200 through 201 removed outlier: 3.535A pdb=" N HIS B 151 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 106 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER B 72 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU B 108 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 19 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL B 21 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 24 through 25 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 280 through 284 removed outlier: 3.549A 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: 3.699A pdb=" N THR B 232 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.588A pdb=" N VAL B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 314 through 317 Processing sheet with id=AB7, first strand: chain 'B' and resid 358 through 359 Processing sheet with id=AB8, first strand: chain 'B' and resid 634 through 639 removed outlier: 4.144A pdb=" N GLN B 634 " --> pdb=" O HIS B1640 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 636 " --> pdb=" O ALA B1638 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B1638 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B1646 " --> pdb=" O ILE B1641 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 713 through 716 removed outlier: 3.988A pdb=" N VAL B 781 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 644 " --> pdb=" O VAL B 781 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 783 " --> pdb=" O THR B 642 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 642 " --> pdb=" O PHE B 783 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 763 through 768 removed outlier: 6.267A pdb=" N VAL B 764 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE B 759 " --> pdb=" O VAL B 764 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLY B 766 " --> pdb=" O PHE B 757 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE B 757 " --> pdb=" O GLY B 766 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 742 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 668 " --> pdb=" O ASP B 742 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 744 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 666 " --> pdb=" O VAL B 744 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 839 through 840 removed outlier: 3.530A pdb=" N PHE B1090 " --> pdb=" O CYS B1151 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 839 through 840 Processing sheet with id=AC4, first strand: chain 'B' and resid 892 through 893 removed outlier: 6.470A pdb=" N THR B 892 " --> pdb=" O HIS B 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 940 through 941 Processing sheet with id=AC6, first strand: chain 'B' and resid 1136 through 1138 removed outlier: 3.710A pdb=" N ARG B1101 " --> pdb=" O SER B1193 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1256 through 1259 removed outlier: 3.584A pdb=" N GLU B1256 " --> pdb=" O ALA B1273 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1293 through 1294 removed outlier: 3.675A pdb=" N UNK B1459 " --> pdb=" O UNK B1495 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N UNK B1495 " --> pdb=" O UNK B1459 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1293 through 1294 removed outlier: 5.256A pdb=" N UNK B1458 " --> pdb=" O UNK B1289 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N UNK B1460 " --> pdb=" O UNK B1287 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N UNK B1287 " --> pdb=" O UNK B1460 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1515 through 1516 Processing sheet with id=AD2, first strand: chain 'B' and resid 1734 through 1736 removed outlier: 6.469A pdb=" N TYR B1734 " --> pdb=" O TYR B2142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 4178 through 4183 Processing sheet with id=AD4, first strand: chain 'G' and resid 200 through 201 removed outlier: 3.535A pdb=" N HIS G 151 " --> pdb=" O ILE G 170 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA G 106 " --> pdb=" O SER G 72 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER G 72 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU G 108 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU G 19 " --> pdb=" O CYS G 206 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL G 21 " --> pdb=" O PRO G 204 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 24 through 25 Processing sheet with id=AD6, first strand: chain 'G' and resid 181 through 184 Processing sheet with id=AD7, first strand: chain 'G' and resid 280 through 284 removed outlier: 3.549A pdb=" N PHE G 389 " --> pdb=" O PHE G 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 230 through 233 removed outlier: 3.700A pdb=" N THR G 232 " --> pdb=" O TYR G 246 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 290 through 292 removed outlier: 3.588A pdb=" N VAL G 300 " --> pdb=" O ALA G 292 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 314 through 317 Processing sheet with id=AE2, first strand: chain 'G' and resid 358 through 359 Processing sheet with id=AE3, first strand: chain 'G' and resid 634 through 639 removed outlier: 4.143A pdb=" N GLN G 634 " --> pdb=" O HIS G1640 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN G 636 " --> pdb=" O ALA G1638 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA G1638 " --> pdb=" O ASN G 636 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG G1646 " --> pdb=" O ILE G1641 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 713 through 716 removed outlier: 3.988A pdb=" N VAL G 781 " --> pdb=" O ILE G 644 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE G 644 " --> pdb=" O VAL G 781 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE G 783 " --> pdb=" O THR G 642 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR G 642 " --> pdb=" O PHE G 783 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 763 through 768 removed outlier: 6.266A pdb=" N VAL G 764 " --> pdb=" O ILE G 759 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE G 759 " --> pdb=" O VAL G 764 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLY G 766 " --> pdb=" O PHE G 757 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE G 757 " --> pdb=" O GLY G 766 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP G 742 " --> pdb=" O VAL G 668 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL G 668 " --> pdb=" O ASP G 742 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL G 744 " --> pdb=" O VAL G 666 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL G 666 " --> pdb=" O VAL G 744 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 839 through 840 removed outlier: 3.530A pdb=" N PHE G1090 " --> pdb=" O CYS G1151 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 839 through 840 Processing sheet with id=AE8, first strand: chain 'G' and resid 892 through 893 removed outlier: 6.471A pdb=" N THR G 892 " --> pdb=" O HIS G 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'G' and resid 940 through 941 Processing sheet with id=AF1, first strand: chain 'G' and resid 1136 through 1138 removed outlier: 3.709A pdb=" N ARG G1101 " --> pdb=" O SER G1193 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE G1074 " --> pdb=" O SER G1239 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 1256 through 1259 removed outlier: 3.584A pdb=" N GLU G1256 " --> pdb=" O ALA G1273 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 1293 through 1294 removed outlier: 3.678A pdb=" N UNK G1459 " --> pdb=" O UNK G1495 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N UNK G1495 " --> pdb=" O UNK G1459 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 1293 through 1294 removed outlier: 5.208A pdb=" N UNK G1458 " --> pdb=" O UNK G1289 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N UNK G1460 " --> pdb=" O UNK G1287 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N UNK G1287 " --> pdb=" O UNK G1460 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 1515 through 1516 Processing sheet with id=AF6, first strand: chain 'G' and resid 1734 through 1736 removed outlier: 6.468A pdb=" N TYR G1734 " --> pdb=" O TYR G2142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'G' and resid 4178 through 4183 Processing sheet with id=AF8, first strand: chain 'I' and resid 200 through 201 removed outlier: 3.535A pdb=" N HIS I 151 " --> pdb=" O ILE I 170 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA I 106 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER I 72 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU I 108 " --> pdb=" O GLU I 70 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU I 19 " --> pdb=" O CYS I 206 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL I 21 " --> pdb=" O PRO I 204 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 24 through 25 Processing sheet with id=AG1, first strand: chain 'I' and resid 181 through 184 Processing sheet with id=AG2, first strand: chain 'I' and resid 280 through 284 removed outlier: 3.549A pdb=" N PHE I 389 " --> pdb=" O PHE I 223 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 230 through 233 removed outlier: 3.699A pdb=" N THR I 232 " --> pdb=" O TYR I 246 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 290 through 292 removed outlier: 3.588A pdb=" N VAL I 300 " --> pdb=" O ALA I 292 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 314 through 317 Processing sheet with id=AG6, first strand: chain 'I' and resid 358 through 359 Processing sheet with id=AG7, first strand: chain 'I' and resid 634 through 639 removed outlier: 4.143A pdb=" N GLN I 634 " --> pdb=" O HIS I1640 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN I 636 " --> pdb=" O ALA I1638 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA I1638 " --> pdb=" O ASN I 636 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG I1646 " --> pdb=" O ILE I1641 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 713 through 716 removed outlier: 3.988A pdb=" N VAL I 781 " --> pdb=" O ILE I 644 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE I 644 " --> pdb=" O VAL I 781 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE I 783 " --> pdb=" O THR I 642 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR I 642 " --> pdb=" O PHE I 783 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 763 through 768 removed outlier: 6.267A pdb=" N VAL I 764 " --> pdb=" O ILE I 759 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE I 759 " --> pdb=" O VAL I 764 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLY I 766 " --> pdb=" O PHE I 757 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE I 757 " --> pdb=" O GLY I 766 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP I 742 " --> pdb=" O VAL I 668 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL I 668 " --> pdb=" O ASP I 742 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL I 744 " --> pdb=" O VAL I 666 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL I 666 " --> pdb=" O VAL I 744 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 839 through 840 removed outlier: 3.530A pdb=" N PHE I1090 " --> pdb=" O CYS I1151 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 839 through 840 Processing sheet with id=AH3, first strand: chain 'I' and resid 892 through 893 removed outlier: 6.471A pdb=" N THR I 892 " --> pdb=" O HIS I 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'I' and resid 940 through 941 Processing sheet with id=AH5, first strand: chain 'I' and resid 1136 through 1138 removed outlier: 3.710A pdb=" N ARG I1101 " --> pdb=" O SER I1193 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE I1074 " --> pdb=" O SER I1239 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 1256 through 1259 removed outlier: 3.585A pdb=" N GLU I1256 " --> pdb=" O ALA I1273 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 1293 through 1294 removed outlier: 3.673A pdb=" N UNK I1459 " --> pdb=" O UNK I1495 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N UNK I1495 " --> pdb=" O UNK I1459 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 1293 through 1294 removed outlier: 5.252A pdb=" N UNK I1458 " --> pdb=" O UNK I1289 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N UNK I1460 " --> pdb=" O UNK I1287 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N UNK I1287 " --> pdb=" O UNK I1460 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 1515 through 1516 Processing sheet with id=AI1, first strand: chain 'I' and resid 1734 through 1736 removed outlier: 6.469A pdb=" N TYR I1734 " --> pdb=" O TYR I2142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'I' and resid 4178 through 4183 Processing sheet with id=AI3, first strand: chain 'E' and resid 200 through 201 removed outlier: 3.534A pdb=" N HIS E 151 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA E 106 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N SER E 72 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU E 108 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU E 19 " --> pdb=" O CYS E 206 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL E 21 " --> pdb=" O PRO E 204 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 24 through 25 Processing sheet with id=AI5, first strand: chain 'E' and resid 181 through 184 Processing sheet with id=AI6, first strand: chain 'E' and resid 280 through 284 removed outlier: 3.548A pdb=" N PHE E 389 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'E' and resid 230 through 233 removed outlier: 3.699A pdb=" N THR E 232 " --> pdb=" O TYR E 246 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 290 through 292 removed outlier: 3.588A pdb=" N VAL E 300 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 314 through 317 Processing sheet with id=AJ1, first strand: chain 'E' and resid 358 through 359 Processing sheet with id=AJ2, first strand: chain 'E' and resid 634 through 639 removed outlier: 4.143A pdb=" N GLN E 634 " --> pdb=" O HIS E1640 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN E 636 " --> pdb=" O