Starting phenix.real_space_refine on Thu Mar 21 07:01:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcp_6575/03_2024/3jcp_6575.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcp_6575/03_2024/3jcp_6575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcp_6575/03_2024/3jcp_6575.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcp_6575/03_2024/3jcp_6575.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcp_6575/03_2024/3jcp_6575.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcp_6575/03_2024/3jcp_6575.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 381 5.16 5 C 65921 2.51 5 N 17703 2.21 5 O 20165 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 309": "NH1" <-> "NH2" Residue "Q GLU 352": "OE1" <-> "OE2" Residue "Q GLU 355": "OE1" <-> "OE2" Residue "Q GLU 401": "OE1" <-> "OE2" Residue "R GLU 199": "OE1" <-> "OE2" Residue "T GLU 252": "OE1" <-> "OE2" Residue "U GLU 141": "OE1" <-> "OE2" Residue "W PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 68": "OE1" <-> "OE2" Residue "Z GLU 218": "OE1" <-> "OE2" Residue "Z GLU 290": "OE1" <-> "OE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 104170 Number of models: 1 Model: "" Number of chains: 47 Chain: "1" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1757 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "2" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1824 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain: "3" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1573 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1684 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain: "5" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1581 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "6" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1585 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "7" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1644 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain: "8" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1757 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "9" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1824 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1921 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 232} Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1915 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain: "C" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1904 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "D" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1890 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "E" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1861 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "F" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1795 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain: "G" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1896 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 9, 'TRANS': 234} Chain: "H" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2877 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 3, 'PTRANS': 21, 'TRANS': 356} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'TYR:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "I" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2652 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 16, 'TRANS': 333} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "J" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2914 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 356} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Chain: "K" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2835 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2829 Classifications: {'peptide': 358} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 339} Chain breaks: 1 Chain: "M" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2754 Classifications: {'peptide': 357} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 339} Chain breaks: 2 Chain: "N" Number of atoms: 6570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 6570 Classifications: {'peptide': 850} Link IDs: {'PTRANS': 23, 'TRANS': 826} Chain breaks: 1 Chain: "O" Number of atoms: 2912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2912 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'CIS': 8, 'PTRANS': 9, 'TRANS': 358} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 126 Chain: "P" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3470 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 420} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 Chain: "Q" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3469 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PTRANS': 7, 'TRANS': 419} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3187 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 3, 'PTRANS': 6, 'TRANS': 390} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "S" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3384 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'CIS': 8, 'PTRANS': 8, 'TRANS': 422} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 117 Chain: "T" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2201 Classifications: {'peptide': 267} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 258} Chain: "U" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2049 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 246} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1912 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 238} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "W" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1534 Classifications: {'peptide': 197} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 187} Chain: "X" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1032 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "Y" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 243 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 1, 'TRANS': 32} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "Z" Number of atoms: 5688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5688 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 718} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "a" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1921 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 232} Chain: "b" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1915 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain: "c" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1904 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "d" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1890 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "e" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1861 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "f" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1795 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain: "g" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1896 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 9, 'TRANS': 234} Chain: "h" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1574 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "i" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1684 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain: "j" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1578 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "k" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1585 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "l" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1644 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Time building chain proxies: 38.80, per 1000 atoms: 0.37 Number of scatterers: 104170 At special positions: 0 Unit cell: (338.1, 220.5, 216.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 381 16.00 O 20165 8.00 N 17703 7.00 C 65921 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: 35.65 Conformation dependent library (CDL) restraints added in 14.3 seconds 26450 Ramachandran restraints generated. 13225 Oldfield, 0 Emsley, 13225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 24966 Finding SS restraints... Secondary structure from input PDB file: 497 helices and 104 sheets defined 51.