ALA E1638 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA E1638 " --> pdb=" O ASN E 636 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG E1646 " --> pdb=" O ILE E1641 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 713 through 716 removed outlier: 3.988A pdb=" N VAL E 781 " --> pdb=" O ILE E 644 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 644 " --> pdb=" O VAL E 781 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE E 783 " --> pdb=" O THR E 642 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR E 642 " --> pdb=" O PHE E 783 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'E' and resid 763 through 768 removed outlier: 6.268A pdb=" N VAL E 764 " --> pdb=" O ILE E 759 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE E 759 " --> pdb=" O VAL E 764 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLY E 766 " --> pdb=" O PHE E 757 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE E 757 " --> pdb=" O GLY E 766 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP E 742 " --> pdb=" O VAL E 668 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E 668 " --> pdb=" O ASP E 742 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL E 744 " --> pdb=" O VAL E 666 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL E 666 " --> pdb=" O VAL E 744 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'E' and resid 839 through 840 removed outlier: 3.531A pdb=" N PHE E1090 " --> pdb=" O CYS E1151 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'E' and resid 839 through 840 Processing sheet with id=AJ7, first strand: chain 'E' and resid 892 through 893 removed outlier: 6.471A pdb=" N THR E 892 " --> pdb=" O HIS E 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'E' and resid 940 through 941 Processing sheet with id=AJ9, first strand: chain 'E' and resid 1136 through 1138 removed outlier: 3.709A pdb=" N ARG E1101 " --> pdb=" O SER E1193 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE E1074 " --> pdb=" O SER E1239 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'E' and resid 1256 through 1259 removed outlier: 3.585A pdb=" N GLU E1256 " --> pdb=" O ALA E1273 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'E' and resid 1293 through 1294 removed outlier: 3.672A pdb=" N UNK E1459 " --> pdb=" O UNK E1495 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNK E1495 " --> pdb=" O UNK E1459 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'E' and resid 1293 through 1294 removed outlier: 5.263A pdb=" N UNK E1458 " --> pdb=" O UNK E1289 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N UNK E1460 " --> pdb=" O UNK E1287 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N UNK E1287 " --> pdb=" O UNK E1460 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'E' and resid 1515 through 1516 Processing sheet with id=AK5, first strand: chain 'E' and resid 1734 through 1736 removed outlier: 6.468A pdb=" N TYR E1734 " --> pdb=" O TYR E2142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK5 Processing sheet with id=AK6, first strand: chain 'E' and resid 4178 through 4183 4947 hydrogen bonds defined for protein. 14241 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: 85.50 Time building geometry restraints manager: 35.32 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: 41198 1.34 - 1.46: 26565 1.46 - 1.58: 54745 1.58 - 1.70: 0 1.70 - 1.82: 1020 Bond restraints: 123528 Sorted by residual: bond pdb=" C LEU I2023 " pdb=" N PRO I2024 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.22e+00 bond pdb=" C LEU E2023 " pdb=" N PRO E2024 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.14e+00 bond pdb=" C LEU B2023 " pdb=" N PRO B2024 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.14e+00 bond pdb=" C LEU G2023 " pdb=" N PRO G2024 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.11e+00 bond pdb=" C ASP B1828 " pdb=" N PRO B1829 " ideal model delta sigma weight residual 1.331 1.360 -0.029 1.27e-02 6.20e+03 5.10e+00 ... (remaining 123523 not shown) Histogram of bond angle deviations from ideal: 98.25 - 106.23: 3305 106.23 - 114.21: 71071 114.21 - 122.19: 70088 122.19 - 130.17: 23282 130.17 - 138.15: 690 Bond angle restraints: 168436 Sorted by residual: angle pdb=" C GLN I2291 " pdb=" N GLU I2292 " pdb=" CA GLU I2292 " ideal model delta sigma weight residual 121.54 132.25 -10.71 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C GLN B2291 " pdb=" N GLU B2292 " pdb=" CA GLU B2292 " ideal model delta sigma weight residual 121.54 132.23 -10.69 1.91e+00 2.74e-01 3.13e+01 angle pdb=" C GLN E2291 " pdb=" N GLU E2292 " pdb=" CA GLU E2292 " ideal model delta sigma weight residual 121.54 132.22 -10.68 1.91e+00 2.74e-01 3.13e+01 angle pdb=" C GLN G2291 " pdb=" N GLU G2292 " pdb=" CA GLU G2292 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.11e+01 angle pdb=" C MET I4639 " pdb=" N GLU I4640 " pdb=" CA GLU I4640 " ideal model delta sigma weight residual 121.80 133.47 -11.67 2.44e+00 1.68e-01 2.29e+01 ... (remaining 168431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.60: 70590 15.60 - 31.21: 2355 31.21 - 46.81: 639 46.81 - 62.42: 52 62.42 - 78.02: 96 Dihedral angle restraints: 73732 sinusoidal: 23656 harmonic: 50076 Sorted by residual: dihedral pdb=" CA LEU B2472 " pdb=" C LEU B2472 " pdb=" N PRO B2473 " pdb=" CA PRO B2473 " ideal model delta harmonic sigma weight residual -180.00 -127.75 -52.25 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA LEU G2472 " pdb=" C LEU G2472 " pdb=" N PRO G2473 " pdb=" CA PRO G2473 " ideal model delta harmonic sigma weight residual 180.00 -127.78 -52.22 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA LEU E2472 " pdb=" C LEU E2472 " pdb=" N PRO E2473 " pdb=" CA PRO E2473 " ideal model delta harmonic sigma weight residual -180.00 -127.79 -52.21 0 5.00e+00 4.00e-02 1.09e+02 ... (remaining 73729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 17853 0.078 - 0.155: 1674 0.155 - 0.233: 133 0.233 - 0.311: 35 0.311 - 0.389: 9 Chirality restraints: 19704 Sorted by residual: chirality pdb=" CG LEU B 131 " pdb=" CB LEU B 131 " pdb=" CD1 LEU B 131 " pdb=" CD2 LEU B 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CG LEU G 131 " pdb=" CB LEU G 131 " pdb=" CD1 LEU G 131 " pdb=" CD2 LEU G 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CG LEU E 131 " pdb=" CB LEU E 131 " pdb=" CD1 LEU E 131 " pdb=" CD2 LEU E 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 19701 not shown) Planarity restraints: 22192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP G2807 " -0.061 5.00e-02 4.00e+02 9.16e-02 1.34e+01 pdb=" N PRO G2808 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO G2808 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO G2808 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP I2807 " 0.061 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO I2808 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO I2808 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO I2808 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP E2807 " -0.061 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO E2808 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO E2808 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO E2808 " -0.050 5.00e-02 4.00e+02 ... (remaining 22189 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 16 2.08 - 2.78: 30692 2.78 - 3.49: 156730 3.49 - 4.19: 268170 4.19 - 4.90: 444807 Nonbonded interactions: 900415 Sorted by model distance: nonbonded pdb=" CB UNK E1297 " pdb=" O UNK E1452 " model vdw 1.373 3.440 nonbonded pdb=" O UNK E1487 " pdb=" CB UNK E1551 " model vdw 1.374 3.440 nonbonded pdb=" O UNK I3557 " pdb=" CB UNK I3561 " model vdw 1.374 3.440 nonbonded pdb=" CB UNK I1297 " pdb=" O UNK I1452 " model vdw 1.374 3.440 nonbonded pdb=" O UNK I1487 " pdb=" CB UNK I1551 " model vdw 1.374 3.440 ... (remaining 900410 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.520 Construct map_model_manager: 0.090 Extract box with map and model: 17.120 Check model and map are aligned: 1.300 Set scattering table: 0.830 Process input model: 284.130 Find NCS groups from input model: 6.440 Set up NCS constraints: 0.620 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 316.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 : 0.004 0.053 123528 Z= 0.260 Angle : 0.860 16.515 168436 Z= 0.445 Chirality : 0.047 0.389 19704 Planarity : 0.007 0.092 22192 Dihedral : 9.824 78.022 41164 Min Nonbonded Distance : 1.373 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.29 % Favored : 89.53 % Rotamer: Outliers : 0.39 % Allowed : 3.09 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.31 % 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: -4.87 (0.05), residues: 13356 helix: -3.69 (0.04), residues: 5484 sheet: -2.01 (0.16), residues: 992 loop : -3.02 (0.06), residues: 6880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP G5019 HIS 0.012 0.002 HIS B 720 PHE 0.031 0.002 PHE E2012 TYR 0.030 0.002 TYR B1711 ARG 0.009 0.001 ARG I1141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2245 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 2205 time to evaluate : 9.012 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 17 LYS cc_start: 0.9046 (mttt) cc_final: 0.8791 (pttt) REVERT: F 73 LYS cc_start: 0.9374 (tttm) cc_final: 0.9079 (mmtm) REVERT: A 17 LYS cc_start: 0.9056 (mttt) cc_final: 0.8771 (pttt) REVERT: A 73 LYS cc_start: 0.9396 (tttm) cc_final: 0.9073 (mmtm) REVERT: H 17 LYS cc_start: 0.9048 (mttt) cc_final: 0.8779 (pttt) REVERT: H 73 LYS cc_start: 0.9411 (tttm) cc_final: 0.9060 (mmtm) REVERT: J 17 LYS cc_start: 0.9073 (mttt) cc_final: 0.8764 (pttt) REVERT: B 196 MET cc_start: 0.7827 (mmp) cc_final: 0.7369 (mmm) REVERT: B 214 VAL cc_start: 0.9508 (t) cc_final: 0.9276 (m) REVERT: B 316 PHE cc_start: 0.8971 (m-80) cc_final: 0.8581 (m-80) REVERT: B 746 CYS cc_start: 0.8181 (m) cc_final: 0.6770 (m) REVERT: B 757 PHE cc_start: 0.6507 (m-10) cc_final: 0.5813 (m-10) REVERT: B 961 MET cc_start: 0.3181 (mmp) cc_final: 0.0067 (mmt) REVERT: B 1115 LEU cc_start: 0.9240 (tp) cc_final: 0.9037 (tp) REVERT: B 1600 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8033 (pt) REVERT: B 2101 MET cc_start: 0.8721 (ttp) cc_final: 0.8374 (tmm) REVERT: B 2165 LEU cc_start: 0.9358 (mp) cc_final: 0.9108 (pp) REVERT: B 2258 LEU cc_start: 0.9134 (tt) cc_final: 0.8534 (tt) REVERT: B 2347 GLU cc_start: 0.7761 (pp20) cc_final: 0.7450 (pm20) REVERT: B 2435 ARG cc_start: 0.9011 (mtt-85) cc_final: 0.8565 (tpp-160) REVERT: B 2440 MET cc_start: 0.6797 (mmp) cc_final: 0.6470 (mmp) REVERT: B 2874 MET cc_start: -0.1025 (mtp) cc_final: -0.1289 (mmt) REVERT: B 2932 MET cc_start: -0.2997 (ttm) cc_final: -0.3380 (tpt) REVERT: B 3758 MET cc_start: 0.7992 (tpt) cc_final: 0.7768 (tpp) REVERT: B 3780 LEU cc_start: 0.9450 (mp) cc_final: 0.8562 (mp) REVERT: B 3805 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9122 (pp) REVERT: B 3852 LYS cc_start: 0.9461 (mttt) cc_final: 0.9220 (tptp) REVERT: B 3917 ILE cc_start: 0.9374 (mt) cc_final: 0.9000 (tp) REVERT: B 3984 ARG cc_start: 0.8146 (ptt180) cc_final: 0.7927 (ptm-80) REVERT: B 4000 MET cc_start: 0.7637 (ttt) cc_final: 0.7416 (tmm) REVERT: B 4001 MET cc_start: 0.8013 (mmt) cc_final: 0.7508 (mmt) REVERT: B 4021 LYS cc_start: 0.9258 (ttpt) cc_final: 0.8930 (ptmm) REVERT: B 4034 ASN cc_start: 0.7614 (t160) cc_final: 0.7167 (t0) REVERT: B 4680 LYS cc_start: 0.9421 (mttt) cc_final: 0.8990 (ttmt) REVERT: B 4686 LEU cc_start: 0.9209 (tp) cc_final: 0.8757 (tp) REVERT: B 4769 MET cc_start: 0.5200 (ptm) cc_final: 0.4936 (ptt) REVERT: B 4813 LEU cc_start: 0.9361 (tp) cc_final: 0.8959 (tp) REVERT: B 4821 LYS cc_start: 0.9310 (tmmm) cc_final: 0.9097 (ttpp) REVERT: B 4880 MET cc_start: 0.7774 (mtp) cc_final: 0.7564 (ttt) REVERT: B 4950 VAL cc_start: 0.9289 (m) cc_final: 0.9076 (t) REVERT: B 4958 CYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6615 (t) REVERT: B 5013 MET cc_start: 0.8627 (mtp) cc_final: 0.6662 (mtm) REVERT: B 5036 LEU cc_start: 0.5510 (tp) cc_final: 0.5211 (tp) REVERT: G 78 LEU cc_start: 0.9498 (tp) cc_final: 0.9193 (pp) REVERT: G 214 VAL cc_start: 0.9541 (t) cc_final: 0.9319 (m) REVERT: G 316 PHE cc_start: 0.8970 (m-80) cc_final: 0.8456 (m-80) REVERT: G 539 LEU cc_start: 0.9025 (mp) cc_final: 0.8785 (tt) REVERT: G 746 CYS cc_start: 0.8155 (m) cc_final: 0.6742 (m) REVERT: G 757 PHE cc_start: 0.6621 (m-10) cc_final: 0.5923 (m-10) REVERT: G 961 MET cc_start: 0.3715 (mmp) cc_final: 0.0378 (mmt) REVERT: G 1115 LEU cc_start: 0.9209 (tp) cc_final: 0.8966 (tp) REVERT: G 1600 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8091 (pt) REVERT: G 1969 LEU cc_start: 0.9198 (tp) cc_final: 0.8987 (tp) REVERT: G 2101 MET cc_start: 0.8826 (ttp) cc_final: 0.8412 (tmm) REVERT: G 2165 LEU cc_start: 0.9395 (mp) cc_final: 0.9077 (pp) REVERT: G 2295 LEU cc_start: 0.9033 (mt) cc_final: 0.8769 (mt) REVERT: G 2347 GLU cc_start: 0.7742 (pp20) cc_final: 0.7390 (pm20) REVERT: G 2423 MET cc_start: 0.7446 (ppp) cc_final: 0.6265 (ppp) REVERT: G 2435 ARG cc_start: 0.9071 (mtt-85) cc_final: 0.8605 (tpp-160) REVERT: G 2440 MET cc_start: 0.6761 (mmp) cc_final: 0.6442 (mmp) REVERT: G 2874 MET cc_start: -0.0992 (mtp) cc_final: -0.1329 (mmt) REVERT: G 2932 MET cc_start: -0.2574 (ttm) cc_final: -0.2818 (tpt) REVERT: G 3805 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9084 (pp) REVERT: G 3829 PHE cc_start: 0.9077 (m-80) cc_final: 0.8733 (m-10) REVERT: G 3852 LYS cc_start: 0.9487 (mttt) cc_final: 0.9274 (tptp) REVERT: G 3917 ILE cc_start: 0.9411 (mt) cc_final: 0.9027 (tp) REVERT: G 4000 MET cc_start: 0.7652 (ttt) cc_final: 0.7426 (tmm) REVERT: G 4021 LYS cc_start: 0.9306 (ttpt) cc_final: 0.8911 (ptmm) REVERT: G 4022 ASP cc_start: 0.8630 (m-30) cc_final: 0.8355 (m-30) REVERT: G 4026 MET cc_start: 0.9139 (ttt) cc_final: 0.8906 (tpt) REVERT: G 4034 ASN cc_start: 0.7569 (t160) cc_final: 0.7135 (t0) REVERT: G 4680 LYS cc_start: 0.9420 (mttt) cc_final: 0.8988 (ttmt) REVERT: G 4686 LEU cc_start: 