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.87 Creating SS restraints... Processing helix chain '1' and resid 76 through 98 Processing helix chain '1' and resid 104 through 119 removed outlier: 3.543A pdb=" N ALA 1 109 " --> pdb=" O ILE 1 105 " (cutoff:3.500A) Processing helix chain '1' and resid 161 through 173 Proline residue: 1 167 - end of helix Processing helix chain '1' and resid 195 through 214 Processing helix chain '2' and resid 90 through 109 removed outlier: 3.518A pdb=" N TYR 2 109 " --> pdb=" O THR 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 111 through 116 removed outlier: 4.188A pdb=" N ASP 2 115 " --> pdb=" O PRO 2 112 " (cutoff:3.500A) Processing helix chain '2' and resid 121 through 139 removed outlier: 3.582A pdb=" N VAL 2 132 " --> pdb=" O TYR 2 128 " (cutoff:3.500A) Processing helix chain '2' and resid 177 through 192 removed outlier: 3.553A pdb=" N HIS 2 182 " --> pdb=" O GLY 2 178 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN 2 185 " --> pdb=" O ALA 2 181 " (cutoff:3.500A) Proline residue: 2 186 - end of helix Processing helix chain '2' and resid 197 through 201 Processing helix chain '2' and resid 202 through 221 Processing helix chain '2' and resid 252 through 258 Processing helix chain '3' and resid 67 through 90 removed outlier: 3.756A pdb=" N ASP 3 76 " --> pdb=" O GLN 3 72 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE 3 77 " --> pdb=" O ALA 3 73 " (cutoff:3.500A) Processing helix chain '3' and resid 93 through 109 Processing helix chain '3' and resid 149 through 161 removed outlier: 3.881A pdb=" N ILE 3 153 " --> pdb=" O GLY 3 149 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR 3 154 " --> pdb=" O SER 3 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLY 3 155 " --> pdb=" O THR 3 151 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR 3 156 " --> pdb=" O PHE 3 152 " (cutoff:3.500A) Processing helix chain '3' and resid 166 through 185 Processing helix chain '3' and resid 208 through 213 Processing helix chain '4' and resid 77 through 100 Processing helix chain '4' and resid 104 through 119 removed outlier: 3.533A pdb=" N ALA 4 108 " --> pdb=" O ARG 4 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS 4 113 " --> pdb=" O LEU 4 109 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS 4 118 " --> pdb=" O GLN 4 114 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR 4 119 " --> pdb=" O HIS 4 115 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 171 Processing helix chain '4' and resid 176 through 195 Processing helix chain '5' and resid 3 through 9 removed outlier: 4.163A pdb=" N ASN 5 8 " --> pdb=" O PRO 5 4 " (cutoff:3.500A) Processing helix chain '5' and resid 56 through 79 removed outlier: 3.597A pdb=" N LEU 5 73 " --> pdb=" O TYR 5 69 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 98 Processing helix chain '5' and resid 142 through 154 removed outlier: 3.613A pdb=" N SER 5 152 " --> pdb=" O GLY 5 148 " (cutoff:3.500A) Processing helix chain '5' and resid 159 through 177 Processing helix chain '6' and resid 49 through 72 removed outlier: 3.510A pdb=" N VAL 6 54 " --> pdb=" O ALA 6 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA 6 57 " --> pdb=" O THR 6 53 " (cutoff:3.500A) Processing helix chain '6' and resid 76 through 93 removed outlier: 3.769A pdb=" N ARG 6 93 " --> pdb=" O ALA 6 89 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 148 removed outlier: 4.501A pdb=" N PHE 6 138 " --> pdb=" O GLY 6 134 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR 6 139 " --> pdb=" O TYR 6 135 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR 6 140 " --> pdb=" O SER 6 136 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER 6 142 " --> pdb=" O PHE 6 138 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU 6 143 " --> pdb=" O TYR 6 139 " (cutoff:3.500A) Processing helix chain '6' and resid 153 through 172 removed outlier: 3.517A pdb=" N GLY 6 157 " --> pdb=" O THR 6 153 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU 6 158 " --> pdb=" O THR 6 154 " (cutoff:3.500A) Processing helix chain '7' and resid 123 through 146 removed outlier: 3.532A pdb=" N GLN 7 137 " --> pdb=" O TRP 7 133 " (cutoff:3.500A) Processing helix chain '7' and resid 150 through 165 Processing helix chain '7' and resid 207 through 219 Processing helix chain '7' and resid 224 through 243 Processing helix chain '7' and resid 268 through 280 Processing helix chain '8' and resid 76 through 98 Processing helix chain '8' and resid 104 through 119 removed outlier: 3.543A pdb=" N ALA 8 109 " --> pdb=" O ILE 8 105 " (cutoff:3.500A) Processing helix chain '8' and resid 161 through 173 Proline residue: 8 167 - end of helix Processing helix chain '8' and resid 195 through 214 Processing helix chain '9' and resid 90 through 109 removed outlier: 3.519A pdb=" N TYR 9 109 " --> pdb=" O THR 9 105 " (cutoff:3.500A) Processing helix chain '9' and resid 111 through 116 removed outlier: 4.188A pdb=" N ASP 9 115 " --> pdb=" O PRO 9 112 " (cutoff:3.500A) Processing helix chain '9' and resid 121 through 139 removed outlier: 3.582A pdb=" N VAL 9 132 " --> pdb=" O TYR 9 128 " (cutoff:3.500A) Processing helix chain '9' and resid 177 through 192 removed outlier: 3.553A pdb=" N HIS 9 182 " --> pdb=" O GLY 9 178 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN 9 185 " --> pdb=" O ALA 9 181 " (cutoff:3.500A) Proline residue: 9 186 - end of helix Processing helix chain '9' and resid 197 through 201 Processing helix chain '9' and resid 202 through 221 Processing helix chain '9' and resid 252 through 258 Processing helix chain 'A' and resid 11 through 16 removed outlier: 4.048A pdb=" N HIS A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 38 removed outlier: 4.233A pdb=" N ASN A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 86 through 109 removed outlier: 3.831A pdb=" N LEU A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 131 removed outlier: 3.609A pdb=" N LEU A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 190 Processing helix chain 'A' and resid 198 through 215 Processing helix chain 'A' and resid 237 through 252 Processing helix chain 'B' and resid 18 through 31 Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 78 through 97 removed outlier: 3.523A pdb=" N ASP B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 124 Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 184 through 200 removed outlier: 3.513A pdb=" N GLU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 19 through 32 Processing helix chain 'C' and resid 80 through 103 Processing helix chain 'C' and resid 107 through 125 removed outlier: 3.508A pdb=" N LEU C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'D' and resid 17 through 30 removed outlier: 3.548A pdb=" N GLU D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 101 removed outlier: 3.626A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 123 removed outlier: 3.703A pdb=" N GLN D 122 " --> pdb=" O GLN D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 179 Processing helix chain 'D' and resid 187 through 204 removed outlier: 3.504A pdb=" N GLU D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 243 removed outlier: 4.019A pdb=" N GLN D 243 " --> pdb=" O GLU D 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.803A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA E 30 " --> pdb=" O TYR E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 83 through 104 removed outlier: 4.150A pdb=" N SER E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 119 through 123 removed outlier: 4.062A pdb=" N PHE E 123 " --> pdb=" O ALA E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 187 Processing helix chain 'E' and resid 192 through 208 Processing helix chain 'E' and resid 232 through 248 Processing helix chain 'F' and resid 3 through 7 Processing helix chain 'F' and resid 19 through 32 removed outlier: 3.588A pdb=" N ILE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 100 removed outlier: 3.822A pdb=" N ALA F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.753A pdb=" N LEU F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 182 removed outlier: 5.480A pdb=" N ASP F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE F 179 " --> pdb=" O THR F 175 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 201 removed outlier: 3.536A pdb=" N SER F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 4.351A pdb=" N LYS F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 11 Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.735A pdb=" N ALA G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 removed outlier: 3.576A pdb=" N GLY G 85 " --> pdb=" O LEU G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 123 removed outlier: 3.577A pdb=" N LEU G 116 " --> pdb=" O PHE G 112 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 183 Processing helix chain 'G' and resid 188 through 208 removed outlier: 4.231A pdb=" N ASP G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN G 207 " --> pdb=" O ALA G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 247 Processing helix chain 'H' and resid 25 through 52 removed outlier: 3.667A pdb=" N TYR H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Proline residue: H 44 - end of helix removed outlier: 4.080A pdb=" N ALA H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR H 52 " --> pdb=" O LYS H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 74 Processing helix chain 'H' and resid 75 through 77 No H-bonds generated for 'chain 'H' and resid 75 through 77' Processing helix chain 'H' and resid 214 through 225 removed outlier: 3.754A pdb=" N GLU H 223 " --> pdb=" O GLU H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 231 Processing helix chain 'H' and resid 232 through 239 Processing helix chain 'H' and resid 255 through 268 Processing helix chain 'H' and resid 276 through 280 removed outlier: 3.609A pdb=" N VAL H 280 " --> pdb=" O GLY H 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 276 through 280' Processing helix chain 'H' and resid 285 through 301 Processing helix chain 'H' and resid 310 through 315 removed outlier: 4.246A pdb=" N VAL H 314 " --> pdb=" O GLU H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 343 removed outlier: 3.853A pdb=" N GLY H 342 " --> pdb=" O THR H 338 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE H 343 " --> pdb=" O GLN H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 361 Processing helix chain 'H' and resid 362 through 367 Processing helix chain 'H' and resid 381 through 394 removed outlier: 3.578A pdb=" N LYS H 394 " --> pdb=" O ARG H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 411 removed outlier: 3.605A pdb=" N LEU H 410 " --> pdb=" O LEU H 406 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 433 removed outlier: 4.042A pdb=" N SER H 421 " --> pdb=" O ALA H 417 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA H 426 " --> pdb=" O VAL H 422 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY H 427 " --> pdb=" O CYS H 423 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N MET H 428 " --> pdb=" O THR H 424 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 