0.9205 (tp) cc_final: 0.8735 (tp) REVERT: G 4769 MET cc_start: 0.5345 (ptm) cc_final: 0.5060 (ptt) REVERT: G 4813 LEU cc_start: 0.9387 (tp) cc_final: 0.9055 (tp) REVERT: G 4821 LYS cc_start: 0.9272 (tmmm) cc_final: 0.9047 (ttpp) REVERT: G 4950 VAL cc_start: 0.9318 (m) cc_final: 0.9109 (t) REVERT: G 5013 MET cc_start: 0.8734 (mtp) cc_final: 0.6586 (mtm) REVERT: I 196 MET cc_start: 0.7812 (mmp) cc_final: 0.7280 (mmp) REVERT: I 214 VAL cc_start: 0.9488 (t) cc_final: 0.9275 (m) REVERT: I 316 PHE cc_start: 0.8800 (m-80) cc_final: 0.8461 (m-80) REVERT: I 746 CYS cc_start: 0.8145 (m) cc_final: 0.6584 (m) REVERT: I 748 LEU cc_start: 0.8881 (tp) cc_final: 0.8677 (tt) REVERT: I 757 PHE cc_start: 0.6680 (m-10) cc_final: 0.5951 (m-10) REVERT: I 961 MET cc_start: 0.3586 (mmp) cc_final: 0.0328 (mmt) REVERT: I 1115 LEU cc_start: 0.9224 (tp) cc_final: 0.8990 (tp) REVERT: I 1600 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8134 (pt) REVERT: I 2101 MET cc_start: 0.8658 (ttp) cc_final: 0.8389 (tmm) REVERT: I 2165 LEU cc_start: 0.9302 (mp) cc_final: 0.9080 (pp) REVERT: I 2347 GLU cc_start: 0.7890 (pp20) cc_final: 0.7578 (pm20) REVERT: I 2435 ARG cc_start: 0.9044 (mtt-85) cc_final: 0.8585 (tpp-160) REVERT: I 2440 MET cc_start: 0.6787 (mmp) cc_final: 0.6406 (mmp) REVERT: I 2457 LEU cc_start: 0.9138 (mt) cc_final: 0.8763 (tt) REVERT: I 3758 MET cc_start: 0.7931 (tpt) cc_final: 0.7728 (tpp) REVERT: I 3829 PHE cc_start: 0.9012 (m-80) cc_final: 0.8294 (m-10) REVERT: I 3917 ILE cc_start: 0.9383 (mt) cc_final: 0.9027 (tp) REVERT: I 4000 MET cc_start: 0.7657 (ttt) cc_final: 0.7450 (tmm) REVERT: I 4021 LYS cc_start: 0.9260 (ttpt) cc_final: 0.8924 (ptmm) REVERT: I 4022 ASP cc_start: 0.8550 (m-30) cc_final: 0.8313 (m-30) REVERT: I 4026 MET cc_start: 0.9055 (ttt) cc_final: 0.8850 (tpt) REVERT: I 4034 ASN cc_start: 0.7805 (t160) cc_final: 0.7309 (t0) REVERT: I 4680 LYS cc_start: 0.9401 (mttt) cc_final: 0.8957 (ttmt) REVERT: I 4686 LEU cc_start: 0.9187 (tp) cc_final: 0.8692 (tp) REVERT: I 4769 MET cc_start: 0.5176 (ptm) cc_final: 0.4889 (ptt) REVERT: I 4813 LEU cc_start: 0.9355 (tp) cc_final: 0.8967 (tp) REVERT: I 4880 MET cc_start: 0.7775 (mtp) cc_final: 0.7556 (ttt) REVERT: I 5013 MET cc_start: 0.8732 (mtp) cc_final: 0.6731 (mtm) REVERT: I 5036 LEU cc_start: 0.5547 (tp) cc_final: 0.5306 (tp) REVERT: E 196 MET cc_start: 0.7750 (mmp) cc_final: 0.7491 (mmp) REVERT: E 214 VAL cc_start: 0.9475 (t) cc_final: 0.9253 (m) REVERT: E 316 PHE cc_start: 0.8894 (m-80) cc_final: 0.8569 (m-80) REVERT: E 746 CYS cc_start: 0.8151 (m) cc_final: 0.6749 (m) REVERT: E 757 PHE cc_start: 0.6603 (m-10) cc_final: 0.5915 (m-10) REVERT: E 961 MET cc_start: 0.3680 (mmp) cc_final: 0.0400 (mmt) REVERT: E 1115 LEU cc_start: 0.9265 (tp) cc_final: 0.9033 (tp) REVERT: E 1600 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8207 (pt) REVERT: E 2101 MET cc_start: 0.8703 (ttp) cc_final: 0.8353 (tmm) REVERT: E 2120 MET cc_start: 0.8725 (mtp) cc_final: 0.8484 (ttm) REVERT: E 2165 LEU cc_start: 0.9327 (mp) cc_final: 0.9074 (pp) REVERT: E 2347 GLU cc_start: 0.7784 (pp20) cc_final: 0.7449 (pm20) REVERT: E 2435 ARG cc_start: 0.8991 (mtt-85) cc_final: 0.8527 (tpp-160) REVERT: E 3780 LEU cc_start: 0.9481 (mp) cc_final: 0.8661 (mp) REVERT: E 3805 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9051 (pp) REVERT: E 3852 LYS cc_start: 0.9438 (mttt) cc_final: 0.9197 (tptp) REVERT: E 3917 ILE cc_start: 0.9380 (mt) cc_final: 0.9013 (tp) REVERT: E 4000 MET cc_start: 0.7645 (ttt) cc_final: 0.7420 (tmm) REVERT: E 4001 MET cc_start: 0.8031 (mmt) cc_final: 0.7556 (mmt) REVERT: E 4021 LYS cc_start: 0.9237 (ttpt) cc_final: 0.8920 (ptmm) REVERT: E 4034 ASN cc_start: 0.7791 (t160) cc_final: 0.7363 (t0) REVERT: E 4680 LYS cc_start: 0.9399 (mttt) cc_final: 0.8941 (ttmt) REVERT: E 4686 LEU cc_start: 0.9195 (tp) cc_final: 0.8699 (tp) REVERT: E 4769 MET cc_start: 0.5351 (ptm) cc_final: 0.5079 (ptt) REVERT: E 4813 LEU cc_start: 0.9365 (tp) cc_final: 0.9104 (tp) REVERT: E 4950 VAL cc_start: 0.9322 (m) cc_final: 0.9104 (t) REVERT: E 5013 MET cc_start: 0.8647 (mtp) cc_final: 0.6622 (mtm) REVERT: E 5036 LEU cc_start: 0.5459 (tp) cc_final: 0.5191 (tp) outliers start: 40 outliers final: 17 residues processed: 2244 average time/residue: 1.0241 time to fit residues: 3946.8259 Evaluate side-chains 1135 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1110 time to evaluate : 8.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 HIS A 87 HIS H 87 HIS J 87 HIS B 57 ASN ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 HIS ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 HIS B 797 HIS B 921 ASN B 949 ASN B1041 GLN ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1660 GLN B1693 GLN ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1775 HIS B1928 GLN B1972 ASN ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3771 HIS ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3982 HIS ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4054 ASN B4223 ASN B4574 ASN ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4728 HIS B4803 HIS ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4833 ASN B4947 GLN ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 ASN ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 HIS ** G 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 HIS ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 520 ASN ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 725 HIS G 797 HIS G 921 ASN G 949 ASN G1041 GLN ** G1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1660 GLN G1693 GLN ** G1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1775 HIS ** G1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1928 GLN G1972 ASN ** G2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3771 HIS ** G3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3982 HIS ** G4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4054 ASN G4223 ASN G4574 ASN ** G4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G4728 HIS G4803 HIS ** G4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4833 ASN G4947 GLN I 57 ASN I 105 HIS ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 HIS ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 379 HIS ** 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 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 520 ASN ** I 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 725 HIS I 797 HIS I 921 ASN I 949 ASN I1041 GLN ** I1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1660 GLN I1693 GLN ** I1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1775 HIS I1928 GLN I1972 ASN ** I2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3771 HIS ** I3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3830 GLN ** I3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3982 HIS ** I4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I4054 ASN I4223 ASN I4574 ASN ** I4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I4728 HIS I4803 HIS ** I4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I4833 ASN I4947 GLN E 57 ASN ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 HIS ** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 HIS ** 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 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 520 ASN ** E 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 725 HIS E 797 HIS E 921 ASN E 949 ASN E1041 GLN ** E1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1660 GLN E1693 GLN ** E1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1775 HIS ** E1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1928 GLN E1972 ASN ** E2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3771 HIS ** E3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3982 HIS ** E4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4054 ASN E4223 ASN E4574 ASN ** E4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4728 HIS E4803 HIS ** E4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4833 ASN E4947 GLN Total number of N/Q/H flips: 97 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 123528 Z= 0.486 Angle : 0.942 13.613 168436 Z= 0.483 Chirality : 0.045 0.270 19704 Planarity : 0.007 0.100 22192 Dihedral : 6.389 50.771 18156 Min Nonbonded Distance : 1.519 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.54 % Favored : 88.34 % Rotamer: Outliers : 0.29 % Allowed : 4.60 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.23 % 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: -3.14 (0.07), residues: 13356 helix: -1.39 (0.06), residues: 5808 sheet: -2.24 (0.15), residues: 1064 loop : -2.73 (0.07), residues: 6484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP G 260 HIS 0.015 0.003 HIS E 284 PHE 0.036 0.003 PHE B3996 TYR 0.033 0.003 TYR E1712 ARG 0.010 0.001 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1203 time to evaluate : 8.996 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: 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 44 LYS cc_start: 0.9414 (mmpt) cc_final: 0.9202 (mmmt) REVERT: A 44 LYS cc_start: 0.9372 (mmpt) cc_final: 0.9163 (mmmt) REVERT: H 44 LYS cc_start: 0.9347 (mmpt) cc_final: 0.9142 (mmmt) REVERT: H 73 LYS cc_start: 0.9383 (tttm) cc_final: 0.9056 (mmtm) REVERT: B 403 MET cc_start: 0.9263 (mtp) cc_final: 0.8821 (mtp) REVERT: B 562 GLU cc_start: 0.8714 (tp30) cc_final: 0.8363 (tp30) REVERT: B 1100 MET cc_start: 0.8105 (pmm) cc_final: 0.7643 (pmm) REVERT: B 1601 MET cc_start: 0.7967 (mpp) cc_final: 0.7765 (mpp) REVERT: B 1636 MET cc_start: 0.8873 (ppp) cc_final: 0.8530 (ppp) REVERT: B 1637 MET cc_start: 0.7445 (pmm) cc_final: 0.7108 (pmm) REVERT: B 1730 MET cc_start: 0.7626 (ppp) cc_final: 0.7183 (ppp) REVERT: B 2153 MET cc_start: 0.9084 (mmp) cc_final: 0.8804 (mmp) REVERT: B 2295 LEU cc_start: 0.9174 (mt) cc_final: 0.8829 (mt) REVERT: B 2932 MET cc_start: -0.2568 (ttm) cc_final: -0.3052 (tpt) REVERT: B 3673 MET cc_start: 0.9214 (mmm) cc_final: 0.8827 (mmp) REVERT: B 3758 MET cc_start: 0.8348 (tpt) cc_final: 0.8045 (tpp) REVERT: B 3800 LEU cc_start: 0.9450 (tp) cc_final: 0.8916 (tt) REVERT: B 3917 ILE cc_start: 0.9436 (mt) cc_final: 0.9152 (pt) REVERT: B 4001 MET cc_start: 0.8739 (mmt) cc_final: 0.7885 (mmt) REVERT: B 4034 ASN cc_start: 0.7820 (t0) cc_final: 0.7528 (t0) REVERT: B 4057 MET cc_start: 0.8795 (mtm) cc_final: 0.8454 (mtp) REVERT: B 4097 MET cc_start: 0.8443 (mmm) cc_final: 0.8187 (mmm) REVERT: B 4207 MET cc_start: 0.8944 (mmm) cc_final: 0.8716 (mmm) REVERT: B 4686 LEU cc_start: 0.9173 (tp) cc_final: 0.8851 (tp) REVERT: B 4769 MET cc_start: 0.5875 (ptm) cc_final: 0.5286 (ttp) REVERT: G 961 MET cc_start: 0.1973 (mmp) cc_final: 0.1012 (mmp) REVERT: G 1100 MET cc_start: 0.8067 (pmm) cc_final: 0.7559 (pmm) REVERT: G 1601 MET cc_start: 0.7994 (mpp) cc_final: 0.7756 (mpp) REVERT: G 1636 MET cc_start: 0.8903 (ppp) cc_final: 0.8519 (ppp) REVERT: G 1637 MET cc_start: 0.7418 (pmm) cc_final: 0.7059 (pmm) REVERT: G 1730 MET cc_start: 0.7737 (ppp) cc_final: 0.7167 (ppp) REVERT: G 2153 MET cc_start: 0.9130 (mmp) cc_final: 0.8863 (mmp) REVERT: G 2295 LEU cc_start: 0.9198 (mt) cc_final: 0.8837 (mt) REVERT: G 2423 MET cc_start: 0.7751 (ppp) cc_final: 0.6605 (ppp) REVERT: G 2932 MET cc_start: -0.2361 (ttm) cc_final: -0.2636 (tpt) REVERT: G 3673 MET cc_start: 0.9197 (mmm) cc_final: 0.8831 (mmp) REVERT: G 3800 LEU cc_start: 0.9465 (tp) cc_final: 0.8948 (tt) REVERT: G 4034 ASN cc_start: 0.8034 (t0) cc_final: 0.7656 (t0) REVERT: G 4039 MET cc_start: 0.8161 (mmp) cc_final: 0.7571 (mmm) REVERT: G 4057 MET cc_start: 0.8512 (mtm) cc_final: 0.8216 (mtp) REVERT: G 4207 MET cc_start: 0.8937 (mmm) cc_final: 0.8720 (mmm) REVERT: G 4769 MET cc_start: 0.5909 (ptm) cc_final: 0.5396 (ttp) REVERT: G 4989 MET cc_start: 0.7886 (tpp) cc_final: 0.7508 (tpp) REVERT: I 388 LEU cc_start: 0.8887 (tp) cc_final: 0.8547 (pp) REVERT: I 403 MET cc_start: 0.9206 (mtp) cc_final: 0.8785 (mtp) REVERT: I 961 MET cc_start: 0.1849 (mmp) cc_final: 0.0919 (mmp) REVERT: I 1100 MET cc_start: 0.8103 (pmm) cc_final: 0.7605 (pmm) REVERT: I 1601 MET cc_start: 0.8044 (mpp) cc_final: 0.7725 (mpp) REVERT: I 1636 MET cc_start: 0.8773 (ppp) cc_final: 0.8463 (ppp) REVERT: I 1637 MET cc_start: 0.7346 (pmm) cc_final: 0.6893 (pmm) REVERT: I 1730 MET cc_start: 0.7604 (ppp) cc_final: 0.7140 (ppp) REVERT: I 2153 MET cc_start: 0.9078 (mmp) cc_final: 0.8828 (mmp) REVERT: I 2295 LEU cc_start: 0.9154 (mt) cc_final: 0.8924 (mt) REVERT: I 2457 LEU cc_start: 0.9180 (mt) cc_final: 0.8950 (tt) REVERT: I 3673 MET cc_start: 0.9172 (mmm) cc_final: 0.8791 (mmp) REVERT: I 3723 MET cc_start: 0.9127 (mmm) cc_final: 0.8900 (mmt) REVERT: I 3758 MET cc_start: 0.8276 (tpt) cc_final: 0.7988 (tpp) REVERT: I 3800 LEU cc_start: 0.9482 (tp) cc_final: 0.8864 (tt) REVERT: I 4001 MET cc_start: 0.8566 (mmt) cc_final: 0.7823 (mmt) REVERT: I 4034 ASN cc_start: 0.7920 (t0) cc_final: 0.7627 (t0) REVERT: I 4057 MET cc_start: 0.8788 (mtm) cc_final: 0.8413 (mtt) REVERT: I 4097 MET cc_start: 0.7286 (mtp) cc_final: 0.6967 (mtm) REVERT: I 4207 MET cc_start: 0.8933 (mmm) cc_final: 0.8706 (mmm) REVERT: I 4686 LEU cc_start: 0.9140 (tp) cc_final: 0.8843 (tp) REVERT: I 4769 MET cc_start: 0.5865 (ptm) cc_final: 0.5281 (ttp) REVERT: I 4989 MET cc_start: 0.8005 (tpp) cc_final: 0.7784 (tpp) REVERT: E 403 MET cc_start: 0.9242 (mtp) cc_final: 0.8821 (mtp) REVERT: E 568 LEU cc_start: 0.8941 (mp) cc_final: 0.8315 (tt) REVERT: E 961 MET cc_start: 0.1790 (mmp) cc_final: 0.0936 (mmp) REVERT: E 1100 MET cc_start: 0.8080 (pmm) cc_final: 0.7609 (pmm) REVERT: E 1601 MET cc_start: 0.7994 (mpp) cc_final: 0.7687 (mpp) REVERT: E 1636 MET cc_start: 0.8911 (ppp) cc_final: 0.8541 (ppp) REVERT: E 1637 MET cc_start: 0.7472 (pmm) cc_final: 0.7106 (pmm) REVERT: E 1730 MET cc_start: 0.7595 (ppp) cc_final: 0.7107 (ppp) REVERT: E 2153 MET cc_start: 0.9043 (mmp) cc_final: 0.8802 (mmp) REVERT: E 2295 LEU cc_start: 0.9146 (mt) cc_final: 0.8897 (mt) REVERT: E 2457 LEU cc_start: 0.9207 (mt) cc_final: 0.8972 (tt) REVERT: E 3673 MET cc_start: 0.9234 (mmm) cc_final: 0.8885 (mmp) REVERT: E 3800 LEU cc_start: 0.9448 (tp) cc_final: 0.8915 (tt) REVERT: E 3917 ILE cc_start: 0.9436 (mt) cc_final: 0.9157 (pt) REVERT: E 4034 ASN cc_start: 0.7994 (t0) cc_final: 0.7723 (t0) REVERT: E 4057 MET cc_start: 0.8871 (mtm) cc_final: 0.8444 (mtp) REVERT: E 4097 MET cc_start: 0.8316 (mmm) cc_final: 0.8058 (mmm) REVERT: E 4686 LEU cc_start: 0.9155 (tp) cc_final: 0.8836 (tp) REVERT: E 4769 MET cc_start: 0.5908 (ptm) cc_final: 0.5370 (ttp) REVERT: E 4989 MET cc_start: 0.7892 (tpp) cc_final: 0.7542 (tpp) outliers start: 30 outliers final: 21 residues processed: 1229 average time/residue: 1.0440 time to fit residues: 2290.1332 Evaluate side-chains 852 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 831 time to evaluate : 8.