455 removed outlier: 3.849A pdb=" N LYS H 455 " --> pdb=" O ILE H 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 86 Proline residue: I 74 - end of helix Proline residue: I 78 - end of helix Processing helix chain 'I' and resid 116 through 128 removed outlier: 3.699A pdb=" N ARG I 127 " --> pdb=" O LEU I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 225 removed outlier: 3.819A pdb=" N ILE I 218 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU I 220 " --> pdb=" O SER I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 231 removed outlier: 3.539A pdb=" N HIS I 231 " --> pdb=" O LEU I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 231 through 237 removed outlier: 3.539A pdb=" N TYR I 235 " --> pdb=" O HIS I 231 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU I 236 " --> pdb=" O PRO I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 268 removed outlier: 3.746A pdb=" N LYS I 261 " --> pdb=" O THR I 257 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA I 262 " --> pdb=" O LEU I 258 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL I 263 " --> pdb=" O LEU I 259 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA I 264 " --> pdb=" O ALA I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 302 removed outlier: 3.634A pdb=" N ALA I 302 " --> pdb=" O ALA I 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 342 removed outlier: 4.234A pdb=" N GLN I 330 " --> pdb=" O GLU I 326 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU I 335 " --> pdb=" O ARG I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 367 Processing helix chain 'I' and resid 381 through 396 removed outlier: 3.608A pdb=" N ILE I 391 " --> pdb=" O LYS I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 409 Processing helix chain 'I' and resid 415 through 433 removed outlier: 3.625A pdb=" N GLN I 420 " --> pdb=" O GLY I 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 440 through 450 Processing helix chain 'J' and resid 29 through 65 removed outlier: 3.618A pdb=" N ILE J 34 " --> pdb=" O THR J 30 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU J 39 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN J 40 " --> pdb=" O SER J 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL J 41 " --> pdb=" O LYS J 37 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG J 42 " --> pdb=" O THR J 38 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN J 49 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LYS J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL J 55 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU J 62 " --> pdb=" O ILE J 58 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 151 Processing helix chain 'J' and resid 153 through 164 Processing helix chain 'J' and resid 164 through 170 Processing helix chain 'J' and resid 171 through 178 Processing helix chain 'J' and resid 194 through 207 removed outlier: 3.671A pdb=" N LEU J 198 " --> pdb=" O GLY J 194 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL J 202 " --> pdb=" O LEU J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 219 Processing helix chain 'J' and resid 224 through 240 removed outlier: 3.966A pdb=" N VAL J 230 " --> pdb=" O GLY J 226 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG J 231 " --> pdb=" O SER J 227 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU J 232 " --> pdb=" O ARG J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 280 removed outlier: 3.736A pdb=" N LEU J 275 " --> pdb=" O THR J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 305 Processing helix chain 'J' and resid 320 through 335 Processing helix chain 'J' and resid 342 through 350 removed outlier: 3.644A pdb=" N VAL J 346 " --> pdb=" O ASN J 342 " (cutoff:3.500A) Processing helix chain 'J' and resid 354 through 372 removed outlier: 3.517A pdb=" N GLY J 360 " --> pdb=" O ALA J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 394 removed outlier: 4.065A pdb=" N PHE J 382 " --> pdb=" O THR J 378 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY J 387 " --> pdb=" O GLU J 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 54 removed outlier: 3.854A pdb=" N LYS K 53 " --> pdb=" O PHE K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 89 removed outlier: 4.067A pdb=" N LEU K 61 " --> pdb=" O GLU K 57 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE K 68 " --> pdb=" O GLN K 64 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS K 69 " --> pdb=" O GLU K 65 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP K 70 " --> pdb=" O ASP K 66 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS K 74 " --> pdb=" O ASP K 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS K 80 " --> pdb=" O LYS K 76 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU K 85 " --> pdb=" O ARG K 81 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS K 87 " --> pdb=" O GLN K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 188 Processing helix chain 'K' and resid 188 through 194 removed outlier: 3.888A pdb=" N VAL K 193 " --> pdb=" O GLU K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 231 removed outlier: 3.810A pdb=" N VAL K 223 " --> pdb=" O LYS K 219 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS K 224 " --> pdb=" O THR K 220 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS K 231 " --> pdb=" O ALA K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 264 removed outlier: 4.107A pdb=" N VAL K 254 " --> pdb=" O GLY K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 278 removed outlier: 3.591A pdb=" N SER K 276 " --> pdb=" O GLU K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 306 removed outlier: 4.098A pdb=" N VAL K 292 " --> pdb=" O SER K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 330 Processing helix chain 'K' and resid 345 through 360 removed outlier: 3.723A pdb=" N SER K 358 " --> pdb=" O GLY K 354 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS K 359 " --> pdb=" O THR K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 375 removed outlier: 3.729A pdb=" N ILE K 373 " --> pdb=" O ASP K 369 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG K 374 " --> pdb=" O SER K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 379 through 397 removed outlier: 3.661A pdb=" N GLN K 388 " --> pdb=" O ALA K 384 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL K 395 " --> pdb=" O GLY K 391 " (cutoff:3.500A) Processing helix chain 'K' and resid 403 through 416 removed outlier: 4.434A pdb=" N LYS K 416 " --> pdb=" O ALA K 412 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 98 removed outlier: 3.850A pdb=" N GLN L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP L 83 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU L 84 " --> pdb=" O ASN L 80 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU L 87 " --> pdb=" O ASP L 83 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR L 88 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP L 89 " --> pdb=" O GLU L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 184 Processing helix chain 'L' and resid 186 through 197 Processing helix chain 'L' and resid 198 through 203 removed outlier: 4.120A pdb=" N LYS L 202 " --> pdb=" O GLU L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 240 removed outlier: 3.709A pdb=" N ALA L 232 " --> pdb=" O LYS L 228 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS L 233 " --> pdb=" O THR L 229 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE L 239 " --> pdb=" O VAL L 235 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY L 240 " --> pdb=" O ALA L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 253 removed outlier: 3.648A pdb=" N ASP L 253 " --> pdb=" O GLY L 250 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 274 removed outlier: 3.649A pdb=" N ALA L 270 " --> pdb=" O MET L 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 314 removed outlier: 3.529A pdb=" N LEU L 308 " --> pdb=" O THR L 304 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU L 309 " --> pdb=" O LEU L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 329 through 333 removed outlier: 3.647A pdb=" N THR L 332 " --> pdb=" O ARG L 329 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 339 Processing helix chain 'L' and resid 353 through 365 Processing helix chain 'L' and resid 375 through 383 removed outlier: 3.798A pdb=" N ALA L 379 " --> pdb=" O ASP L 375 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 406 Processing helix chain 'L' and resid 411 through 426 removed outlier: 4.039A pdb=" N LYS L 417 " --> pdb=" O ASP L 413 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL L 425 " --> pdb=" O LYS L 421 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS L 426 " --> pdb=" O VAL L 422 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 38 removed outlier: 3.607A pdb=" N LEU M 12 " --> pdb=" O ASP M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix removed outlier: 3.651A pdb=" N LEU M 18 " --> pdb=" O GLY M 14 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP M 19 " --> pdb=" O ASP M 15 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN M 24 " --> pdb=" O GLN M 20 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU M 29 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR M 32 " --> pdb=" O GLN M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 72 No H-bonds generated for 'chain 'M' and resid 71 through 72' Processing helix chain 'M' and resid 186 through 197 Processing helix chain 'M' and resid 197 through 203 Processing helix chain 'M' and resid 227 through 239 Processing helix chain 'M' and resid 248 through 252 Processing helix chain 'M' and resid 257 through 274 removed outlier: 3.576A pdb=" N ALA