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.0370 overall best weight: 2.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 HIS ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS B 156 GLN ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1598 GLN B1688 HIS B1719 HIS ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 ASN ** B2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2127 GLN ** B2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2349 ASN ** B2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3766 GLN B3809 ASN ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4803 HIS B4806 ASN ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 HIS ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 HIS G 156 GLN ** G 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 379 HIS ** 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 495 ASN G 597 HIS ** G1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1598 GLN G1688 HIS G1693 GLN G1719 HIS ** G1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1972 ASN ** G2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2127 GLN ** G2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2349 ASN ** G2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G3766 GLN G3809 ASN ** G3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4803 HIS ** G4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4806 ASN ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS I 156 GLN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1598 GLN I1688 HIS I1719 HIS ** I1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1972 ASN ** I2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2127 GLN ** I2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2349 ASN ** I2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I3766 GLN I3809 ASN ** I3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I4803 HIS ** I4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I4806 ASN ** I4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 HIS E 156 GLN ** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 GLN ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 HIS ** E1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1598 GLN E1688 HIS E1719 HIS ** E1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1972 ASN ** E2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2127 GLN ** E2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2349 ASN ** E2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E3643 ASN E3766 GLN E3809 ASN ** E3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4803 HIS ** E4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4806 ASN ** E4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 123528 Z= 0.205 Angle : 0.655 10.855 168436 Z= 0.334 Chirality : 0.039 0.218 19704 Planarity : 0.005 0.095 22192 Dihedral : 5.819 53.579 18156 Min Nonbonded Distance : 1.493 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.00 % Favored : 89.85 % Rotamer: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.20 % 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: -2.45 (0.07), residues: 13356 helix: -0.59 (0.06), residues: 5832 sheet: -2.08 (0.15), residues: 1076 loop : -2.57 (0.07), residues: 6448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G4767 HIS 0.010 0.001 HIS I4983 PHE 0.018 0.002 PHE B 414 TYR 0.026 0.001 TYR I1712 ARG 0.010 0.001 ARG E 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1218 time to evaluate : 8.993 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: 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 44 LYS cc_start: 0.9415 (mmpt) cc_final: 0.9184 (mmmt) REVERT: F 73 LYS cc_start: 0.9329 (tttm) cc_final: 0.9035 (mmtm) REVERT: A 44 LYS cc_start: 0.9340 (mmpt) cc_final: 0.9122 (mmmt) REVERT: A 73 LYS cc_start: 0.9338 (tttm) cc_final: 0.9044 (mmtm) REVERT: H 44 LYS cc_start: 0.9381 (mmpt) cc_final: 0.9113 (mmmt) REVERT: H 73 LYS cc_start: 0.9328 (tttm) cc_final: 0.9022 (mmtm) REVERT: J 35 LYS cc_start: 0.9171 (ttpp) cc_final: 0.8962 (tttm) REVERT: J 44 LYS cc_start: 0.9374 (mmpt) cc_final: 0.9094 (mmmt) REVERT: J 73 LYS cc_start: 0.9311 (tttm) cc_final: 0.9104 (mmtm) REVERT: B 150 MET cc_start: 0.8179 (tpt) cc_final: 0.7889 (tpt) REVERT: B 168 ASP cc_start: 0.8949 (m-30) cc_final: 0.8312 (p0) REVERT: B 316 PHE cc_start: 0.9079 (m-80) cc_final: 0.8559 (m-80) REVERT: B 403 MET cc_start: 0.9197 (mtp) cc_final: 0.8793 (mtp) REVERT: B 568 LEU cc_start: 0.8995 (mp) cc_final: 0.8718 (tt) REVERT: B 1100 MET cc_start: 0.7868 (pmm) cc_final: 0.7207 (pmm) REVERT: B 1601 MET cc_start: 0.7942 (mpp) cc_final: 0.7723 (mpp) REVERT: B 1730 MET cc_start: 0.7503 (ppp) cc_final: 0.6938 (ppp) REVERT: B 2153 MET cc_start: 0.9051 (mmp) cc_final: 0.8727 (mmp) REVERT: B 2423 MET cc_start: 0.7379 (ppp) cc_final: 0.7159 (ptm) REVERT: B 2932 MET cc_start: -0.2780 (ttm) cc_final: -0.3219 (tpt) REVERT: B 3673 MET cc_start: 0.9263 (mmm) cc_final: 0.8915 (mmp) REVERT: B 3758 MET cc_start: 0.8306 (tpt) cc_final: 0.8006 (tpp) REVERT: B 3780 LEU cc_start: 0.9630 (mp) cc_final: 0.8574 (mp) REVERT: B 3917 ILE cc_start: 0.9474 (mt) cc_final: 0.9225 (pt) REVERT: B 4026 MET cc_start: 0.8247 (tpt) cc_final: 0.7902 (tpt) REVERT: B 4034 ASN cc_start: 0.7736 (t0) cc_final: 0.7512 (t0) REVERT: B 4039 MET cc_start: 0.7766 (mmp) cc_final: 0.7328 (mmm) REVERT: B 4057 MET cc_start: 0.8720 (mtm) cc_final: 0.8389 (mtt) REVERT: B 4062 PHE cc_start: 0.8533 (m-10) cc_final: 0.8319 (m-10) REVERT: B 4207 MET cc_start: 0.8976 (mmm) cc_final: 0.8773 (mmm) REVERT: B 4245 MET cc_start: 0.8322 (mmm) cc_final: 0.7943 (mmt) REVERT: B 4769 MET cc_start: 0.5659 (ptm) cc_final: 0.4926 (ttp) REVERT: B 4989 MET cc_start: 0.7732 (tpp) cc_final: 0.7356 (tpp) REVERT: G 150 MET cc_start: 0.8099 (tpt) cc_final: 0.7859 (tpt) REVERT: G 168 ASP cc_start: 0.8911 (m-30) cc_final: 0.8221 (p0) REVERT: G 316 PHE cc_start: 0.9114 (m-80) cc_final: 0.8481 (m-80) REVERT: G 403 MET cc_start: 0.9449 (mtm) cc_final: 0.8711 (mtm) REVERT: G 568 LEU cc_start: 0.8994 (mp) cc_final: 0.8550 (tt) REVERT: G 961 MET cc_start: 0.1712 (mmp) cc_final: 0.0896 (mmp) REVERT: G 1100 MET cc_start: 0.7833 (pmm) cc_final: 0.7141 (pmm) REVERT: G 1601 MET cc_start: 0.7946 (mpp) cc_final: 0.7717 (mpp) REVERT: G 1637 MET cc_start: 0.7222 (pmm) cc_final: 0.6997 (pmm) REVERT: G 1730 MET cc_start: 0.7392 (ppp) cc_final: 0.6922 (ppp) REVERT: G 2153 MET cc_start: 0.9090 (mmp) cc_final: 0.8784 (mmp) REVERT: G 2228 MET cc_start: 0.8367 (ppp) cc_final: 0.8000 (tmm) REVERT: G 2423 MET cc_start: 0.7672 (ppp) cc_final: 0.6715 (ppp) REVERT: G 2932 MET cc_start: -0.2418 (ttm) cc_final: -0.2711 (tpt) REVERT: G 3673 MET cc_start: 0.9253 (mmm) cc_final: 0.8929 (mmp) REVERT: G 3780 LEU cc_start: 0.9612 (mp) cc_final: 0.9288 (mp) REVERT: G 3928 GLU cc_start: 0.8645 (pp20) cc_final: 0.8425 (pp20) REVERT: G 3955 MET cc_start: 0.8686 (ptp) cc_final: 0.8043 (ptp) REVERT: G 4026 MET cc_start: 0.8699 (tpt) cc_final: 0.8251 (tpt) REVERT: G 4034 ASN cc_start: 0.7958 (t0) cc_final: 0.7683 (t0) REVERT: G 4039 MET cc_start: 0.8111 (mmp) cc_final: 0.7738 (mmm) REVERT: G 4057 MET cc_start: 0.8582 (mtm) cc_final: 0.8184 (mtp) REVERT: G 4207 MET cc_start: 0.8894 (mmm) cc_final: 0.8644 (mmm) REVERT: G 4245 MET cc_start: 0.8468 (mmm) cc_final: 0.8091 (mmt) REVERT: G 4769 MET cc_start: 0.5691 (ptm) cc_final: 0.5020 (ttp) REVERT: G 4837 LEU cc_start: 0.9504 (tp) cc_final: 0.9281 (tt) REVERT: G 4989 MET cc_start: 0.7809 (tpp) cc_final: 0.7314 (tpp) REVERT: I 168 ASP cc_start: 0.8833 (m-30) cc_final: 0.8247 (p0) REVERT: I 316 PHE cc_start: 0.9037 (m-80) cc_final: 0.8532 (m-80) REVERT: I 403 MET cc_start: 0.9124 (mtp) cc_final: 0.8684 (mtp) REVERT: I 961 MET cc_start: 0.1329 (mmp) cc_final: 0.0708 (mmp) REVERT: I 1100 MET cc_start: 0.7883 (pmm) cc_final: 0.7201 (pmm) REVERT: I 1601 MET cc_start: 0.7964 (mpp) cc_final: 0.7735 (mpp) REVERT: I 1637 MET cc_start: 0.6928 (pmm) cc_final: 0.6655 (pmm) REVERT: I 1730 MET cc_start: 0.7451 (ppp) cc_final: 0.6891 (ppp) REVERT: I 2153 MET cc_start: 0.9087 (mmp) cc_final: 0.8676 (mmp) REVERT: I 2423 MET cc_start: 0.7042 (ppp) cc_final: 0.6801 (ptm) REVERT: I 2457 LEU cc_start: 0.9157 (mt) cc_final: 0.8950 (tt) REVERT: I 3673 MET cc_start: 0.9263 (mmm) cc_final: 0.8907 (mmp) REVERT: I 3758 MET cc_start: 0.8272 (tpt) cc_final: 0.7970 (tpp) REVERT: I 3800 LEU cc_start: 0.9431 (tp) cc_final: 0.8939 (tt) REVERT: I 3917 ILE cc_start: 0.9453 (mt) cc_final: 0.9135 (pt) REVERT: I 4026 MET cc_start: 0.8329 (tpt) cc_final: 0.8029 (tpt) REVERT: I 4034 ASN cc_start: 0.7878 (t0) cc_final: 0.7616 (t0) REVERT: I 4039 MET cc_start: 0.7717 (mmp) cc_final: 0.7057 (mmm) REVERT: I 4057 MET cc_start: 0.8705 (mtm) cc_final: 0.8308 (mtt) REVERT: I 4097 MET cc_start: 0.7255 (mtp) cc_final: 0.6990 (mtm) REVERT: I 4207 MET cc_start: 0.8959 (mmm) cc_final: 0.8749 (mmm) REVERT: I 4245 MET cc_start: 0.8395 (mmm) cc_final: 0.8005 (mmt) REVERT: I 4769 MET cc_start: 0.5662 (ptm) cc_final: 0.4969 (ttp) REVERT: E 168 ASP cc_start: 0.8936 (m-30) cc_final: 0.8365 (p0) REVERT: E 316 PHE cc_start: 0.9048 (m-80) cc_final: 0.8552 (m-80) REVERT: E 403 MET cc_start: 0.9200 (mtp) cc_final: 0.8799 (mtp) REVERT: E 961 MET cc_start: 0.1520 (mmp) cc_final: 0.1012 (mmp) REVERT: E 1100 MET cc_start: 0.7833 (pmm) cc_final: 0.7162 (pmm) REVERT: E 1601 MET cc_start: 0.7993 (mpp) cc_final: 0.7790 (mpp) REVERT: E 1637 MET cc_start: 0.7222 (pmm) cc_final: 0.6965 (pmm) REVERT: E 1730 MET cc_start: 0.7389 (ppp) cc_final: 0.6833 (ppp) REVERT: E 2153 MET cc_start: 0.9041 (mmp) cc_final: 0.8684 (mmp) REVERT: E 2457 LEU cc_start: 0.9158 (mt) cc_final: 0.8931 (tt) REVERT: E 3673 MET cc_start: 0.9264 (mmm) cc_final: 0.8964 (mmp) REVERT: E 3917 ILE cc_start: 0.9438 (mt) cc_final: 0.9107 (pt) REVERT: E 4000 MET cc_start: 0.6217 (tmm) cc_final: 0.5978 (tmm) REVERT: E 4026 MET cc_start: 0.8239 (tpt) cc_final: 0.8025 (tpt) REVERT: E 4034 ASN cc_start: 0.7870 (t0) cc_final: 0.7552 (t0) REVERT: E 4039 MET cc_start: 0.7787 (mmp) cc_final: 0.7344 (mmm) REVERT: E 4057 MET cc_start: 0.8776 (mtm) cc_final: 0.8430 (mtt) REVERT: E 4058 ILE cc_start: 0.9368 (pt) cc_final: 0.9086 (tp) REVERT: E 4062 PHE cc_start: 0.8837 (m-10) cc_final: 0.8596 (m-10) REVERT: E 4245 MET cc_start: 0.8369 (mmm) cc_final: 0.7990 (mmt) REVERT: E 4769 MET cc_start: 0.5685 (ptm) cc_final: 0.4009 (ttp) REVERT: E 4874 MET cc_start: 0.7939 (mmm) cc_final: 0.7730 (mmm) REVERT: E 4989 MET cc_start: 0.7861 (tpp) cc_final: 0.7384 (tpp) outliers start: 4 outliers final: 0 residues processed: 1222 average time/residue: 0.9174 time to fit residues: 2000.5930 Evaluate side-chains 872 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 872 time to evaluate : 8.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 38 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1663 HIS B1693 GLN ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 ASN ** B1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3970 GLN ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4078 GLN ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4803 HIS ** B4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5031 GLN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 399 GLN ** G 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1663 HIS ** G1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1972 ASN ** G1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4078 GLN ** G4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G4156 HIS G4803 HIS ** G4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4886 HIS ** G4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G5031 GLN ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 520 ASN ** I 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1663 HIS I1693 GLN ** I1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1972 ASN ** I1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I4078 GLN ** I4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I4156 HIS I4803 HIS ** I4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I4886 HIS ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1663 HIS ** E1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1693 GLN ** E1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1972 ASN ** E1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4078 GLN ** E4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4156 HIS E4803 HIS ** E4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4886 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 123528 Z= 0.447 Angle : 0.860 14.208 168436 Z= 0.439 Chirality : 0.043 0.248 19704 Planarity : 0.006 0.090 22192 Dihedral : 6.212 53.699 18156 Min Nonbonded Distance : 1.506 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.04 % Favored : 86.86 % Rotamer: Outliers : 0.12 % Allowed : 5.03 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.19 % 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: -2.60 (0.07), residues: 13356 helix: -0.67 (0.06), residues: 5864 sheet: -2.27 (0.15), residues: 1064 loop : -2.69 (0.07), residues: 6428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G2886 HIS 0.013 0.002 HIS E4978 PHE 0.030 0.003 PHE G2012 TYR 0.028 0.003 TYR I1712 ARG 0.008 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 989 time to evaluate : 9.292 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: 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 44 LYS cc_start: 0.9524 (mmpt) cc_final: 0.9234 (mmmt) REVERT: F 73 LYS cc_start: 0.9465 (tttm) cc_final: 0.9070 (tmtt) REVERT: A 44 LYS cc_start: 0.9504 (mmpt) cc_final: 0.9222 (mmmt) REVERT: A 73 LYS cc_start: 0.9477 (tttm) cc_final: 0.9069 (tmtt) REVERT: H 44 LYS cc_start: 0.9501 (mmpt) cc_final: 0.9230 (mmmt) REVERT: J 35 LYS cc_start: 0.9119 (ttpp) cc_final: 0.8887 (tttm) REVERT: J 44 LYS cc_start: 0.9505 (mmpt) cc_final: 0.9254 (mmmt) REVERT: B 180 LEU cc_start: 0.9315 (tp) cc_final: 0.9091 (tp) REVERT: B 403 MET cc_start: 0.9231 (mtp) cc_final: 0.8863 (mtp) REVERT: B 1100 MET cc_start: 0.7879 (pmm) cc_final: 0.7531 (pmm) REVERT: B 1601 MET cc_start: 0.8117 (mpp) cc_final: 0.7913 (mpp) REVERT: B 1637 MET cc_start: 0.7489 (pmm) cc_final: 0.7205 (pmm) REVERT: B 1730 MET cc_start: 0.7853 (ppp) cc_final: 0.7289 (ppp) REVERT: B 2932 MET cc_start: -0.2686 (ttm) cc_final: -0.3090 (tpt) REVERT: B 3673 MET cc_start: 0.9277 (mmm) cc_final: 0.8981 (mmp) REVERT: B 3758 MET cc_start: 0.8391 (tpt) cc_final: 0.8103 (tpp) REVERT: B 3800 LEU cc_start: 0.9442 (tp) cc_final: 0.8838 (tt) REVERT: B 4000 MET cc_start: 0.6803 (tmm) cc_final: 0.6567 (tmm) REVERT: B 4026 MET cc_start: 0.7980 (tpt) cc_final: 0.7712 (tpt) REVERT: B 4039 MET cc_start: 0.8248 (mmp) cc_final: 0.7469 (mmm) REVERT: B 4057 MET cc_start: 0.8557 (mtm) cc_final: 0.8283 (mtt) REVERT: B 4064 MET cc_start: 0.8686 (pmm) cc_final: 0.8346 (pmm) REVERT: B 4174 PHE cc_start: 0.8439 (m-10) cc_final: 0.8229 (m-10) REVERT: B 4207 MET cc_start: 0.9160 (mmm) cc_final: 0.8939 (mmm) REVERT: B 4682 GLU cc_start: 0.9241 (tt0) cc_final: 0.8998 (pt0) REVERT: B 4769 MET cc_start: 0.5645 (ptm) cc_final: 0.4942 (ttp) REVERT: B 5020 ASP cc_start: 0.8753 (p0) cc_final: 0.8400 (p0) REVERT: G 180 LEU cc_start: 0.9314 (tp) cc_final: 0.9093 (tp) REVERT: G 1100 MET cc_start: 0.7830 (pmm) cc_final: 0.7506 (pmm) REVERT: G 1601 MET cc_start: 0.8128 (mpp) cc_final: 0.7914 (mpp) REVERT: G 1637 MET cc_start: 0.7691 (pmm) cc_final: 0.7341 (pmm) REVERT: G 1730 MET cc_start: 0.7773 (ppp) cc_final: 0.7255 (ppp) REVERT: G 2153 MET cc_start: 0.9198 (mmp) cc_final: 0.8868 (mmp) REVERT: G 2178 MET cc_start: 0.9073 (ppp) cc_final: 0.8829 (ppp) REVERT: G 2228 MET cc_start: 0.8660 (ppp) cc_final: 0.8209 (tmm) REVERT: G 2932 MET cc_start: -0.2384 (ttm) cc_final: -0.2696 (tpt) REVERT: G 3673 MET cc_start: 0.9281 (mmm) cc_final: 0.9008 (mmp) REVERT: G 4000 MET cc_start: 0.7156 (tmm) cc_final: 0.6862 (tmm) REVERT: G 4039 MET cc_start: 0.8349 (mmp) cc_final: 0.7877 (mmm) REVERT: G 4057 MET cc_start: 0.8483 (mtm) cc_final: 0.8133 (mtp) REVERT: G 4231 MET cc_start: 0.8548 (tpp) cc_final: 0.8300 (tpp) REVERT: G 4245 MET cc_start: 0.8404 (mmm) cc_final: 0.8148 (mmt) REVERT: G 4769 MET cc_start: 0.5959 (ptm) cc_final: 0.5543 (ttp) REVERT: G 4989 MET cc_start: 0.7877 (tpp) cc_final: 0.7620 (tpp) REVERT: I 150 MET cc_start: 0.8149 (tpt) cc_final: 0.7945 (tpt) REVERT: I 180 LEU cc_start: 0.9281 (tp) cc_final: 0.9065 (tp) REVERT: I 403 MET cc_start: 0.9238 (mtp) cc_final: 0.8876 (mtp) REVERT: I 568 LEU cc_start: 0.9163 (mp) cc_final: 0.8853 (tt) REVERT: I 1100 MET cc_start: 0.7865 (pmm) cc_final: 0.7550 (pmm) REVERT: I 1579 MET cc_start: 0.9284 (pmm) cc_final: 0.9036 (pmm) REVERT: I 1601 MET cc_start: 0.8144 (mpp) cc_final: 0.7918 (mpp) REVERT: I 1637 MET cc_start: 0.7605 (pmm) cc_final: 0.7188 (pmm) REVERT: I 1730 MET cc_start: 0.7842 (ppp) cc_final: 0.7276 (ppp) REVERT: I 2101 MET cc_start: 0.8481 (tmm) cc_final: 0.8269 (tmm) REVERT: I 2153 MET cc_start: 0.9152 (mmp) cc_final: 0.8764 (mmp) REVERT: I 2457 LEU cc_start: 0.9208 (mt) cc_final: 0.8966 (tt) REVERT: I 3673 MET cc_start: 0.9282 (mmm) cc_final: 0.8910 (mmp) REVERT: I 3758 MET cc_start: 0.8347 (tpt) cc_final: 0.8051 (tpp) REVERT: I 3800 LEU cc_start: 0.9460 (tp) cc_final: 0.8874 (tt) REVERT: I 3955 MET cc_start: 0.8660 (ptm) cc_final: 0.8376 (ptp) REVERT: I 4000 MET cc_start: 0.6884 (tmm) cc_final: 0.6682 (tmm) REVERT: I 4026 MET cc_start: 0.8015 (tpt) cc_final: 0.7694 (tpt) REVERT: I 4034 ASN cc_start: 0.8003 (t0) cc_final: 0.7791 (t0) REVERT: I 4039 MET cc_start: 0.8068 (mmp) cc_final: 0.7337 (mmm) REVERT: I 4057 MET cc_start: 0.8515 (mtm) cc_final: 0.8230 (mtt) REVERT: I 4064 MET cc_start: 0.8655 (pmm) cc_final: 0.8354 (pmm) REVERT: I 4207 MET cc_start: 0.9144 (mmm) cc_final: 0.8924 (mmm) REVERT: I 4231 MET cc_start: 0.8503 (tpp) cc_final: 0.8300 (tpp) REVERT: I 4682 GLU cc_start: 0.9240 (tt0) cc_final: 0.9009 (pt0) REVERT: I 4769 MET cc_start: 0.5721 (ptm) cc_final: 0.5050 (ttp) REVERT: I 5020 ASP cc_start: 0.8809 (p0) cc_final: 0.8462 (p0) REVERT: E 180 LEU cc_start: 0.9286 (tp) cc_final: 0.9066 (tp) REVERT: E 403 MET cc_start: 0.9227 (mtp) cc_final: 0.8875 (mtp) REVERT: E 568 LEU cc_start: 0.9127 (mp) cc_final: 0.8754 (tt) REVERT: E 1100 MET cc_start: 0.7833 (pmm) cc_final: 0.7559 (pmm) REVERT: E 1637 MET cc_start: 0.7634 (pmm) cc_final: 0.7286 (pmm) REVERT: E 1730 MET cc_start: 0.7829 (ppp) cc_final: 0.7240 (ppp) REVERT: E 2153 MET cc_start: 0.9169 (mmp) cc_final: 0.8794 (mmp) REVERT: E 3673 MET cc_start: 0.9305 (mmm) cc_final: 0.8970 (mmp) REVERT: E 3780 LEU cc_start: 0.9672 (mp) cc_final: 0.9021 (mt) REVERT: E 3800 LEU cc_start: 0.9441 (tp) cc_final: 0.8862 (tt) REVERT: E 4034 ASN cc_start: 0.8078 (t0) cc_final: 0.7797 (t0) REVERT: E 4039 MET cc_start: 0.8149 (mmp) cc_final: 0.7343 (mmm) REVERT: E 4057 MET cc_start: 0.8678 (mtm) cc_final: 0.8334 (mtt) REVERT: E 4231 MET cc_start: 0.8447 (tpp) cc_final: 0.8208 (tpp) REVERT: E 4245 MET cc_start: 0.8416 (mmm) cc_final: 0.8125 (mmt) REVERT: E 4682 GLU cc_start: 0.9257 (tt0) cc_final: 0.9041 (pt0) REVERT: E 4769 MET cc_start: 0.5711 (ptm) cc_final: 0.4448 (ttp) REVERT: E 4989 MET cc_start: 0.7893 (tpp) cc_final: 0.7616 (tpp) REVERT: E 5020 ASP cc_start: 0.8740 (p0) cc_final: 0.8381 (p0) outliers start: 12 outliers final: 12 residues processed: 1001 average time/residue: 0.9350 time to fit residues: 1682.0506 Evaluate side-chains 788 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 776 time to evaluate : 9.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.0010 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 ASN ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1688 HIS ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 ASN B2005 GLN B2902 HIS B3643 ASN ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4803 HIS ** B4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 HIS ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 520 ASN G 949 ASN ** G1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1688 HIS ** G1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1972 ASN G2005 GLN G2324 ASN G2902 HIS G3643 ASN ** G3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4803 HIS ** G4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN I 412 ASN ** I 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 597 HIS I 949 ASN ** I1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1688 HIS ** I1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1972 ASN I2005 GLN ** I2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2902 HIS I3643 ASN ** I3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I4803 HIS ** I4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 399 GLN ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1972 ASN E2005 GLN ** E2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2902 HIS ** E3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4803 HIS ** E4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 123528 Z= 0.158 Angle : 0.637 10.500 168436 Z= 0.320 Chirality : 0.040 0.245 19704 Planarity : 0.004 0.079 22192 Dihedral : 5.594 52.302 18156 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.70 % Favored : 90.15 % Rotamer: Outliers : 0.04 % Allowed : 2.14 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: -1.99 (0.07), residues: 13356 helix: -0.09 (0.07), residues: 5860 sheet: -2.04 (0.16), residues: 1040 loop : -2.42 (0.08), residues: 6456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G3661 HIS 0.012 0.001 HIS G4983 PHE 0.026 0.001 PHE I 195 TYR 0.027 0.002 TYR E1089 ARG 0.010 0.001 ARG E 392 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1173 time to evaluate : 9.055 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: 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 35 LYS cc_start: 0.9204 (ttpp) cc_final: 0.8885 (tttm) REVERT: F 44 LYS cc_start: 0.9492 (mmpt) cc_final: 0.9187 (mmmt) REVERT: F 73 LYS cc_start: 0.9343 (tttm) cc_final: 0.9104 (mmtm) REVERT: A 44 LYS cc_start: 0.9450 (mmpt) cc_final: 0.9154 (mmmt) REVERT: A 73 LYS cc_start: 0.9362 (tttm) cc_final: 0.9104 (mmtm) REVERT: H 35 LYS cc_start: 0.9161 (ttpp) cc_final: 0.8859 (tttm) REVERT: H 44 LYS cc_start: 0.9433 (mmpt) cc_final: 0.9157 (mmmt) REVERT: H 73 LYS cc_start: 0.9392 (tttm) cc_final: 0.9147 (mmtm) REVERT: J 44 LYS cc_start: 0.9439 (mmpt) cc_final: 0.9160 (mmmt) REVERT: J 73 LYS cc_start: 0.9358 (tttm) cc_final: 0.9138 (mmtm) REVERT: B 76 ARG cc_start: 0.8858 (mmp80) cc_final: 0.8625 (mmp80) REVERT: B 180 LEU cc_start: 0.9295 (tp) cc_final: 0.9041 (tp) REVERT: B 316 PHE cc_start: 0.9059 (m-80) cc_final: 0.8543 (m-80) REVERT: B 403 MET cc_start: 0.9153 (mtp) cc_final: 0.8754 (mtp) REVERT: B 961 MET cc_start: 0.0846 (mmm) cc_final: 0.0378 (tpp) REVERT: B 1100 MET cc_start: 0.7862 (pmm) cc_final: 0.7462 (pmm) REVERT: B 1601 MET cc_start: 0.8028 (mpp) cc_final: 0.7800 (mpp) REVERT: B 1730 MET cc_start: 0.7464 (ppp) cc_final: 0.6941 (ppp) REVERT: B 2153 MET cc_start: 0.9069 (mmp) cc_final: 0.8829 (mmp) REVERT: B 2211 MET cc_start: 0.8932 (mmt) cc_final: 0.8710 (mmm) REVERT: B 2932 MET cc_start: -0.2567 (ttm) cc_final: -0.2873 (tpt) REVERT: B 3673 MET cc_start: 0.9285 (mmm) cc_final: 0.8904 (mmm) REVERT: B 3723 MET cc_start: 0.9109 (mmt) cc_final: 0.8874 (mmp) REVERT: B 3917 ILE cc_start: 0.9466 (mt) cc_final: 0.9251 (pt) REVERT: B 4058 ILE cc_start: 0.9342 (pt) cc_final: 0.9121 (tp) REVERT: B 4097 MET cc_start: 0.7313 (mmm) cc_final: 0.7044 (mmm) REVERT: B 4146 LEU cc_start: 0.9412 (pp) cc_final: 0.9170 (tt) REVERT: B 4183 ILE cc_start: 0.9362 (pt) cc_final: 0.9090 (mm) REVERT: B 4193 ILE cc_start: 0.8517 (mp) cc_final: 0.8306 (mp) REVERT: B 4207 MET cc_start: 0.9098 (mmm) cc_final: 0.8854 (mmm) REVERT: B 4769 MET cc_start: 0.5260 (ptm) cc_final: 0.4709 (ttp) REVERT: B 4877 ASP cc_start: 0.8405 (m-30) cc_final: 0.8193 (m-30) REVERT: B 4938 ASP cc_start: 0.8896 (m-30) cc_final: 0.8621 (m-30) REVERT: B 4989 MET cc_start: 0.7818 (tpp) cc_final: 0.7529 (tpp) REVERT: G 76 ARG cc_start: 0.8914 (mmp80) cc_final: 0.8684 (mmp80) REVERT: G 180 LEU cc_start: 0.9295 (tp) cc_final: 0.9045 (tp) REVERT: G 316 PHE cc_start: 0.9067 (m-80) cc_final: 0.8469 (m-80) REVERT: G 1100 MET cc_start: 0.7808 (pmm) cc_final: 0.7546 (pmm) REVERT: G 1601 MET cc_start: 0.8034 (mpp) cc_final: 0.7783 (mpp) REVERT: G 1730 MET cc_start: 0.7520 (ppp) cc_final: 0.6997 (ppp) REVERT: G 2228 MET cc_start: 0.8428 (ppp) cc_final: 0.7914 (tmm) REVERT: G 2932 MET cc_start: -0.2276 (ttm) cc_final: -0.2607 (tpt) REVERT: G 3673 MET cc_start: 0.9297 (mmm) cc_final: 0.8908 (mmm) REVERT: G 3780 LEU cc_start: 0.9618 (mp) cc_final: 0.9328 (mp) REVERT: G 3917 ILE cc_start: 0.9194 (pt) cc_final: 0.8884 (tp) REVERT: G 4057 MET cc_start: 0.8542 (mtm) cc_final: 0.8300 (mtp) REVERT: G 4060 LYS cc_start: 0.9188 (pttt) cc_final: 0.8610 (mmpt) REVERT: G 4193 ILE cc_start: 0.8522 (mp) cc_final: 0.8276 (mp) REVERT: G 4207 MET cc_start: 0.9251 (mmp) cc_final: 0.8764 (mmm) REVERT: G 4231 MET cc_start: 0.8490 (tpp) cc_final: 0.8225 (tpp) REVERT: G 4702 ASP cc_start: 0.8680 (m-30) cc_final: 0.8446 (m-30) REVERT: G 4769 MET cc_start: 0.5603 (ptm) cc_final: 0.5038 (ttp) REVERT: G 4938 ASP cc_start: 0.8835 (m-30) cc_final: 0.8604 (m-30) REVERT: G 4989 MET cc_start: 0.7805 (tpp) cc_final: 0.7508 (tpp) REVERT: I 180 LEU cc_start: 0.9187 (tp) cc_final: 0.8930 (tp) REVERT: I 316 PHE cc_start: 0.9027 (m-80) cc_final: 0.8547 (m-80) REVERT: I 403 MET cc_start: 0.9175 (mtp) cc_final: 0.8795 (mtp) REVERT: I 746 CYS cc_start: 0.7942 (m) cc_final: 0.6683 (m) REVERT: I 757 PHE cc_start: 0.5915 (m-10) cc_final: 0.5371 (m-10) REVERT: I 1100 MET cc_start: 0.7892 (pmm) cc_final: 0.7516 (pmm) REVERT: I 1579 MET cc_start: 0.9266 (pmm) cc_final: 0.8967 (pmm) REVERT: I 1601 MET cc_start: 0.8045 (mpp) cc_final: 0.7806 (mpp) REVERT: I 1636 MET cc_start: 0.8670 (ppp) cc_final: 0.8458 (ppp) REVERT: I 1720 LEU cc_start: 0.7101 (tt) cc_final: 0.6789 (tt) REVERT: I 1730 MET cc_start: 0.7500 (ppp) cc_final: 0.6922 (ppp) REVERT: I 2153 MET cc_start: 0.9114 (mmp) cc_final: 0.8731 (mmp) REVERT: I 3673 MET cc_start: 0.9283 (mmm) cc_final: 0.8884 (mmm) REVERT: I 3917 ILE cc_start: 0.9447 (mt) cc_final: 0.9152 (pt) REVERT: I 4019 LEU cc_start: 0.9405 (tt) cc_final: 0.9121 (tt) REVERT: I 4039 MET cc_start: 0.7838 (mmp) cc_final: 0.7486 (mmm) REVERT: I 4057 MET cc_start: 0.8556 (mtm) cc_final: 0.8320 (mtt) REVERT: I 4097 MET cc_start: 0.6971 (mmm) cc_final: 0.6606 (mmm) REVERT: I 4183 ILE cc_start: 0.9368 (pt) cc_final: 0.9093 (mm) REVERT: I 4207 MET cc_start: 0.9092 (mmm) cc_final: 0.8836 (mmm) REVERT: I 4231 MET cc_start: 0.8380 (tpp) cc_final: 0.8121 (tpp) REVERT: I 4769 MET cc_start: 0.5451 (ptm) cc_final: 0.4834 (ttp) REVERT: I 4938 ASP cc_start: 0.8899 (m-30) cc_final: 0.8670 (m-30) REVERT: I 4989 MET cc_start: 0.7708 (tpp) cc_final: 0.7473 (tpp) REVERT: E 180 LEU cc_start: 0.9260 (tp) cc_final: 0.8996 (tp) REVERT: E 316 PHE cc_start: 0.9013 (m-80) cc_final: 0.8542 (m-80) REVERT: E 403 MET cc_start: 0.9133 (mtp) cc_final: 0.8477 (mtp) REVERT: E 568 LEU cc_start: 0.9089 (mp) cc_final: 0.8731 (tt) REVERT: E 1100 MET cc_start: 0.7816 (pmm) cc_final: 0.7544 (pmm) REVERT: E 1601 MET cc_start: 0.8033 (mpp) cc_final: 0.7764 (mpp) REVERT: E 1730 MET cc_start: 0.7516 (ppp) cc_final: 0.7054 (ppp) REVERT: E 2153 MET cc_start: 0.9101 (mmp) cc_final: 0.8727 (mmp) REVERT: E 2457 LEU cc_start: 0.9143 (mt) cc_final: 0.8931 (tt) REVERT: E 3673 MET cc_start: 0.9308 (mmm) cc_final: 0.8845 (mmm) REVERT: E 3723 MET cc_start: 0.9126 (mmt) cc_final: 0.8896 (mmp) REVERT: E 3780 LEU cc_start: 0.9605 (mp) cc_final: 0.9230 (mp) REVERT: E 3917 ILE cc_start: 0.9453 (mt) cc_final: 0.9154 (pt) REVERT: E 4034 ASN cc_start: 0.7933 (t0) cc_final: 0.7715 (t0) REVERT: E 4039 MET cc_start: 0.8008 (mmp) cc_final: 0.7644 (mmm) REVERT: E 4097 MET cc_start: 0.7512 (mmm) cc_final: 0.7292 (mmm) REVERT: E 4159 ARG cc_start: 0.8724 (mtm180) cc_final: 0.8362 (mpp80) REVERT: E 4207 MET cc_start: 0.9129 (mmp) cc_final: 0.8716 (mmm) REVERT: E 4769 MET cc_start: 0.5563 (ptm) cc_final: 0.5073 (ttp) REVERT: E 4989 MET cc_start: 0.7789 (tpp) cc_final: 0.7490 (tpp) outliers start: 4 outliers final: 1 residues processed: 1177 average time/residue: 0.9481 time to fit residues: 2009.2289 Evaluate side-chains 883 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 882 time to evaluate : 9.