M 270 " --> pdb=" O ALA M 266 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 286 Processing helix chain 'M' and resid 294 through 297 Processing helix chain 'M' and resid 298 through 315 removed outlier: 3.574A pdb=" N GLN M 302 " --> pdb=" O ASP M 298 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE M 315 " --> pdb=" O GLN M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 367 removed outlier: 3.520A pdb=" N ILE M 363 " --> pdb=" O GLN M 359 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS M 367 " --> pdb=" O ILE M 363 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 383 Processing helix chain 'M' and resid 387 through 405 removed outlier: 4.185A pdb=" N LEU M 391 " --> pdb=" O ASN M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 411 through 421 Processing helix chain 'N' and resid 6 through 15 removed outlier: 4.296A pdb=" N ARG N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 40 removed outlier: 4.372A pdb=" N ASP N 33 " --> pdb=" O ASN N 29 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLN N 34 " --> pdb=" O ASN N 30 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N SER N 37 " --> pdb=" O ASP N 33 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLU N 38 " --> pdb=" O GLN N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 51 Processing helix chain 'N' and resid 55 through 57 No H-bonds generated for 'chain 'N' and resid 55 through 57' Processing helix chain 'N' and resid 58 through 72 Processing helix chain 'N' and resid 75 through 86 Processing helix chain 'N' and resid 95 through 120 removed outlier: 3.764A pdb=" N MET N 108 " --> pdb=" O LYS N 104 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR N 109 " --> pdb=" O SER N 105 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL N 110 " --> pdb=" O ILE N 106 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN N 111 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS N 119 " --> pdb=" O LYS N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 126 Processing helix chain 'N' and resid 130 through 148 Processing helix chain 'N' and resid 149 through 161 removed outlier: 3.763A pdb=" N ALA N 153 " --> pdb=" O GLU N 149 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 177 Processing helix chain 'N' and resid 178 through 197 removed outlier: 3.973A pdb=" N VAL N 183 " --> pdb=" O THR N 179 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE N 186 " --> pdb=" O ASN N 182 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 216 Processing helix chain 'N' and resid 221 through 233 removed outlier: 3.530A pdb=" N LEU N 225 " --> pdb=" O ASP N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 249 removed outlier: 3.507A pdb=" N ALA N 238 " --> pdb=" O ASP N 234 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 263 Processing helix chain 'N' and resid 266 through 280 removed outlier: 3.768A pdb=" N GLU N 271 " --> pdb=" O GLN N 267 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE N 272 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU N 273 " --> pdb=" O LEU N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 290 removed outlier: 3.529A pdb=" N LEU N 287 " --> pdb=" O ASP N 283 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 307 Processing helix chain 'N' and resid 310 through 319 removed outlier: 3.557A pdb=" N LEU N 314 " --> pdb=" O ASP N 310 " (cutoff:3.500A) Processing helix chain 'N' and resid 325 through 340 removed outlier: 3.734A pdb=" N HIS N 329 " --> pdb=" O PHE N 325 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA N 331 " --> pdb=" O LEU N 327 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL N 334 " --> pdb=" O THR N 330 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY N 337 " --> pdb=" O SER N 333 " (cutoff:3.500A) Processing helix chain 'N' and resid 346 through 352 Processing helix chain 'N' and resid 353 through 359 removed outlier: 3.773A pdb=" N GLY N 357 " --> pdb=" O LEU N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 360 through 375 removed outlier: 3.839A pdb=" N LEU N 371 " --> pdb=" O ALA N 367 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY N 372 " --> pdb=" O THR N 368 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL N 373 " --> pdb=" O ALA N 369 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE N 374 " --> pdb=" O SER N 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 380 through 387 removed outlier: 3.684A pdb=" N LYS N 384 " --> pdb=" O LEU N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 388 through 390 No H-bonds generated for 'chain 'N' and resid 388 through 390' Processing helix chain 'N' and resid 397 through 413 removed outlier: 4.147A pdb=" N LEU N 405 " --> pdb=" O LYS N 401 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR N 406 " --> pdb=" O GLY N 402 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY N 409 " --> pdb=" O LEU N 405 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU N 410 " --> pdb=" O TYR N 406 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE N 411 " --> pdb=" O GLY N 407 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR N 412 " --> pdb=" O LEU N 408 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 432 removed outlier: 4.114A pdb=" N GLY N 432 " --> pdb=" O VAL N 428 " (cutoff:3.500A) Processing helix chain 'N' and resid 436 through 455 removed outlier: 4.549A pdb=" N GLY N 451 " --> pdb=" O SER N 447 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 472 Processing helix chain 'N' and resid 476 through 489 removed outlier: 4.384A pdb=" N ALA N 480 " --> pdb=" O THR N 476 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA N 481 " --> pdb=" O SER N 477 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY N 486 " --> pdb=" O ALA N 482 " (cutoff:3.500A) Processing helix chain 'N' and resid 494 through 508 Processing helix chain 'N' and resid 511 through 525 removed outlier: 3.732A pdb=" N LEU N 517 " --> pdb=" O ILE N 513 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA N 518 " --> pdb=" O THR N 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL N 519 " --> pdb=" O ARG N 515 " (cutoff:3.500A) Processing helix chain 'N' and resid 532 through 542 Processing helix chain 'N' and resid 544 through 560 removed outlier: 3.573A pdb=" N ARG N 548 " --> pdb=" O GLU N 544 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE N 553 " --> pdb=" O TYR N 549 " (cutoff:3.500A) Processing helix chain 'N' and resid 564 through 578 Processing helix chain 'N' and resid 580 through 595 removed outlier: 3.989A pdb=" N GLY N 592 " --> pdb=" O VAL N 588 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE N 593 " --> pdb=" O ILE N 589 " (cutoff:3.500A) Processing helix chain 'N' and resid 600 through 611 removed outlier: 4.711A pdb=" N ARG N 604 " --> pdb=" O THR N 600 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU N 608 " --> pdb=" O ARG N 604 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU N 609 " --> pdb=" O ILE N 605 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS N 611 " --> pdb=" O GLN N 607 " (cutoff:3.500A) Processing helix chain 'N' and resid 614 through 629 removed outlier: 3.839A pdb=" N ALA N 622 " --> pdb=" O ARG N 618 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE N 623 " --> pdb=" O CYS N 619 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA N 624 " --> pdb=" O GLY N 620 " (cutoff:3.500A) Processing helix chain 'N' and resid 634 through 645 removed outlier: 3.772A pdb=" N LEU N 641 " --> pdb=" O ALA N 637 " (cutoff:3.500A) Proline residue: N 643 - end of helix Processing helix chain 'N' and resid 649 through 665 Processing helix chain 'N' and resid 674 through 688 Processing helix chain 'N' and resid 694 through 707 Processing helix chain 'N' and resid 726 through 738 removed outlier: 3.624A pdb=" N VAL N 730 " --> pdb=" O ASP N 726 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY N 732 " --> pdb=" O LYS N 728 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU N 733 " --> pdb=" O SER N 729 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN N 738 " --> pdb=" O VAL N 734 " (cutoff:3.500A) Processing helix chain 'N' and resid 745 through 751 Processing helix chain 'N' and resid 875 through 881 removed outlier: 3.578A pdb=" N ARG N 880 " --> pdb=" O PRO N 876 " (cutoff:3.500A) Processing helix chain 'N' and resid 919 through 925 Processing helix chain 'O' and resid 4 through 12 removed outlier: 3.822A pdb=" N SER O 12 " --> pdb=" O ASP O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 34 removed outlier: 3.617A pdb=" N GLN O 28 " --> pdb=" O PRO O 24 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU O 30 " --> pdb=" O PHE O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 63 Processing helix chain 'O' and resid 85 through 90 removed outlier: 3.867A pdb=" N LYS O 90 " --> pdb=" O LYS O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 104 removed outlier: 3.949A pdb=" N LEU O 96 " --> pdb=" O PHE O 92 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP O 100 " --> pdb=" O LEU O 96 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP O 101 " --> pdb=" O LYS O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 139 removed outlier: 3.726A pdb=" N LEU O 139 " --> pdb=" O ARG O 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 160 removed outlier: 4.219A pdb=" N LYS O 159 " --> pdb=" O LYS O 155 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS O 160 " --> pdb=" O THR O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 182 removed outlier: 3.815A pdb=" N SER O 173 " --> pdb=" O ASN O 169 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS O 182 " --> pdb=" O TYR O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 200 removed outlier: 3.590A pdb=" N TYR O 190 " --> pdb=" O ASN O 186 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 223 removed outlier: 3.840A pdb=" N GLN O 212 " --> pdb=" O ALA O 208 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU O 222 " --> pdb=" O SER O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 243 Processing helix chain 'O' and resid 246 through 258 removed outlier: 3.706A pdb=" N TRP O 250 " --> pdb=" O SER O 246 " (cutoff:3.500A) Processing helix chain 'O' and resid 271 through 277 removed outlier: 3.877A pdb=" N ILE O 277 " --> pdb=" O GLN O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 279 through 299 removed outlier: 3.646A pdb=" N SER O 285 " --> pdb=" O ALA O 281 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR O 295 " --> pdb=" O ILE O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 316 Processing helix chain 'O' and resid 320 through 325 Processing helix chain 'O' and resid 361 through 381 removed outlier: 4.094A pdb=" N LYS O 365 " --> pdb=" O ASP O 361 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS O 367 " --> pdb=" O ILE O 363 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP O 368 " --> pdb=" O THR O 364 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG O 369 " --> pdb=" O LYS O 365 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN O 374 " --> pdb=" O LEU O 370 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS O 379 " --> pdb=" O ASP O 375 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU O 380 " --> pdb=" O GLN O 376 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 25 removed outlier: 3.671A pdb=" N ASP P 12 " --> pdb=" O LYS P 8 " (cutoff:3.500A) Proline residue: P 22 - end of helix Processing helix chain 'P' and resid 34 through 46 removed outlier: 3.789A pdb=" N LEU P 42 " --> pdb=" O GLN P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 70 removed outlier: 3.698A pdb=" N LEU P 59 " --> pdb=" O SER P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 71 through 86 removed outlier: 3.558A pdb=" N HIS P 86 " --> pdb=" O LEU P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 106 removed outlier: 4.642A pdb=" N GLN P 94 " --> pdb=" O LYS P 90 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR P 95 " --> pdb=" O LEU P 91 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET P 96 " --> pdb=" O SER P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 122 removed outlier: 3.557A pdb=" N GLU P 120 " --> pdb=" O ILE P 116 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE P 122 " --> pdb=" O VAL P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 123 through 126 Processing helix chain 'P' and resid 132 through 137 Processing helix chain 'P' and resid 137 through 150 Processing helix chain 'P' and resid 153 through 161 Processing helix chain 'P' and resid 172 through 191 removed outlier: 3.544A pdb=" N GLN P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE P 179 " --> pdb=" O GLU P 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 209 removed outlier: 3.729A pdb=" N ALA P 196 " --> pdb=" O ASP P 192 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU P 199 " --> pdb=" O GLN P 195 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU P 204 " --> pdb=" O SER P 200 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS P 205 " --> pdb=" O ARG P 201 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS P 206 " --> pdb=" O LYS P 202 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR P 207 " --> pdb=" O ILE P 203 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 232 Processing helix chain 'P' and resid 233 through 251 removed outlier: 3.626A pdb=" N THR P 247 " --> pdb=" O GLU P 243 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA P 249 " --> pdb=" O TYR P 245 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE P 250 " --> pdb=" O GLN P 246 " (cutoff:3.500A) Processing helix chain 'P' and resid 253 through 271 Proline residue: P 259 - end of helix removed outlier: 3.978A pdb=" N TYR P 266 " --> pdb=" O SER P 262 " (cutoff:3.500A) Processing helix chain 'P' and resid 274 through 281 Processing helix chain 'P' and resid 294 through 305 removed outlier: 4.456A pdb=" N THR P 304 " --> pdb=" O VAL P 300 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR P 305 " --> pdb=" O LYS P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 309 through 318 removed outlier: 4.487A pdb=" N ILE P 313 " --> pdb=" O MET P 309 " (cutoff:3.500A) Processing helix chain 'P' and resid 333 through 336 removed outlier: 3.776A pdb=" N HIS P 336 " --> pdb=" O ALA P 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 333 through 336' Processing helix chain 'P' and resid 337 through 357 removed outlier: 3.613A pdb=" N VAL P 352 " --> pdb=" O HIS P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 370 Processing helix chain 'P' and resid 372 through 386 Processing helix chain 'P' and resid 405 through 409 removed outlier: 4.033A pdb=" N SER P 409 " --> pdb=" O LYS P 406 " (cutoff:3.500A) Processing helix chain 'P' and resid 410 through 441 removed outlier: 4.680A pdb=" N GLU P 427 " --> pdb=" O LEU P 423 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU P 432 " --> pdb=" O THR P 428 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR P 434 " --> pdb=" O GLY P 430 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS P 435 " --> pdb=" O HIS P 431 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 18 Processing helix chain 'Q' and resid 19 through 33 removed outlier: 3.528A pdb=" N GLN Q 25 " --> pdb=" O ASN Q 21 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL Q 26 " --> pdb=" O GLU Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 69 removed outlier: 3.528A pdb=" N GLU Q 60 " --> pdb=" O THR Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 87 removed outlier: 3.516A pdb=" N GLU Q 76 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) Proline residue: Q 79 - end of helix Processing helix chain 'Q' and resid 89 through 106 Processing helix chain 'Q' and resid 110 through 128 removed outlier: 3.679A pdb=" N LYS Q 126 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 148 Processing helix chain 'Q' and resid 150 through 166 Processing helix chain 'Q' and resid 170 through 188 Processing helix chain 'Q' and resid 190 through 208 removed outlier: 3.621A pdb=" N SER Q 207 " --> pdb=" O THR Q 203 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE Q 208 " --> pdb=" O ALA Q 204 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 229 removed outlier: 4.353A pdb=" N GLU Q 228 " --> pdb=" O ILE Q 224 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP Q 229 " --> pdb=" O LEU Q 225 " (cutoff:3.500A) Processing helix chain 'Q' and resid 231 through 250 Processing helix chain 'Q' and resid 256 through 273 Processing helix chain 'Q' and resid 274 through 284 removed outlier: 3.530A pdb=" N VAL Q 278 " --> pdb=" O LEU Q 274 " (cutoff:3.500A) Processing helix chain 'Q' and resid 284 through 289 Processing helix chain 'Q' and resid 293 through 309 Processing helix chain 'Q' and resid 310 through 321 removed outlier: 3.791A pdb=" N PHE Q 314 " --> pdb=" O SER Q 310 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN Q 315 " --> pdb=" O LEU Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 328 through 350 removed outlier: 4.253A pdb=" N ASN Q 336 " --> pdb=" O ARG Q 332 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR Q 341 " --> pdb=" O ALA Q 337 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU Q 342 " --> pdb=" O LEU Q 338 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU Q 343 " --> pdb=" O TYR Q 339 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU Q 344 " --> pdb=" O ASP Q 340 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE Q 350 " --> pdb=" O ASN Q 346 " (cutoff:3.500A) Processing helix chain 'Q' and resid 358 through 366 Processing helix chain 'Q' and resid 373 through 378 removed outlier: 3.607A pdb=" N SER Q 378 " --> pdb=" O GLU Q 374 " (cutoff:3.500A) Processing helix chain 'Q' and resid 408 through 431 removed outlier: 3.761A pdb=" N GLU Q 414 " --> pdb=" O ASP Q 410 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU Q 415 " --> pdb=" O SER Q 411 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN Q 420 " --> pdb=" O VAL Q 416 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS Q 421 " --> pdb=" O GLY Q 417 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL Q 422 " --> pdb=" O GLN Q 418 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 35 Processing helix chain 'R' and resid 39 through 57 removed outlier: 4.368A pdb=" N ALA R 46 " --> pdb=" O GLN R 42 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA R 47 " --> pdb=" O ARG R 43 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE R 49 " --> pdb=" O GLU R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 70 removed outlier: 3.688A pdb=" N TYR R 65 " --> pdb=" O PRO R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 124 removed outlier: 3.696A pdb=" N TYR R 99 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 145 removed outlier: 3.723A pdb=" N ALA R 133 " --> pdb=" O GLU R 129 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR R 141 " --> pdb=" O LEU R 137 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA R 142 " --> pdb=" O GLY R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 159 Processing helix chain 'R' and resid 163 through 181 removed outlier: 3.600A pdb=" N ASP R 169 " --> pdb=" O GLY R 165 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET R 171 " --> pdb=" O LYS R 167 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR R 181 " --> pdb=" O LEU R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 198 removed outlier: 4.094A pdb=" N ILE R 198 " --> pdb=" O VAL R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 218 removed outlier: 3.631A pdb=" N ASN R 208 " --> pdb=" O TRP R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 234 removed outlier: 4.020A pdb=" N LEU R 230 " --> pdb=" O GLU R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 261 Processing helix chain 'R' and resid 262 through 269 Processing helix chain 'R' and resid 273 through 280 Processing helix chain 'R' and resid 290 through 297 Processing helix chain 'R' and resid 303 through 316 removed outlier: 4.391A pdb=" N LEU R 309 " --> pdb=" O PHE R 305 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN R 314 " --> pdb=" O GLU R 310 " (cutoff:3.500A) Processing helix chain 'R' and resid 319 through 326 removed outlier: 3.645A pdb=" N ARG R 324 " --> pdb=" O LYS R 320 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA R 326 " --> pdb=" O LEU R 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 340 removed outlier: 3.678A pdb=" N TYR R 338 " --> pdb=" O ARG R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 355 Processing helix chain 'R' and resid 360 through 370 Processing helix chain 'R' and resid 400 through 402 No H-bonds generated for 'chain 'R' and resid 400 through 402' Processing helix chain 'R' and resid 403 through 421 removed outlier: 4.212A pdb=" N GLY R 407 " --> pdb=" O LEU R 403 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL R 421 " --> pdb=" O TYR R 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 22 Processing helix chain 'S' and resid 24 through 38 Processing helix chain 'S' and resid 44 through 56 removed outlier: 3.680A pdb=" N ASP S 49 " --> pdb=" O THR S 45 " (cutoff:3.500A) Proline residue: S 50 - end of helix removed outlier: 3.783A pdb=" N ILE S 53 " --> pdb=" O ASP S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 58 through 69 removed outlier: 3.539A pdb=" N GLN S 66 " --> pdb=" O SER S 62 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 129 through 144 removed outlier: 3.556A pdb=" N GLU S 133 " --> pdb=" O GLU S 129 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU S 144 " --> pdb=" O LEU S 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 152 through 164 Processing helix chain 'S' and resid 180 through 192 removed outlier: 3.600A pdb=" N ILE S 187 " --> pdb=" O LEU S 183 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR S 188 " --> pdb=" O TRP S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 204 through 221 Processing helix chain 'S' and resid 229 through 242 removed outlier: 3.609A pdb=" N LEU S 233 " --> pdb=" O THR S 229 " (cutoff:3.500A) Processing helix chain 'S' and resid 248 through 257 removed outlier: 3.754A pdb=" N ASP S 252 " --> pdb=" O ASP S 248 " (cutoff:3.500A) Processing helix chain 'S' and resid 265 through 283 removed outlier: 3.593A pdb=" N ASN S 280 " --> pdb=" O LEU S 276 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE S 282 " --> pdb=" O LYS S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 286 through 294 Processing helix chain 'S' and resid 308 through 324 removed outlier: 3.618A pdb=" N GLN S 312 " --> pdb=" O GLY S 308 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN S 321 " --> pdb=" O HIS S 317 " (cutoff:3.500A) Processing helix chain 'S' and resid 329 through 334 removed outlier: 4.294A pdb=" N PHE S 333 " --> pdb=" O GLU S 329 " (cutoff:3.500A) Processing helix chain 'S' and resid 343 through 355 removed outlier: 3.744A pdb=" N LEU S 354 " --> pdb=" O LYS S 350 " (cutoff:3.500A) Processing helix chain 'S' and resid 356 through 375 removed outlier: 5.747A pdb=" N GLN S 369 " --> pdb=" O THR S 365 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU S 370 " --> pdb=" O LYS S 366 " (cutoff:3.500A) Processing helix chain 'S' and resid 382 through 395 removed outlier: 3.614A pdb=" N ASN S 386 " --> pdb=" O ARG S 382 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE S 394 " --> pdb=" O THR S 390 " (cutoff:3.500A) Processing helix chain 'S' and resid 404 through 413 removed outlier: 3.701A pdb=" N LEU S 411 " --> pdb=" O ILE S 407 " (cutoff:3.500A) Processing helix chain 'S' and resid 417 through 429 removed outlier: 3.861A pdb=" N TYR S 421 " --> pdb=" O GLN S 417 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP S 429 " --> pdb=" O ARG S 425 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 467 Processing helix chain 'S' and resid 469 through 488 removed outlier: 3.998A pdb=" N LEU S 476 " --> pdb=" O HIS S 472 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG S 480 " --> pdb=" O LEU S 476 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR S 481 " --> pdb=" O VAL S 477 " (cutoff:3.500A) Proline residue: S 482 - end of helix removed outlier: 3.696A pdb=" N GLN S 488 " --> pdb=" O ASP S 484 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 17 Processing helix chain 'T' and resid 19 through 37 removed outlier: 4.217A pdb=" N LYS T 25 " --> pdb=" O ALA T 21 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU T 26 " --> pdb=" O ALA T 22 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU T 27 " --> pdb=" O CYS T 23 " (cutoff:3.500A) Proline residue: T 28 - end of helix removed outlier: 3.623A pdb=" N ILE T 35 " --> pdb=" O LYS T 31 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS T 36 " --> pdb=" O ILE T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 72 removed outlier: 4.201A pdb=" N THR T 58 " --> pdb=" O ASP T 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 90 Proline residue: T 87 - end of helix Processing helix chain 'T' and resid 100 through 116 removed outlier: 3.771A pdb=" N LYS T 104 " --> pdb=" O ASP T 100 " (cutoff:3.500A) Processing helix chain 'T' and resid 118 through 129 Processing helix chain 'T' and resid 132 through 137 Processing helix chain 'T' and resid 139 through 155 Proline residue: T 145 - end of helix removed outlier: 3.769A pdb=" N GLU T 154 " --> pdb=" O ARG T 150 " (cutoff:3.500A) Processing helix chain 'T' and resid 157 through 167 removed outlier: 3.506A pdb=" N GLN T 165 " --> pdb=" O TRP T 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 167 through 172 Processing helix chain 'T' and resid 174 through 197 removed outlier: 3.607A pdb=" N THR T 178 " --> pdb=" O PHE T 174 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP T 179 " --> pdb=" O ASP T 175 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE T 180 " --> pdb=" O SER T 176 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU T 188 " --> pdb=" O ALA T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 210 Processing helix chain 'T' and resid 213 through 224 removed outlier: 3.847A pdb=" N THR T 217 " --> pdb=" O ASN T 213 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE T 220 " --> pdb=" O GLU T 216 " (cutoff:3.500A) Processing helix chain 'T' and resid 253 through 270 removed outlier: 3.610A pdb=" N THR T 257 " --> pdb=" O GLU T 253 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 25 Processing helix chain 'U' and resid 70 through 84 removed outlier: 3.524A pdb=" N GLU U 78 " --> pdb=" O GLU U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 87 No H-bonds generated for 'chain 'U' and resid 85 through 87' Processing helix chain 'U' and resid 101 through 114 removed outlier: 4.132A pdb=" N LYS U 105 " --> pdb=" O ALA U 101 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE U 110 " --> pdb=" O ILE U 106 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS U 111 " --> pdb=" O ASN U 107 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR U 113 " --> pdb=" O LEU U 109 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 173 Processing helix chain 'U' and resid 190 through 195 removed outlier: 3.520A pdb=" N LEU U 194 " --> pdb=" O LEU U 190 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS U 195 " --> pdb=" O THR U 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 190 through 195' Processing helix chain 'U' and resid 197 through 215 removed outlier: 3.945A pdb=" N LEU U 204 " --> pdb=" O LEU U 200 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS U 205 " --> pdb=" O GLN U 201 " (cutoff:3.500A) Processing helix chain 'U' and resid 224 through 231 removed outlier: 3.506A pdb=" N ASP U 231 " --> pdb=" O GLY U 227 " (cutoff:3.500A) Processing helix chain 'U' and resid 263 through 277 removed outlier: 3.796A pdb=" N VAL U 267 " --> pdb=" O LYS U 263 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR U 269 " --> pdb=" O LEU U 265 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN U 270 " --> pdb=" O THR U 266 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP U 271 " --> pdb=" O VAL U 267 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL U 275 " --> pdb=" O ASP U 271 " (cutoff:3.500A) Processing helix chain 'U' and resid 278 through 286 removed outlier: 4.407A pdb=" N VAL U 282 " --> pdb=" O ILE U 278 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER U 284 " --> pdb=" O ASN U 280 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE U 286 " --> pdb=" O VAL U 282 " (cutoff:3.500A) Processing helix chain 'U' and resid 290 through 306 removed outlier: 4.129A pdb=" N VAL U 306 " --> pdb=" O GLN U 302 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 45 removed outlier: 3.678A pdb=" N ALA V 43 " --> pdb=" O LYS V 39 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL V 45 " --> pdb=" O GLY V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 99 removed outlier: 3.834A pdb=" N GLN V 88 " --> pdb=" O ASP V 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 131 Processing helix chain 'V' and resid 144 through 149 removed outlier: 3.631A pdb=" N LYS V 148 " --> pdb=" O GLN V 145 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY V 149 " --> pdb=" O SER V 146 " (cutoff:3.500A) Processing helix chain 'V' and resid 185 through 190 removed outlier: 3.830A pdb=" N ILE V 189 " --> pdb=" O ILE V 185 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 215 removed outlier: 3.690A pdb=" N THR V 210 " --> pdb=" O THR V 206 " (cutoff:3.500A) Processing helix chain 'V' and resid 231 through 236 Processing helix chain 'V' and resid 243 through 245 No H-bonds generated for 'chain 'V' and resid 243 through 245' Processing helix chain 'V' and resid 246 through 267 removed outlier: 3.941A pdb=" N LYS V 259 " --> pdb=" O ILE V 255 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU V 260 " --> pdb=" O GLU V 256 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU V 261 " --> pdb=" O GLU V 257 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR V 262 " --> pdb=" O GLU V 258 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU V 263 " --> pdb=" O LYS V 259 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS V 267 " --> pdb=" O GLU V 263 " (cutoff:3.500A) Processing helix chain 'V' and resid 278 through 286 removed outlier: 3.918A pdb=" N GLU V 282 " --> pdb=" O LYS V 278 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA V 284 " --> pdb=" O LEU V 280 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU V 286 " --> pdb=" O GLU V 282 " (cutoff:3.500A) Processing helix chain 'V' and resid 287 through 294 Processing helix chain 'W' and resid 24 through 44 removed outlier: 3.697A pdb=" N ASP W 31 " --> pdb=" O GLU W 27 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER W 32 " --> pdb=" O ALA W 28 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 76 Processing helix chain 'W' and resid 86 through 100 Processing helix chain 'W' and resid 121 through 136 Processing helix chain 'W' and resid 152 through 162 removed outlier: 3.519A pdb=" N ALA W 159 " --> pdb=" O ASP W 155 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN W 162 " --> pdb=" O ILE W 158 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 169 Processing helix chain 'W' and resid 180 through 188 removed outlier: 3.934A pdb=" N SER W 187 " --> pdb=" O GLU W 183 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER W 188 " --> pdb=" O ASN W 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 131 removed outlier: 4.456A pdb=" N ASN X 123 " --> pdb=" O LYS X 119 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU X 129 " --> pdb=" O MET X 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 71 through 89 Processing helix chain 'Z' and resid 111 through 125 removed outlier: 4.805A pdb=" N LEU Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER Z 120 " --> pdb=" O ALA Z 116 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 140 removed outlier: 3.536A pdb=" N LEU Z 140 " --> pdb=" O ARG Z 136 " (cutoff:3.500A) Processing helix chain 'Z' and resid 151 through 170 removed outlier: 4.136A pdb=" N ARG Z 155 " --> pdb=" O HIS Z 151 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU Z 159 " --> pdb=" O ARG Z 155 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE Z 161 " --> pdb=" O LEU Z 157 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL Z 164 " --> pdb=" O GLU Z 160 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL Z 169 " --> pdb=" O TYR Z 165 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU Z 170 " --> pdb=" O ASN Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 171 through 173 No H-bonds generated for 'chain 'Z' and resid 171 through 173' Processing helix chain 'Z' and resid 197 through 214 removed outlier: 3.707A pdb=" N ILE Z 207 " --> pdb=" O LEU Z 203 " (cutoff:3.500A) Proline residue: Z 209 - end of helix removed outlier: 3.539A pdb=" N HIS Z 214 " --> pdb=" O TYR Z 210 " (cutoff:3.500A) Processing helix chain 'Z' and resid 219 through 226 Processing helix chain 'Z' and resid 231 through 236 Processing helix chain 'Z' and resid 243 through 253 removed outlier: 3.596A pdb=" N GLN Z 247 " --> pdb=" O GLN Z 243 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA Z 251 " --> pdb=" O GLN Z 247 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N CYS Z 252 " --> pdb=" O TYR Z 248 " (cutoff:3.500A) Processing helix chain 'Z' and resid 262 through 266 Processing helix chain 'Z' and resid 278 through 286 removed outlier: 3.716A pdb=" N ALA Z 283 " --> pdb=" O THR Z 279 " (cutoff:3.500A) Processing helix chain 'Z' and resid 292 through 301 removed outlier: 4.500A pdb=" N SER Z 296 " --> pdb=" O ASP Z 292 " (cutoff:3.500A) Processing helix chain 'Z' and resid 303 through 317 removed outlier: 3.552A pdb=" N GLN Z 317 " --> pdb=" O ILE Z 313 " (cutoff:3.500A) Processing helix chain 'Z' and resid 317 through 323 removed outlier: 4.197A pdb=" N TYR Z 323 " --> pdb=" O THR Z 319 " (cutoff:3.500A) Processing helix chain 'Z' and resid 344 through 349 removed outlier: 3.803A pdb=" N LEU Z 348 " --> pdb=" O LYS Z 344 " (cutoff:3.500A) Processing helix chain 'Z' and resid 352 through 365 removed outlier: 4.042A pdb=" N ASP Z 356 " --> pdb=" O LYS Z 352 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER Z 360 " --> pdb=" O ASP Z 356 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS Z 361 " --> pdb=" O ILE Z 357 " (cutoff:3.500A) Processing helix chain 'Z' and resid 376 through 391 removed outlier: 4.318A pdb=" N ALA Z 382 " --> pdb=" O GLN Z 378 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE Z 385 " --> pdb=" O LEU Z 381 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN Z 387 " --> pdb=" O SER Z 383 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY Z 388 " --> pdb=" O SER Z 384 " (cutoff:3.500A) Processing helix chain 'Z' and resid 397 through 402 Processing helix chain 'Z' and resid 404 through 410 removed outlier: 3.709A pdb=" N THR Z 410 " --> pdb=" O TRP Z 406 " (cutoff:3.500A) Processing helix chain 'Z' and resid 412 through 426 removed outlier: 3.821A pdb=" N THR Z 416 " --> pdb=" O GLY Z 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE Z 422 " --> pdb=" O ALA Z 418 " (cutoff:3.500A) Processing helix chain 'Z' and resid 432 through 441 removed outlier: 4.095A pdb=" N LEU Z 436 " --> pdb=" O GLY Z 432 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR Z 441 " --> pdb=" O ASP Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 444 through 459 removed outlier: 4.022A pdb=" N ALA Z 451 " --> pdb=" O VAL Z 447 " (cutoff:3.500A) Processing helix chain 'Z' and resid 470 through 478 removed outlier: 3.922A pdb=" N GLN Z 475 " --> pdb=" O LEU Z 471 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP Z 476 " --> pdb=" O LEU Z 472 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR Z 477 " --> pdb=" O LEU Z 473 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 498 Processing helix chain 'Z' and resid 502 through 516 removed outlier: 3.974A pdb=" N LEU Z 506 " --> pdb=" O ASN Z 502 " (cutoff:3.500A) Proline residue: Z 511 - end of helix Processing helix chain 'Z' and resid 522 through 532 removed outlier: 3.888A pdb=" N LEU Z 528 " --> pdb=" O ALA Z 524 " (cutoff:3.500A) Processing helix chain 'Z' and resid 539 through 550 removed outlier: 3.640A pdb=" N MET Z 547 " --> pdb=" O THR Z 543 " (cutoff:3.500A) Processing helix chain 'Z' and resid 559 through 574 removed outlier: 3.590A pdb=" N VAL Z 563 " --> pdb=" O LYS Z 559 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU Z 566 " --> pdb=" O TRP Z 562 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA Z 569 " --> pdb=" O PHE Z 565 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU Z 573 " --> pdb=" O ALA Z 569 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR Z 574 " --> pdb=" O LEU Z 570 " (cutoff:3.500A) Processing helix chain 'Z' and resid 579 through 588 removed outlier: 5.443A pdb=" N LEU Z 585 " --> pdb=" O VAL Z 581 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU Z 586 " --> pdb=" O ASP Z 582 " (cutoff:3.500A) Processing helix chain 'Z' and resid 593 through 598 removed outlier: 4.335A pdb=" N ALA Z 598 " --> pdb=" O PRO Z 594 " (cutoff:3.500A) Processing helix chain 'Z' and resid 598 through 603 removed outlier: 3.779A pdb=" N LEU Z 602 " --> pdb=" O ALA Z 598 " (cutoff:3.500A) Processing helix chain 'Z' and resid 614 through 621 Processing helix chain 'Z' and resid 743 through 749 removed outlier: 4.166A pdb=" N LEU Z 748 " --> pdb=" O ALA Z 744 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY Z 749 " --> pdb=" O LEU Z 745 " (cutoff:3.500A) Processing helix chain 'Z' and resid 754 through 767 removed outlier: 3.547A pdb=" N ARG Z 759 " --> pdb=" O GLU Z 755 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY Z 762 " --> pdb=" O LEU Z 758 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N HIS Z 763 " --> pdb=" O ARG Z 759 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS Z 766 " --> pdb=" O GLY Z 762 " (cutoff:3.500A) Processing helix chain 'Z' and resid 769 through 785 Proline residue: Z 777 - end of helix removed outlier: 4.037A pdb=" N GLY Z 781 " --> pdb=" O PRO Z 777 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE Z 782 " --> pdb=" O LEU Z 778 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL Z 783 " --> pdb=" O ALA Z 779 " (cutoff:3.500A) Processing helix chain 'Z' and resid 791 through 800 removed outlier: 3.991A pdb=" N THR Z 797 " --> pdb=" O PHE Z 793 " (cutoff:3.500A) Processing helix chain 'Z' and resid 804 through 819 removed outlier: 3.878A pdb=" N SER Z 808 " --> pdb=" O ASP Z 804 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET Z 815 " --> pdb=" O SER Z 811 " (cutoff:3.500A) Processing helix chain 'Z' and resid 824 through 826 No H-bonds generated for 'chain 'Z' and resid 824 through 826' Processing helix chain 'Z' and resid 827 through 836 removed outlier: 3.922A pdb=" N LEU Z 831 " --> pdb=" O LEU Z 827 