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 37 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 overall best weight: 7.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN B 949 ASN ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1665 HIS ** B1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 ASN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3970 GLN ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4109 GLN B4803 HIS B4805 ASN B4886 HIS ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 949 ASN ** G1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1972 ASN ** G2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G4109 GLN G4156 HIS G4803 HIS G4805 ASN ** G4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 949 ASN ** I1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1972 ASN ** I2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I4109 GLN I4803 HIS I4805 ASN I5031 GLN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1972 ASN ** E2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2169 GLN ** E2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4020 GLN ** E4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4109 GLN E4803 HIS E4805 ASN E5031 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 123528 Z= 0.415 Angle : 0.817 14.707 168436 Z= 0.416 Chirality : 0.043 0.265 19704 Planarity : 0.005 0.087 22192 Dihedral : 5.942 54.386 18156 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.84 % Favored : 87.02 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.19 % 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: -2.31 (0.07), residues: 13356 helix: -0.36 (0.07), residues: 5812 sheet: -2.21 (0.16), residues: 1036 loop : -2.57 (0.08), residues: 6508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B5019 HIS 0.011 0.002 HIS I3895 PHE 0.030 0.003 PHE E2012 TYR 0.022 0.002 TYR G4863 ARG 0.017 0.001 ARG B4722 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 995 time to evaluate : 9.213 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: 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 35 LYS cc_start: 0.9174 (ttpp) cc_final: 0.8894 (tttm) REVERT: F 44 LYS cc_start: 0.9542 (mmpt) cc_final: 0.9276 (mmmt) REVERT: F 73 LYS cc_start: 0.9470 (tttm) cc_final: 0.9107 (tmtt) REVERT: A 44 LYS cc_start: 0.9539 (mmpt) cc_final: 0.9267 (mmmt) REVERT: A 73 LYS cc_start: 0.9466 (tttm) cc_final: 0.9090 (tmtt) REVERT: H 35 LYS cc_start: 0.9070 (ttpp) cc_final: 0.8826 (tttm) REVERT: H 44 LYS cc_start: 0.9522 (mmpt) cc_final: 0.9250 (mmmt) REVERT: H 73 LYS cc_start: 0.9460 (tttm) cc_final: 0.9147 (mmtm) REVERT: J 44 LYS cc_start: 0.9529 (mmpt) cc_final: 0.9281 (mmmt) REVERT: J 73 LYS cc_start: 0.9472 (tttm) cc_final: 0.9051 (tmtt) REVERT: B 180 LEU cc_start: 0.9343 (tp) cc_final: 0.9125 (tp) REVERT: B 403 MET cc_start: 0.9220 (mtp) cc_final: 0.8846 (mtp) REVERT: B 1100 MET cc_start: 0.7794 (pmm) cc_final: 0.7290 (pmm) REVERT: B 1601 MET cc_start: 0.8148 (mpp) cc_final: 0.7939 (mpp) REVERT: B 1730 MET cc_start: 0.7832 (ppp) cc_final: 0.7272 (ppp) REVERT: B 2198 MET cc_start: 0.9198 (mpp) cc_final: 0.8959 (mpp) REVERT: B 2423 MET cc_start: 0.7028 (ppp) cc_final: 0.6816 (ptm) REVERT: B 2932 MET cc_start: -0.2133 (ttm) cc_final: -0.2636 (tpt) REVERT: B 3673 MET cc_start: 0.9365 (mmm) cc_final: 0.8992 (mmp) REVERT: B 3800 LEU cc_start: 0.9518 (mt) cc_final: 0.9198 (tt) REVERT: B 3955 MET cc_start: 0.8581 (ptm) cc_final: 0.8317 (ptp) REVERT: B 4026 MET cc_start: 0.8730 (tpp) cc_final: 0.8514 (tpt) REVERT: B 4039 MET cc_start: 0.7918 (mmm) cc_final: 0.7690 (mmm) REVERT: B 4057 MET cc_start: 0.8659 (mtm) cc_final: 0.8430 (mtp) REVERT: B 4064 MET cc_start: 0.8701 (pmm) cc_final: 0.8272 (pmm) REVERT: B 4097 MET cc_start: 0.7624 (mmm) cc_final: 0.7348 (mmm) REVERT: B 4174 PHE cc_start: 0.8378 (m-10) cc_final: 0.8173 (m-10) REVERT: B 4769 MET cc_start: 0.5854 (ptm) cc_final: 0.4399 (ttp) REVERT: B 4938 ASP cc_start: 0.8968 (m-30) cc_final: 0.8756 (m-30) REVERT: B 4989 MET cc_start: 0.7827 (tpp) cc_final: 0.7535 (tpp) REVERT: G 180 LEU cc_start: 0.9331 (tp) cc_final: 0.9090 (tp) REVERT: G 231 LEU cc_start: 0.9015 (mt) cc_final: 0.8576 (tp) REVERT: G 961 MET cc_start: 0.2265 (mmp) cc_final: 0.1785 (mmp) REVERT: G 1100 MET cc_start: 0.7815 (pmm) cc_final: 0.7324 (pmm) REVERT: G 1579 MET cc_start: 0.9306 (pmm) cc_final: 0.9074 (pmm) REVERT: G 1601 MET cc_start: 0.8156 (mpp) cc_final: 0.7938 (mpp) REVERT: G 1730 MET cc_start: 0.7877 (ppp) cc_final: 0.7370 (ppp) REVERT: G 2178 MET cc_start: 0.9053 (ppp) cc_final: 0.8810 (ppp) REVERT: G 2198 MET cc_start: 0.9091 (mpp) cc_final: 0.8880 (mpp) REVERT: G 2228 MET cc_start: 0.8635 (ppp) cc_final: 0.8119 (tmm) REVERT: G 2932 MET cc_start: -0.2262 (ttm) cc_final: -0.2575 (tpt) REVERT: G 3673 MET cc_start: 0.9417 (mmm) cc_final: 0.9023 (mmm) REVERT: G 3917 ILE cc_start: 0.9336 (pt) cc_final: 0.9135 (pt) REVERT: G 3955 MET cc_start: 0.8681 (ptm) cc_final: 0.8415 (ptp) REVERT: G 3999 MET cc_start: 0.9038 (pmm) cc_final: 0.8798 (pmm) REVERT: G 4026 MET cc_start: 0.8226 (tpt) cc_final: 0.7962 (tpt) REVERT: G 4039 MET cc_start: 0.8174 (mmp) cc_final: 0.7796 (mmm) REVERT: G 4057 MET cc_start: 0.8526 (mtm) cc_final: 0.8161 (mtp) REVERT: G 4060 LYS cc_start: 0.9218 (pttt) cc_final: 0.8617 (mmpt) REVERT: G 4207 MET cc_start: 0.9341 (mmp) cc_final: 0.9037 (mmm) REVERT: G 4231 MET cc_start: 0.8823 (tpp) cc_final: 0.8608 (tpp) REVERT: G 4769 MET cc_start: 0.5910 (ptm) cc_final: 0.5403 (ttp) REVERT: G 4796 MET cc_start: 0.8645 (mmm) cc_final: 0.8390 (tpp) REVERT: G 4938 ASP cc_start: 0.8981 (m-30) cc_final: 0.8756 (m-30) REVERT: G 5013 MET cc_start: 0.8926 (tpp) cc_final: 0.8471 (tpp) REVERT: G 5020 ASP cc_start: 0.8672 (p0) cc_final: 0.8256 (p0) REVERT: I 180 LEU cc_start: 0.9316 (tp) cc_final: 0.9115 (tp) REVERT: I 403 MET cc_start: 0.9205 (mtp) cc_final: 0.8803 (mtp) REVERT: I 568 LEU cc_start: 0.9200 (mp) cc_final: 0.8899 (tt) REVERT: I 961 MET cc_start: 0.2415 (mmp) cc_final: 0.1920 (mmp) REVERT: I 1100 MET cc_start: 0.7949 (pmm) cc_final: 0.7464 (pmm) REVERT: I 1579 MET cc_start: 0.9289 (pmm) cc_final: 0.9067 (pmm) REVERT: I 1601 MET cc_start: 0.8173 (mpp) cc_final: 0.7943 (mpp) REVERT: I 1730 MET cc_start: 0.7841 (ppp) cc_final: 0.7265 (ppp) REVERT: I 2153 MET cc_start: 0.9179 (mmp) cc_final: 0.8795 (mmp) REVERT: I 3673 MET cc_start: 0.9296 (mmm) cc_final: 0.8866 (mmm) REVERT: I 3723 MET cc_start: 0.9155 (mmp) cc_final: 0.8794 (mmp) REVERT: I 3955 MET cc_start: 0.8674 (ptm) cc_final: 0.8375 (ptp) REVERT: I 4001 MET cc_start: 0.8534 (mmt) cc_final: 0.7873 (mmt) REVERT: I 4026 MET cc_start: 0.8171 (tpt) cc_final: 0.7951 (tpt) REVERT: I 4039 MET cc_start: 0.8158 (mmp) cc_final: 0.7848 (mmm) REVERT: I 4057 MET cc_start: 0.8497 (mtm) cc_final: 0.8157 (mtt) REVERT: I 4064 MET cc_start: 0.8740 (pmm) cc_final: 0.8347 (pmm) REVERT: I 4097 MET cc_start: 0.7532 (mmm) cc_final: 0.7289 (mmm) REVERT: I 4231 MET cc_start: 0.8752 (tpp) cc_final: 0.8530 (tpp) REVERT: I 4769 MET cc_start: 0.5822 (ptm) cc_final: 0.4927 (ttp) REVERT: E 180 LEU cc_start: 0.9327 (tp) cc_final: 0.9113 (tp) REVERT: E 403 MET cc_start: 0.9204 (mtp) cc_final: 0.8817 (mtp) REVERT: E 568 LEU cc_start: 0.9172 (mp) cc_final: 0.8872 (tt) REVERT: E 961 MET cc_start: 0.2556 (mmp) cc_final: 0.2098 (mmp) REVERT: E 1100 MET cc_start: 0.7753 (pmm) cc_final: 0.7282 (pmm) REVERT: E 1579 MET cc_start: 0.9311 (pmm) cc_final: 0.9061 (pmm) REVERT: E 1601 MET cc_start: 0.8092 (mpp) cc_final: 0.7805 (mpp) REVERT: E 1637 MET cc_start: 0.7502 (pmm) cc_final: 0.7289 (pmm) REVERT: E 1730 MET cc_start: 0.7810 (ppp) cc_final: 0.7254 (ppp) REVERT: E 2153 MET cc_start: 0.9189 (mmp) cc_final: 0.8806 (mmp) REVERT: E 3673 MET cc_start: 0.9332 (mmm) cc_final: 0.8919 (mmm) REVERT: E 3800 LEU cc_start: 0.9535 (mt) cc_final: 0.9184 (tt) REVERT: E 3955 MET cc_start: 0.8505 (ptm) cc_final: 0.8291 (ptp) REVERT: E 4039 MET cc_start: 0.8190 (mmp) cc_final: 0.7852 (mmm) REVERT: E 4057 MET cc_start: 0.8830 (mtm) cc_final: 0.8574 (mtp) REVERT: E 4097 MET cc_start: 0.7644 (mmm) cc_final: 0.7360 (mmm) REVERT: E 4207 MET cc_start: 0.9286 (mmp) cc_final: 0.9039 (mmm) REVERT: E 4769 MET cc_start: 0.5945 (ptm) cc_final: 0.4430 (ttp) outliers start: 0 outliers final: 0 residues processed: 995 average time/residue: 0.9307 time to fit residues: 1657.3924 Evaluate side-chains 776 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 776 time to evaluate : 8.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 ASN B2253 HIS ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4574 ASN ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 394 GLN ** 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 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1693 GLN ** G1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1972 ASN G3970 GLN ** G3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G4156 HIS ** G4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1775 HIS I1972 ASN I2169 GLN ** I3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I4574 ASN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 949 ASN ** E1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1688 HIS ** E1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1972 ASN ** E3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4574 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 123528 Z= 0.312 Angle : 0.726 11.520 168436 Z= 0.369 Chirality : 0.041 0.262 19704 Planarity : 0.005 0.082 22192 Dihedral : 5.877 54.499 18156 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.95 % Favored : 87.93 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.29 % Twisted General : 0.19 % 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: -2.19 (0.07), residues: 13356 helix: -0.27 (0.07), residues: 5832 sheet: -2.12 (0.16), residues: 1012 loop : -2.51 (0.08), residues: 6512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B5019 HIS 0.008 0.001 HIS B4983 PHE 0.023 0.002 PHE B2012 TYR 0.024 0.002 TYR G4580 ARG 0.006 0.001 ARG I 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 980 time to evaluate : 9.120 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 LYS cc_start: 0.9550 (mmpt) cc_final: 0.9285 (mmmt) REVERT: F 73 LYS cc_start: 0.9442 (tttm) cc_final: 0.9150 (mmtm) REVERT: A 44 LYS cc_start: 0.9560 (mmpt) cc_final: 0.9278 (mmmt) REVERT: A 73 LYS cc_start: 0.9419 (tttm) cc_final: 0.9104 (mmtm) REVERT: H 44 LYS cc_start: 0.9537 (mmpt) cc_final: 0.9267 (mmmt) REVERT: H 73 LYS cc_start: 0.9436 (tttm) cc_final: 0.9135 (mmtm) REVERT: J 44 LYS cc_start: 0.9544 (mmpt) cc_final: 0.9280 (mmmt) REVERT: J 73 LYS cc_start: 0.9449 (tttm) cc_final: 0.9142 (mmtm) REVERT: B 403 MET cc_start: 0.9196 (mtp) cc_final: 0.8815 (mtp) REVERT: B 961 MET cc_start: 0.1566 (mmm) cc_final: 0.1141 (tpp) REVERT: B 1579 MET cc_start: 0.9298 (pmm) cc_final: 0.9078 (pmm) REVERT: B 1601 MET cc_start: 0.8138 (mpp) cc_final: 0.7931 (mpp) REVERT: B 1730 MET cc_start: 0.7768 (ppp) cc_final: 0.7266 (ppp) REVERT: B 1815 LEU cc_start: 0.9280 (pp) cc_final: 0.9044 (pp) REVERT: B 1865 MET cc_start: 0.8786 (mpp) cc_final: 0.8442 (mpp) REVERT: B 3673 MET cc_start: 0.9358 (mmm) cc_final: 0.9002 (mmm) REVERT: B 3955 MET cc_start: 0.8519 (ptm) cc_final: 0.7996 (ptp) REVERT: B 4057 MET cc_start: 0.8635 (mtm) cc_final: 0.8410 (mtp) REVERT: B 4064 MET cc_start: 0.8805 (pmm) cc_final: 0.8368 (pmm) REVERT: B 4097 MET cc_start: 0.7965 (mmm) cc_final: 0.7700 (mmm) REVERT: B 4207 MET cc_start: 0.9284 (mmp) cc_final: 0.8859 (mmm) REVERT: B 4769 MET cc_start: 0.5822 (ptm) cc_final: 0.5259 (ttp) REVERT: B 4989 MET cc_start: 0.7801 (tpp) cc_final: 0.7504 (tpp) REVERT: G 180 LEU cc_start: 0.9313 (tp) cc_final: 0.9065 (tp) REVERT: G 961 MET cc_start: 0.2182 (mmp) cc_final: 0.1859 (mmp) REVERT: G 1579 MET cc_start: 0.9286 (pmm) cc_final: 0.9026 (pmm) REVERT: G 1601 MET cc_start: 0.8152 (mpp) cc_final: 0.7930 (mpp) REVERT: G 1730 MET cc_start: 0.7831 (ppp) cc_final: 0.7279 (ppp) REVERT: G 2228 MET cc_start: 0.8570 (ppp) cc_final: 0.8229 (ppp) REVERT: G 2932 MET cc_start: -0.1886 (ttm) cc_final: -0.2218 (tpt) REVERT: G 3673 MET cc_start: 0.9383 (mmm) cc_final: 0.9018 (mmm) REVERT: G 3816 MET cc_start: 0.8588 (mmp) cc_final: 0.8362 (mmp) REVERT: G 3955 MET cc_start: 0.8602 (ptm) cc_final: 0.8101 (ptp) REVERT: G 4057 MET cc_start: 0.8728 (mtm) cc_final: 0.8318 (mtp) REVERT: G 4207 MET cc_start: 0.9324 (mmp) cc_final: 0.8829 (mmm) REVERT: G 4769 MET cc_start: 0.5731 (ptm) cc_final: 0.5127 (ttp) REVERT: G 4938 ASP cc_start: 0.8950 (m-30) cc_final: 0.8716 (m-30) REVERT: G 4989 MET cc_start: 0.7971 (tpp) cc_final: 0.7632 (tpp) REVERT: I 180 LEU cc_start: 0.9209 (tp) cc_final: 0.8962 (tp) REVERT: I 403 MET cc_start: 0.9180 (mtp) cc_final: 0.8781 (mtp) REVERT: I 568 LEU cc_start: 0.9177 (mp) cc_final: 0.8921 (tt) REVERT: I 1579 MET cc_start: 0.9279 (pmm) cc_final: 0.8994 (pmm) REVERT: I 1601 MET cc_start: 0.8158 (mpp) cc_final: 0.7931 (mpp) REVERT: I 1730 MET cc_start: 0.7732 (ppp) cc_final: 0.7209 (ppp) REVERT: I 1815 LEU cc_start: 0.9208 (pp) cc_final: 0.8964 (pp) REVERT: I 2153 MET cc_start: 0.9190 (mmp) cc_final: 0.8790 (mmp) REVERT: I 3673 MET cc_start: 0.9284 (mmm) cc_final: 0.8931 (mmm) REVERT: I 3932 ASP cc_start: 0.8700 (p0) cc_final: 0.8415 (p0) REVERT: I 3955 MET cc_start: 0.8690 (ptm) cc_final: 0.8096 (ptp) REVERT: I 4039 MET cc_start: 0.7724 (mmp) cc_final: 0.7458 (mmm) REVERT: I 4057 MET cc_start: 0.8556 (mtm) cc_final: 0.8123 (mtt) REVERT: I 4064 MET cc_start: 0.8822 (pmm) cc_final: 0.8412 (pmm) REVERT: I 4097 MET cc_start: 0.7541 (mmm) cc_final: 0.7293 (mmm) REVERT: I 4207 MET cc_start: 0.9271 (mmp) cc_final: 0.8847 (mmm) REVERT: I 4769 MET cc_start: 0.6130 (ptm) cc_final: 0.5172 (ttp) REVERT: I 4938 ASP cc_start: 0.8937 (m-30) cc_final: 0.8691 (m-30) REVERT: E 180 LEU cc_start: 0.9282 (tp) cc_final: 0.9066 (tp) REVERT: E 403 MET cc_start: 0.9176 (mtp) cc_final: 0.8800 (mtp) REVERT: E 568 LEU cc_start: 0.9156 (mp) cc_final: 0.8893 (tt) REVERT: E 1579 MET cc_start: 0.9330 (pmm) cc_final: 0.9072 (pmm) REVERT: E 1601 MET cc_start: 0.8085 (mpp) cc_final: 0.7771 (mpp) REVERT: E 1730 MET cc_start: 0.7772 (ppp) cc_final: 0.7237 (ppp) REVERT: E 2153 MET cc_start: 0.9170 (mmp) cc_final: 0.8775 (mmp) REVERT: E 2423 MET cc_start: 0.6215 (ptm) cc_final: 0.5410 (ptm) REVERT: E 3673 MET cc_start: 0.9346 (mmm) cc_final: 0.8976 (mmm) REVERT: E 3932 ASP cc_start: 0.8735 (p0) cc_final: 0.8464 (p0) REVERT: E 3955 MET cc_start: 0.8507 (ptm) cc_final: 0.7958 (ptp) REVERT: E 4000 MET cc_start: 0.7362 (tmm) cc_final: 0.6986 (tmm) REVERT: E 4039 MET cc_start: 0.7990 (mmp) cc_final: 0.7740 (mmm) REVERT: E 4057 MET cc_start: 0.8820 (mtm) cc_final: 0.8601 (mtp) REVERT: E 4097 MET cc_start: 0.7857 (mmm) cc_final: 0.7623 (mmm) REVERT: E 4207 MET cc_start: 0.9216 (mmp) cc_final: 0.8800 (mmm) REVERT: E 4769 MET cc_start: 0.5748 (ptm) cc_final: 0.4978 (ttp) REVERT: E 4938 ASP cc_start: 0.8964 (m-30) cc_final: 0.8729 (m-30) REVERT: E 4989 MET cc_start: 0.7919 (tpp) cc_final: 0.7602 (tpp) outliers start: 0 outliers final: 0 residues processed: 980 average time/residue: 0.9826 time to fit residues: 1747.4933 Evaluate side-chains 798 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 798 time to evaluate : 9.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.1980 chunk 30 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 overall best weight: 4.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 ASN H 43 ASN B 44 ASN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1660 GLN B1775 HIS B1972 ASN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 949 ASN ** G1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1660 GLN ** G1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1972 ASN G3970 GLN ** G4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G4153 HIS ** G4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 379 HIS ** I 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 949 ASN ** I1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1660 GLN I1972 ASN ** I4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 520 ASN ** E1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1660 GLN ** E1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1972 ASN ** E4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 123528 Z= 0.268 Angle : 0.692 10.609 168436 Z= 0.351 Chirality : 0.041 0.246 19704 Planarity : 0.005 0.082 22192 Dihedral : 5.754 53.195 18156 Min Nonbonded Distance : 1.407 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.30 % Favored : 87.58 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: -2.06 (0.07), residues: 13356 helix: -0.16 (0.07), residues: 5840 sheet: -2.07 (0.16), residues: 1036 loop : -2.44 (0.08), residues: 6480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G3661 HIS 0.008 0.001 HIS B4983 PHE 0.022 0.002 PHE B 195 TYR 0.019 0.002 TYR G4580 ARG 0.006 0.001 ARG E4188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 982 time to evaluate : 10.951 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 LYS cc_start: 0.9565 (mmpt) cc_final: 0.9304 (mmmt) REVERT: F 73 LYS cc_start: 0.9461 (tttm) cc_final: 0.9175 (mmtm) REVERT: A 44 LYS cc_start: 0.9550 (mmpt) cc_final: 0.9268 (mmmt) REVERT: A 73 LYS cc_start: 0.9453 (tttm) cc_final: 0.9173 (mmtm) REVERT: H 44 LYS cc_start: 0.9557 (mmpt) cc_final: 0.9288 (mmmt) REVERT: H 73 LYS cc_start: 0.9436 (tttm) cc_final: 0.9142 (mmtm) REVERT: J 44 LYS cc_start: 0.9543 (mmpt) cc_final: 0.9272 (mmmt) REVERT: B 180 LEU cc_start: 0.9243 (tp) cc_final: 0.9001 (tp) REVERT: B 403 MET cc_start: 0.9193 (mtp) cc_final: 0.8830 (mtp) REVERT: B 961 MET cc_start: 0.1363 (mmm) cc_final: 0.0910 (tpp) REVERT: B 1100 MET cc_start: 0.7945 (pmm) cc_final: 0.7516 (pmm) REVERT: B 1579 MET cc_start: 0.9328 (pmm) cc_final: 0.8955 (pmm) REVERT: B 1601 MET cc_start: 0.8149 (mpp) cc_final: 0.7942 (mpp) REVERT: B 1730 MET cc_start: 0.7762 (ppp) cc_final: 0.7265 (ppp) REVERT: B 1815 LEU cc_start: 0.9302 (pp) cc_final: 0.9045 (pp) REVERT: B 2423 MET cc_start: 0.6063 (ptm) cc_final: 0.5317 (ptm) REVERT: B 3673 MET cc_start: 0.9336 (mmm) cc_final: 0.8992 (mmm) REVERT: B 3955 MET cc_start: 0.8536 (ptm) cc_final: 0.8005 (ptp) REVERT: B 4026 MET cc_start: 0.8649 (tpp) cc_final: 0.8400 (tpt) REVERT: B 4097 MET cc_start: 0.7905 (mmm) cc_final: 0.7636 (mmm) REVERT: B 4207 MET cc_start: 0.9274 (mmp) cc_final: 0.8811 (mmm) REVERT: B 4652 LEU cc_start: 0.9427 (tp) cc_final: 0.9186 (tt) REVERT: B 4769 MET cc_start: 0.5875 (ptm) cc_final: 0.5346 (ttp) REVERT: B 4874 MET cc_start: 0.7418 (mmm) cc_final: 0.7179 (mmp) REVERT: B 4938 ASP cc_start: 0.8906 (m-30) cc_final: 0.8668 (m-30) REVERT: B 4989 MET cc_start: 0.7768 (tpp) cc_final: 0.7351 (tpp) REVERT: G 180 LEU cc_start: 0.9284 (tp) cc_final: 0.9042 (tp) REVERT: G 1100 MET cc_start: 0.8089 (pmm) cc_final: 0.7549 (pmm) REVERT: G 1579 MET cc_start: 0.9299 (pmm) cc_final: 0.9010 (pmm) REVERT: G 1601 MET cc_start: 0.8166 (mpp) cc_final: 0.7944 (mpp) REVERT: G 1730 MET cc_start: 0.7842 (ppp) cc_final: 0.7277 (ppp) REVERT: G 2178 MET cc_start: 0.9047 (ppp) cc_final: 0.8777 (ppp) REVERT: G 2198 MET cc_start: 0.9045 (mpp) cc_final: 0.8836 (mpp) REVERT: G 2228 MET cc_start: 0.8680 (ppp) cc_final: 0.8083 (tmm) REVERT: G 2423 MET cc_start: 0.6429 (ptm) cc_final: 0.5849 (ptm) REVERT: G 2932 MET cc_start: -0.1796 (ttm) cc_final: -0.2152 (tpt) REVERT: G 3673 MET cc_start: 0.9378 (mmm) cc_final: 0.9001 (mmm) REVERT: G 3759 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8728 (tp30) REVERT: G 3955 MET cc_start: 0.8557 (ptm) cc_final: 0.8046 (ptp) REVERT: G 4039 MET cc_start: 0.8171 (mmm) cc_final: 0.7815 (mmm) REVERT: G 4044 MET cc_start: 0.8917 (mpp) cc_final: 0.8694 (mpp) REVERT: G 4057 MET cc_start: 0.8779 (mtm) cc_final: 0.8390 (mtp) REVERT: G 4207 MET cc_start: 0.9266 (mmp) cc_final: 0.8792 (mmm) REVERT: G 4769 MET cc_start: 0.5850 (ptm) cc_final: 0.4758 (ttm) REVERT: G 4796 MET cc_start: 0.8683 (mmm) cc_final: 0.8447 (mmm) REVERT: G 4938 ASP cc_start: 0.8961 (m-30) cc_final: 0.8738 (m-30) REVERT: G 4989 MET cc_start: 0.7882 (tpp) cc_final: 0.7407 (tpp) REVERT: G 5013 MET cc_start: 0.8894 (tpp) cc_final: 0.8403 (tpp) REVERT: I 180 LEU cc_start: 0.9169 (tp) cc_final: 0.8920 (tp) REVERT: I 403 MET cc_start: 0.9167 (mtp) cc_final: 0.8782 (mtp) REVERT: I 568 LEU cc_start: 0.9181 (mp) cc_final: 0.8946 (tt) REVERT: I 1100 MET cc_start: 0.8012 (pmm) cc_final: 0.7591 (pmm) REVERT: I 1579 MET cc_start: 0.9310 (pmm) cc_final: 0.8988 (pmm) REVERT: I 1601 MET cc_start: 0.8180 (mpp) cc_final: 0.7955 (mpp) REVERT: I 1730 MET cc_start: 0.7720 (ppp) cc_final: 0.7197 (ppp) REVERT: I 1815 LEU cc_start: 0.9237 (pp) cc_final: 0.8973 (pp) REVERT: I 2153 MET cc_start: 0.9190 (mmp) cc_final: 0.8761 (mmp) REVERT: I 2423 MET cc_start: 0.5910 (ptm) cc_final: 0.5673 (ptm) REVERT: I 3673 MET cc_start: 0.9312 (mmm) cc_final: 0.8951 (mmm) REVERT: I 3780 LEU cc_start: 0.9676 (mp) cc_final: 0.9452 (mm) REVERT: I 3932 ASP cc_start: 0.8832 (p0) cc_final: 0.8549 (p0) REVERT: I 3955 MET cc_start: 0.8595 (ptm) cc_final: 0.8027 (ptp) REVERT: I 4039 MET cc_start: 0.8060 (mmp) cc_final: 0.7807 (mmm) REVERT: I 4057 MET cc_start: 0.8611 (mtm) cc_final: 0.8277 (mtp) REVERT: I 4064 MET cc_start: 0.8772 (pmm) cc_final: 0.8440 (pmm) REVERT: I 4097 MET cc_start: 0.7475 (mmm) cc_final: 0.7273 (mmm) REVERT: I 4207 MET cc_start: 0.9263 (mmp) cc_final: 0.8783 (mmm) REVERT: I 4231 MET cc_start: 0.8353 (tpp) cc_final: 0.8071 (tpp) REVERT: I 4769 MET cc_start: 0.6022 (ptm) cc_final: 0.5170 (ttp) REVERT: I 4874 MET cc_start: 0.7404 (mmm) cc_final: 0.7172 (mmp) REVERT: I 4938 ASP cc_start: 0.8944 (m-30) cc_final: 0.8703 (m-30) REVERT: E 180 LEU cc_start: 0.9261 (tp) cc_final: 0.9036 (tp) REVERT: E 403 MET cc_start: 0.9150 (mtp) cc_final: 0.8787 (mtp) REVERT: E 568 LEU cc_start: 0.9147 (mp) cc_final: 0.8918 (tt) REVERT: E 1100 MET cc_start: 0.7861 (pmm) cc_final: 0.7469 (pmm) REVERT: E 1579 MET cc_start: 0.9284 (pmm) cc_final: 0.8933 (pmm) REVERT: E 1601 MET cc_start: 0.8103 (mpp) cc_final: 0.7811 (mpp) REVERT: E 1815 LEU cc_start: 0.9285 (pp) cc_final: 0.9045 (pp) REVERT: E 2153 MET cc_start: 0.9182 (mmp) cc_final: 0.8721 (mmp) REVERT: E 3673 MET cc_start: 0.9342 (mmm) cc_final: 0.8969 (mmm) REVERT: E 3759 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8587 (tp30) REVERT: E 3932 ASP cc_start: 0.8836 (p0) cc_final: 0.8577 (p0) REVERT: E 3955 MET cc_start: 0.8492 (ptm) cc_final: 0.7898 (ptp) REVERT: E 4000 MET cc_start: 0.7211 (tmm) cc_final: 0.6904 (tmm) REVERT: E 4039 MET cc_start: 0.8150 (mmp) cc_final: 0.7896 (mmm) REVERT: E 4097 MET cc_start: 0.7916 (mmm) cc_final: 0.7666 (mmm) REVERT: E 4207 MET cc_start: 0.9219 (mmp) cc_final: 0.8790 (mmm) REVERT: E 4769 MET cc_start: 0.5906 (ptm) cc_final: 0.5162 (ttp) REVERT: E 4938 ASP cc_start: 0.8937 (m-30) cc_final: 0.8662 (m-30) REVERT: E 4989 MET cc_start: 0.7843 (tpp) cc_final: 0.7371 (tpp) outliers start: 0 outliers final: 0 residues processed: 982 average time/residue: 0.9366 time to fit residues: 1657.9482 Evaluate side-chains 801 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 801 time to evaluate : 8.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1688 HIS B1972 ASN ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1688 HIS ** G1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1972 ASN ** G1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G4153 HIS ** G4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 ASN ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1688 HIS I1972 ASN ** I1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 HIS ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1972 ASN ** E1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 123528 Z= 0.273 Angle : 0.704 11.247 168436 Z= 0.355 Chirality : 0.041 0.257 19704 Planarity : 0.005 0.078 22192 Dihedral : 5.728 52.869 18156 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.32 % Favored : 87.53 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.29 % 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: -2.04 (0.07), residues: 13356 helix: -0.12 (0.07), residues: 5860 sheet: -2.04 (0.16), residues: 1036 loop : -2.46 (0.08), residues: 6460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B3661 HIS 0.007 0.001 HIS E4983 PHE 0.022 0.002 PHE I 195 TYR 0.032 0.002 TYR E5009 ARG 0.006 0.001 ARG B1964 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 975 time to evaluate : 9.030 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 MET cc_start: 0.8442 (tmm) cc_final: 0.8131 (tmm) REVERT: F 44 LYS cc_start: 0.9567 (mmpt) cc_final: 0.9312 (mmmt) REVERT: F 73 LYS cc_start: 0.9405 (tttm) cc_final: 0.9161 (mmtm) REVERT: A 44 LYS cc_start: 0.9541 (mmpt) cc_final: 0.9271 (mmmt) REVERT: A 73 LYS cc_start: 0.9441 (tttm) cc_final: 0.9187 (mmtm) REVERT: H 29 MET cc_start: 0.8408 (tmm) cc_final: 0.8054 (tmm) REVERT: H 44 LYS cc_start: 0.9553 (mmpt) cc_final: 0.9279 (mmmt) REVERT: H 73 LYS cc_start: 0.9428 (tttm) cc_final: 0.9136 (mmtm) REVERT: J 44 LYS cc_start: 0.9530 (mmpt) cc_final: 0.9276 (mmmt) REVERT: B 316 PHE cc_start: 0.9156 (m-80) cc_final: 0.8632 (m-80) REVERT: B 403 MET cc_start: 0.9188 (mtp) cc_final: 0.8832 (mtp) REVERT: B 961 MET cc_start: 0.1350 (mmm) cc_final: 0.0921 (tpp) REVERT: B 1100 MET cc_start: 0.7745 (pmm) cc_final: 0.7311 (pmm) REVERT: B 1579 MET cc_start: 0.9336 (pmm) cc_final: 0.8890 (pmm) REVERT: B 1601 MET cc_start: 0.8165 (mpp) cc_final: 0.7961 (mpp) REVERT: B 1815 LEU cc_start: 0.9295 (pp) cc_final: 0.9042 (pp) REVERT: B 2932 MET cc_start: -0.1626 (ptm) cc_final: -0.1868 (ptm) REVERT: B 3673 MET cc_start: 0.9372 (mmm) cc_final: 0.9037 (mmm) REVERT: B 3955 MET cc_start: 0.8530 (ptm) cc_final: 0.7972 (ptp) REVERT: B 3968 TYR cc_start: 0.8744 (m-80) cc_final: 0.8544 (m-80) REVERT: B 4026 MET cc_start: 0.8751 (tpp) cc_final: 0.8326 (tpt) REVERT: B 4056 GLU cc_start: 0.8939 (mp0) cc_final: 0.8659 (mp0) REVERT: B 4057 MET cc_start: 0.8884 (mtm) cc_final: 0.8642 (mtp) REVERT: B 4097 MET cc_start: 0.7902 (mmm) cc_final: 0.7646 (mmm) REVERT: B 4207 MET cc_start: 0.9178 (mmp) cc_final: 0.8746 (mmm) REVERT: B 4652 LEU cc_start: 0.9417 (tp) cc_final: 0.9184 (tt) REVERT: B 4769 MET cc_start: 0.5803 (ptm) cc_final: 0.5292 (ttp) REVERT: B 4938 ASP cc_start: 0.8879 (m-30) cc_final: 0.8648 (m-30) REVERT: B 4989 MET cc_start: 0.7692 (tpp) cc_final: 0.7349 (tpp) REVERT: B 5013 MET cc_start: 0.8398 (mtp) cc_final: 0.7888 (ttm) REVERT: G 180 LEU cc_start: 0.9285 (tp) cc_final: 0.9039 (tp) REVERT: G 1100 MET cc_start: 0.7750 (pmm) cc_final: 0.7346 (pmm) REVERT: G 1579 MET cc_start: 0.9309 (pmm) cc_final: 0.8891 (pmm) REVERT: G 1601 MET cc_start: 0.8182 (mpp) cc_final: 0.7964 (mpp) REVERT: G 2198 MET cc_start: 0.9057 (mpp) cc_final: 0.8816 (mpp) REVERT: G 2228 MET cc_start: 0.8612 (ppp) cc_final: 0.8339 (ppp) REVERT: G 2423 MET cc_start: 0.6374 (ptm) cc_final: 0.5768 (ptm) REVERT: G 2932 MET cc_start: -0.1772 (ttm) cc_final: -0.2139 (tpt) REVERT: G 3673 MET cc_start: 0.9395 (mmm) cc_final: 0.9035 (mmm) REVERT: G 3759 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8635 (tp30) REVERT: G 3928 GLU cc_start: 0.8755 (pp20) cc_final: 0.8551 (pp20) REVERT: G 3955 MET cc_start: 0.8552 (ptm) cc_final: 0.7969 (ptp) REVERT: G 3968 TYR cc_start: 0.8829 (m-80) cc_final: 0.8555 (m-80) REVERT: G 4039 MET cc_start: 0.8190 (mmm) cc_final: 0.7821 (mmm) REVERT: G 4057 MET cc_start: 0.8671 (mtm) cc_final: 0.8231 (mtp) REVERT: G 4207 MET cc_start: 0.9214 (mmp) cc_final: 0.8735 (mmm) REVERT: G 4769 MET cc_start: 0.5882 (ptm) cc_final: 0.4743 (ttm) REVERT: G 4938 ASP cc_start: 0.8943 (m-30) cc_final: 0.8715 (m-30) REVERT: G 4989 MET cc_start: 0.7985 (tpp) cc_final: 0.7603 (tpp) REVERT: I 403 MET cc_start: 0.9169 (mtp) cc_final: 0.8767 (mtp) REVERT: I 961 MET cc_start: 0.2041 (mmp) cc_final: 0.1661 (mmp) REVERT: I 1100 MET cc_start: 0.7765 (pmm) cc_final: 0.7340 (pmm) REVERT: I 1579 MET cc_start: 0.9325 (pmm) cc_final: 0.9001 (pmm) REVERT: I 1601 MET cc_start: 0.8192 (mpp) cc_final: 0.7964 (mpp) REVERT: I 1637 MET cc_start: 0.7242 (pmm) cc_final: 0.7010 (pmm) REVERT: I 1815 LEU cc_start: 0.9259 (pp) cc_final: 0.8988 (pp) REVERT: I 2153 MET cc_start: 0.9177 (mmp) cc_final: 0.8761 (mmp) REVERT: I 3673 MET cc_start: 0.9371 (mmm) cc_final: 0.9063 (mmm) REVERT: I 3932 ASP cc_start: 0.8784 (p0) cc_final: 0.8490 (p0) REVERT: I 3955 MET cc_start: 0.8555 (ptm) cc_final: 0.8007 (ptp) REVERT: I 3968 TYR cc_start: 0.8782 (m-80) cc_final: 0.8492 (m-80) REVERT: I 4000 MET cc_start: 0.7210 (tmm) cc_final: 0.6996 (tmm) REVERT: I 4057 MET cc_start: 0.8633 (mtm) cc_final: 0.8144 (mtt) REVERT: I 4159 ARG cc_start: 0.8746 (mtm180) cc_final: 0.8399 (mpp80) REVERT: I 4207 MET cc_start: 0.9168 (mmp) cc_final: 0.8767 (mmm) REVERT: I 4769 MET cc_start: 0.5681 (ptm) cc_final: 0.4735 (ttp) REVERT: I 4938 ASP cc_start: 0.8951 (m-30) cc_final: 0.8700 (m-30) REVERT: E 316 PHE cc_start: 0.9157 (m-80) cc_final: 0.8607 (m-80) REVERT: E 403 MET cc_start: 0.9146 (mtp) cc_final: 0.8800 (mtp) REVERT: E 568 LEU cc_start: 0.9153 (mp) cc_final: 0.8918 (tt) REVERT: E 961 MET cc_start: 0.2373 (mmp) cc_final: 0.2075 (mmp) REVERT: E 1100 MET cc_start: 0.7583 (pmm) cc_final: 0.7164 (pmm) REVERT: E 1579 MET cc_start: 0.9309 (pmm) cc_final: 0.8916 (pmm) REVERT: E 1601 MET cc_start: 0.8111 (mpp) cc_final: 0.7811 (mpp) REVERT: E 1730 MET cc_start: 0.7739 (ppp) cc_final: 0.7327 (ppp) REVERT: E 1815 LEU cc_start: 0.9294 (pp) cc_final: 0.9029 (pp) REVERT: E 2153 MET cc_start: 0.9160 (mmp) cc_final: 0.8749 (mmp) REVERT: E 2423 MET cc_start: 0.5748 (ptm) cc_final: 0.5174 (ptm) REVERT: E 3673 MET cc_start: 0.9357 (mmm) cc_final: 0.8996 (mmm) REVERT: E 3759 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8700 (tp30) REVERT: E 3932 ASP cc_start: 0.8803 (p0) cc_final: 0.8509 (p0) REVERT: E 3955 MET cc_start: 0.8499 (ptm) cc_final: 0.7945 (ptp) REVERT: E 3968 TYR cc_start: 0.8771 (m-80) cc_final: 0.8523 (m-80) REVERT: E 4097 MET cc_start: 0.7923 (mmm) cc_final: 0.7667 (mmm) REVERT: E 4207 MET cc_start: 0.9196 (mmp) cc_final: 0.8773 (mmm) REVERT: E 4769 MET cc_start: 0.5896 (ptm) cc_final: 0.4715 (ttm) REVERT: E 4938 ASP cc_start: 0.8932 (m-30) cc_final: 0.8686 (m-30) REVERT: E 4989 MET cc_start: 0.7919 (tpp) cc_final: 0.7567 (tpp) outliers start: 0 outliers final: 0 residues processed: 975 average time/residue: 0.9288 time to fit residues: 1643.3831 Evaluate side-chains 801 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 801 time to evaluate : 9.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 13 optimal weight: 0.1980 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 HIS ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 ASN ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 ASN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4776 GLN ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1972 ASN G4153 HIS ** G4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 GLN ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1693 GLN I1972 ASN I2931 GLN I3970 GLN ** I4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I4776 GLN E 71 GLN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1972 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 123528 Z= 0.208 Angle : 0.667 12.208 168436 Z= 0.335 Chirality : 0.040 0.233 19704 Planarity : 0.004 0.078 22192 Dihedral : 5.551 52.791 18156 Min Nonbonded Distance : 1.466 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.70 % Favored : 88.15 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: -1.84 (0.07), residues: 13356 helix: 0.05 (0.07), residues: 5864 sheet: -1.85 (0.16), residues: 1084 loop : -2.39 (0.08), residues: 6408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I5019 HIS 0.007 0.001 HIS I4983 PHE 0.031 0.002 PHE B4243 TYR 0.038 0.001 TYR E5009 ARG 0.005 0.000 ARG B1964 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 995 time to evaluate : 9.288 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 LYS cc_start: 0.9538 (mmpt) cc_final: 0.9279 (mmmt) REVERT: F 73 LYS cc_start: 0.9410 (tttm) cc_final: 0.9182 (mmtm) REVERT: A 44 LYS cc_start: 0.9535 (mmpt) cc_final: 0.9258 (mmmt) REVERT: A 73 LYS cc_start: 0.9452 (tttm) cc_final: 0.9095 (mmtm) REVERT: H 44 LYS cc_start: 0.9546 (mmpt) cc_final: 0.9261 (mmmt) REVERT: H 73 LYS cc_start: 0.9424 (tttm) cc_final: 0.9154 (mmtm) REVERT: J 44 LYS cc_start: 0.9537 (mmpt) cc_final: 0.9261 (mmmt) REVERT: B 180 LEU cc_start: 0.9221 (tp) cc_final: 0.9003 (tp) REVERT: B 316 PHE cc_start: 0.9133 (m-80) cc_final: 0.8647 (m-80) REVERT: B 403 MET cc_start: 0.9168 (mtp) cc_final: 0.8778 (mtp) REVERT: B 961 MET cc_start: 0.1123 (mmm) cc_final: 0.0689 (tpp) REVERT: B 1100 MET cc_start: 0.7701 (pmm) cc_final: 0.7295 (pmm) REVERT: B 1579 MET cc_start: 0.9296 (pmm) cc_final: 0.8775 (pmm) REVERT: B 1601 MET cc_start: 0.8171 (mpp) cc_final: 0.7949 (mpp) REVERT: B 1730 MET cc_start: 0.7719 (ppp) cc_final: 0.7300 (ppp) REVERT: B 1815 LEU cc_start: 0.9257 (pp) cc_final: 0.9021 (pp) REVERT: B 2423 MET cc_start: 0.5654 (ptm) cc_final: 0.5104 (ptm) REVERT: B 2932 MET cc_start: -0.1806 (ptm) cc_final: -0.2069 (ptm) REVERT: B 3673 MET cc_start: 0.9395 (mmm) cc_final: 0.9058 (mmm) REVERT: B 3917 ILE cc_start: 0.9484 (mt) cc_final: 0.9187 (pt) REVERT: B 3928 GLU cc_start: 0.8721 (pp20) cc_final: 0.8490 (pp20) REVERT: B 3955 MET cc_start: 0.8466 (ptm) cc_final: 0.7907 (ptp) REVERT: B 4039 MET cc_start: 0.8277 (mmm) cc_final: 0.7929 (mmm) REVERT: B 4056 GLU cc_start: 0.8928 (mp0) cc_final: 0.8701 (mp0) REVERT: B 4057 MET cc_start: 0.8856 (mtm) cc_final: 0.8654 (mtp) REVERT: B 4064 MET cc_start: 0.8792 (pmm) cc_final: 0.8518 (pmm) REVERT: B 4097 MET cc_start: 0.7698 (mmm) cc_final: 0.7400 (mmm) REVERT: B 4207 MET cc_start: 0.9151 (mmp) cc_final: 0.8762 (mmm) REVERT: B 4567 LEU cc_start: 0.9345 (pp) cc_final: 0.9142 (tt) REVERT: B 4652 LEU cc_start: 0.9384 (tp) cc_final: 0.9133 (tt) REVERT: B 4769 MET cc_start: 0.5424 (ptm) cc_final: 0.4341 (ttp) REVERT: B 4938 ASP cc_start: 0.8854 (m-30) cc_final: 0.8616 (m-30) REVERT: B 5013 MET cc_start: 0.8433 (mtp) cc_final: 0.7954 (ttm) REVERT: B 5020 ASP cc_start: 0.8570 (p0) cc_final: 0.8366 (p0) REVERT: G 180 LEU cc_start: 0.9273 (tp) cc_final: 0.9031 (tp) REVERT: G 961 MET cc_start: 0.1827 (mmp) cc_final: 0.1466 (mmp) REVERT: G 1100 MET cc_start: 0.7704 (pmm) cc_final: 0.7282 (pmm) REVERT: G 1601 MET cc_start: 0.8158 (mpp) cc_final: 0.7950 (mpp) REVERT: G 1637 MET cc_start: 0.7348 (pmm) cc_final: 0.7137 (pmm) REVERT: G 1730 MET cc_start: 0.7770 (ppp) cc_final: 0.7329 (ppp) REVERT: G 1815 LEU cc_start: 0.9246 (pp) cc_final: 0.9006 (pp) REVERT: G 2178 MET cc_start: 0.9053 (ppp) cc_final: 0.8715 (ppp) REVERT: G 2198 MET cc_start: 0.9065 (mpp) cc_final: 0.8811 (mpp) REVERT: G 2228 MET cc_start: 0.8637 (ppp) cc_final: 0.7912 (tmm) REVERT: G 2423 MET cc_start: 0.5987 (ptm) cc_final: 0.5333 (ptm) REVERT: G 2932 MET cc_start: -0.1771 (ttm) cc_final: -0.2125 (tpt) REVERT: G 3673 MET cc_start: 0.9404 (mmm) cc_final: 0.9037 (mmm) REVERT: G 3759 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8546 (tp30) REVERT: G 3816 MET cc_start: 0.8550 (mmp) cc_final: 0.8328 (mmp) REVERT: G 3928 GLU cc_start: 0.8730 (pp20) cc_final: 0.8468 (pp20) REVERT: G 3955 MET cc_start: 0.8509 (ptm) cc_final: 0.7919 (ptp) REVERT: G 3968 TYR cc_start: 0.8778 (m-80) cc_final: 0.8511 (m-80) REVERT: G 3974 THR cc_start: 0.8761 (p) cc_final: 0.8518 (t) REVERT: G 4039 MET cc_start: 0.8250 (mmm) cc_final: 0.7857 (mmm) REVERT: G 4057 MET cc_start: 0.8843 (mtm) cc_final: 0.8567 (mtp) REVERT: G 4207 MET cc_start: 0.9183 (mmp) cc_final: 0.8708 (mmm) REVERT: G 4769 MET cc_start: 0.5804 (ptm) cc_final: 0.5124 (ttp) REVERT: G 4938 ASP cc_start: 0.8897 (m-30) cc_final: 0.8675 (m-30) REVERT: G 4989 MET cc_start: 0.7904 (tpp) cc_final: 0.6699 (tpp) REVERT: I 168 ASP cc_start: 0.8706 (m-30) cc_final: 0.8403 (p0) REVERT: I 180 LEU cc_start: 0.9187 (tp) cc_final: 0.8951 (tp) REVERT: I 316 PHE cc_start: 0.9068 (m-80) cc_final: 0.8594 (m-80) REVERT: I 403 MET cc_start: 0.9143 (mtp) cc_final: 0.8727 (mtp) REVERT: I 1100 MET cc_start: 0.7871 (pmm) cc_final: 0.7477 (pmm) REVERT: I 1579 MET cc_start: 0.9297 (pmm) cc_final: 0.8969 (pmm) REVERT: I 1601 MET cc_start: 0.8182 (mpp) cc_final: 0.7956 (mpp) REVERT: I 1730 MET cc_start: 0.7738 (ppp) cc_final: 0.7269 (ppp) REVERT: I 1815 LEU cc_start: 0.9232 (pp) cc_final: 0.8975 (pp) REVERT: I 2153 MET cc_start: 0.9131 (mmp) cc_final: 0.8708 (mmp) REVERT: I 2423 MET cc_start: 0.5242 (ptm) cc_final: 0.4713 (ptm) REVERT: I 3673 MET cc_start: 0.9370 (mmm) cc_final: 0.9053 (mmm) REVERT: I 3723 MET cc_start: 0.9126 (mmt) cc_final: 0.8865 (mmp) REVERT: I 3816 MET cc_start: 0.8451 (mmp) cc_final: 0.8237 (mmp) REVERT: I 3917 ILE cc_start: 0.9448 (mt) cc_final: 0.9152 (pt) REVERT: I 3955 MET cc_start: 0.8474 (ptm) cc_final: 0.7886 (ptp) REVERT: I 3968 TYR cc_start: 0.8740 (m-80) cc_final: 0.8458 (m-80) REVERT: I 4039 MET cc_start: 0.7794 (mmm) cc_final: 0.7518 (mmm) REVERT: I 4057 MET cc_start: 0.8606 (mtm) cc_final: 0.8290 (mtp) REVERT: I 4064 MET cc_start: 0.8771 (pmm) cc_final: 0.8529 (pmm) REVERT: I 4097 MET cc_start: 0.7110 (mmm) cc_final: 0.6819 (mmm) REVERT: I 4159 ARG cc_start: 0.8694 (mtm180) cc_final: 0.8359 (mpp80) REVERT: I 4207 MET cc_start: 0.9126 (mmp) cc_final: 0.8754 (mmm) REVERT: I 4567 LEU cc_start: 0.9350 (pp) cc_final: 0.9138 (tt) REVERT: I 4769 MET cc_start: 0.5662 (ptm) cc_final: 0.4832 (ttp) REVERT: I 4938 ASP cc_start: 0.8911 (m-30) cc_final: 0.8662 (m-30) REVERT: E 180 LEU cc_start: 0.9197 (tp) cc_final: 0.8973 (tp) REVERT: E 316 PHE cc_start: 0.9096 (m-80) cc_final: 0.8611 (m-80) REVERT: E 403 MET cc_start: 0.9137 (mtp) cc_final: 0.8754 (mtp) REVERT: E 1100 MET cc_start: 0.7645 (pmm) cc_final: 0.7217 (pmm) REVERT: E 1601 MET cc_start: 0.8085 (mpp) cc_final: 0.7812 (mpp) REVERT: E 1730 MET cc_start: 0.7732 (ppp) cc_final: 0.7375 (ppp) REVERT: E 2153 MET cc_start: 0.9119 (mmp) cc_final: 0.8685 (mmp) REVERT: E 2423 MET cc_start: 0.5171 (ptm) cc_final: 0.4571 (ptm) REVERT: E 3673 MET cc_start: 0.9367 (mmm) cc_final: 0.9022 (mmm) REVERT: E 3759 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8614 (tp30) REVERT: E 3917 ILE cc_start: 0.9467 (mt) cc_final: 0.9177 (pt) REVERT: E 3955 MET cc_start: 0.8434 (ptm) cc_final: 0.7802 (ptp) REVERT: E 3968 TYR cc_start: 0.8800 (m-80) cc_final: 0.8591 (m-80) REVERT: E 4023 MET cc_start: 0.8431 (tmm) cc_final: 0.8139 (tmm) REVERT: E 4039 MET cc_start: 0.7867 (mmm) cc_final: 0.7628 (mmm) REVERT: E 4097 MET cc_start: 0.7859 (mmm) cc_final: 0.7592 (mmm) REVERT: E 4159 ARG cc_start: 0.8729 (mtm180) cc_final: 0.8371 (mpp80) REVERT: E 4207 MET cc_start: 0.9145 (mmp) cc_final: 0.8724 (mmm) REVERT: E 4769 MET cc_start: 0.5802 (ptm) cc_final: 0.4625 (ttm) REVERT: E 4938 ASP cc_start: 0.8882 (m-30) cc_final: 0.8637 (m-30) REVERT: E 4989 MET cc_start: 0.7869 (tpp) cc_final: 0.6693 (tpp) outliers start: 0 outliers final: 0 residues processed: 995 average time/residue: 0.9339 time to fit residues: 1687.6739 Evaluate side-chains 821 residues out of total 11708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 821 time to evaluate : 8.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 ASN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1972 ASN G4776 GLN ** G4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1972 ASN ** I3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I3970 GLN ** I4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I4034 ASN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1972 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.068998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.054907 restraints weight = 1128082.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.055415 restraints weight = 661380.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.055993 restraints weight = 478513.934| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 123528 Z= 0.234 Angle : 0.676 11.551 168436 Z= 0.340 Chirality : 0.040 0.234 19704 Planarity : 0.004 0.075 22192 Dihedral : 5.511 52.266 18156 Min Nonbonded Distance : 1.459 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.02 % Favored : 87.81 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.29 % 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: -1.82 (0.07), residues: 13356 helix: 0.09 (0.07), residues: 5840 sheet: -1.88 (0.16), residues: 1032 loop : -2.38 (0.08), residues: 6484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E5019 HIS 0.010 0.001 HIS B2253 PHE 0.017 0.002 PHE G2012 TYR 0.035 0.002 TYR E5009 ARG 0.006 0.000 ARG B1964 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30072.69 seconds wall clock time: 496 minutes 31.64 seconds (29791.64 seconds total)