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG Z 832 " --> pdb=" O ALA Z 828 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLN Z 833 " --> pdb=" O GLN Z 829 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU Z 834 " --> pdb=" O LEU Z 830 " (cutoff:3.500A) Processing helix chain 'Z' and resid 841 through 857 Processing helix chain 'Z' and resid 874 through 879 removed outlier: 3.641A pdb=" N LEU Z 878 " --> pdb=" O ASN Z 874 " (cutoff:3.500A) Processing helix chain 'Z' and resid 881 through 887 Processing helix chain 'Z' and resid 897 through 907 removed outlier: 3.883A pdb=" N LEU Z 900 " --> pdb=" O HIS Z 897 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE Z 901 " --> pdb=" O HIS Z 898 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR Z 902 " --> pdb=" O GLN Z 899 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET Z 903 " --> pdb=" O LEU Z 900 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU Z 904 " --> pdb=" O PHE Z 901 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA Z 906 " --> pdb=" O MET Z 903 " (cutoff:3.500A) Processing helix chain 'a' and resid 11 through 16 removed outlier: 4.049A pdb=" N HIS a 15 " --> pdb=" O GLY a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 38 removed outlier: 4.233A pdb=" N ASN a 36 " --> pdb=" O PHE a 32 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR a 38 " --> pdb=" O ALA a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 69 Processing helix chain 'a' and resid 86 through 109 removed outlier: 3.831A pdb=" N LEU a 95 " --> pdb=" O ARG a 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA a 102 " --> pdb=" O LYS a 98 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 131 removed outlier: 3.609A pdb=" N LEU a 124 " --> pdb=" O ARG a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 174 through 190 Processing helix chain 'a' and resid 198 through 215 Processing helix chain 'a' and resid 237 through 252 Processing helix chain 'b' and resid 18 through 31 Processing helix chain 'b' and resid 58 through 61 Processing helix chain 'b' and resid 78 through 97 removed outlier: 3.523A pdb=" N ASP b 87 " --> pdb=" O ARG b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 97 through 102 Processing helix chain 'b' and resid 106 through 124 Processing helix chain 'b' and resid 167 through 179 Processing helix chain 'b' and resid 184 through 200 removed outlier: 3.512A pdb=" N GLU b 198 " --> pdb=" O LEU b 194 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER b 199 " --> pdb=" O THR b 195 " (cutoff:3.500A) Processing helix chain 'b' and resid 218 through 222 Processing helix chain 'b' and resid 239 through 249 Processing helix chain 'c' and resid 2 through 7 Processing helix chain 'c' and resid 19 through 32 Processing helix chain 'c' and resid 80 through 103 Processing helix chain 'c' and resid 107 through 125 removed outlier: 3.508A pdb=" N LEU c 111 " --> pdb=" O PRO c 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR c 122 " --> pdb=" O ILE c 118 " (cutoff:3.500A) Processing helix chain 'c' and resid 168 through 180 Processing helix chain 'c' and resid 185 through 201 Processing helix chain 'c' and resid 207 through 209 No H-bonds generated for 'chain 'c' and resid 207 through 209' Processing helix chain 'c' and resid 231 through 242 Processing helix chain 'd' and resid 17 through 30 removed outlier: 3.548A pdb=" N GLU d 25 " --> pdb=" O GLU d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 78 through 101 removed outlier: 3.625A pdb=" N ILE d 84 " --> pdb=" O ALA d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 123 removed outlier: 3.703A pdb=" N GLN d 122 " --> pdb=" O GLN d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 167 through 179 Processing helix chain 'd' and resid 187 through 204 removed outlier: 3.504A pdb=" N GLU d 201 " --> pdb=" O ARG d 197 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL d 202 " --> pdb=" O SER d 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 225 through 243 removed outlier: 4.019A pdb=" N GLN d 243 " --> pdb=" O GLU d 239 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 34 removed outlier: 3.802A pdb=" N GLU e 29 " --> pdb=" O GLU e 25 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA e 30 " --> pdb=" O TYR e 26 " (cutoff:3.500A) Processing helix chain 'e' and resid 61 through 64 Processing helix chain 'e' and resid 83 through 104 removed outlier: 4.149A pdb=" N SER e 87 " --> pdb=" O ALA e 83 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET e 88 " --> pdb=" O ASP e 84 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 Processing helix chain 'e' and resid 119 through 123 removed outlier: 4.063A pdb=" N PHE e 123 " --> pdb=" O ALA e 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 175 through 187 Processing helix chain 'e' and resid 192 through 208 Processing helix chain 'e' and resid 232 through 248 Processing helix chain 'f' and resid 3 through 7 Processing helix chain 'f' and resid 19 through 32 removed outlier: 3.588A pdb=" N ILE f 29 " --> pdb=" O ALA f 25 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS f 30 " --> pdb=" O LEU f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 77 through 100 removed outlier: 3.822A pdb=" N ALA f 81 " --> pdb=" O LEU f 77 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 122 removed outlier: 3.753A pdb=" N LEU f 111 " --> pdb=" O ARG f 107 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU f 112 " --> pdb=" O ALA f 108 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN f 119 " --> pdb=" O LYS f 115 " (cutoff:3.500A) Processing helix chain 'f' and resid 165 through 182 removed outlier: 5.480A pdb=" N ASP f 177 " --> pdb=" O GLU f 173 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR f 178 " --> pdb=" O ARG f 174 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE f 179 " --> pdb=" O THR f 175 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE f 180 " --> pdb=" O LEU f 176 " (cutoff:3.500A) Processing helix chain 'f' and resid 185 through 201 removed outlier: 3.536A pdb=" N SER f 200 " --> pdb=" O ALA f 196 " (cutoff:3.500A) Processing helix chain 'f' and resid 227 through 232 removed outlier: 4.351A pdb=" N LYS f 232 " --> pdb=" O GLU f 228 " (cutoff:3.500A) Processing helix chain 'g' and resid 7 through 11 Processing helix chain 'g' and resid 21 through 34 removed outlier: 3.735A pdb=" N ALA g 30 " --> pdb=" O TYR g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 104 removed outlier: 3.576A pdb=" N GLY g 85 " --> pdb=" O LEU g 81 " (cutoff:3.500A) Processing helix chain 'g' and resid 108 through 123 removed outlier: 3.576A pdb=" N LEU g 116 " --> pdb=" O PHE g 112 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS g 123 " --> pdb=" O TYR g 119 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 183 Processing helix chain 'g' and resid 188 through 208 removed outlier: 4.231A pdb=" N ASP g 206 " --> pdb=" O LEU g 202 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN g 207 " --> pdb=" O ALA g 203 " (cutoff:3.500A) Processing helix chain 'g' and resid 232 through 247 Processing helix chain 'h' and resid 67 through 90 removed outlier: 3.756A pdb=" N ASP h 76 " --> pdb=" O GLN h 72 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE h 77 " --> pdb=" O ALA h 73 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 109 Processing helix chain 'h' and resid 149 through 161 removed outlier: 3.881A pdb=" N ILE h 153 " --> pdb=" O GLY h 149 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR h 154 " --> pdb=" O SER h 150 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLY h 155 " --> pdb=" O THR h 151 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR h 156 " --> pdb=" O PHE h 152 " (cutoff:3.500A) Processing helix chain 'h' and resid 166 through 185 Processing helix chain 'h' and resid 208 through 213 Processing helix chain 'i' and resid 77 through 100 Processing helix chain 'i' and resid 104 through 119 removed outlier: 3.534A pdb=" N ALA i 108 " --> pdb=" O ARG i 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS i 113 " --> pdb=" O LEU i 109 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS i 118 " --> pdb=" O GLN i 114 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR i 119 " --> pdb=" O HIS i 115 " (cutoff:3.500A) Processing helix chain 'i' and resid 159 through 171 Processing helix chain 'i' and resid 176 through 195 Processing helix chain 'j' and resid 3 through 9 removed outlier: 4.163A pdb=" N ASN j 8 " --> pdb=" O PRO j 4 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 79 removed outlier: 3.596A pdb=" N LEU j 73 " --> pdb=" O TYR j 69 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 98 Processing helix chain 'j' and resid 142 through 154 removed outlier: 3.613A pdb=" N SER j 152 " --> pdb=" O GLY j 148 " (cutoff:3.500A) Processing helix chain 'j' and resid 159 through 177 Processing helix chain 'k' and resid 49 through 72 removed outlier: 3.511A pdb=" N VAL k 54 " --> pdb=" O ALA k 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA k 57 " --> pdb=" O THR k 53 " (cutoff:3.500A) Processing helix chain 'k' and resid 76 through 93 removed outlier: 3.769A pdb=" N ARG k 93 " --> pdb=" O ALA k 89 " (cutoff:3.500A) Processing helix chain 'k' and resid 134 through 148 removed outlier: 4.500A pdb=" N PHE k 138 " --> pdb=" O GLY k 134 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR k 139 " --> pdb=" O TYR k 135 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR k 140 " --> pdb=" O SER k 136 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER k 142 " --> pdb=" O PHE k 138 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU k 143 " --> pdb=" O TYR k 139 " (cutoff:3.500A) Processing helix chain 'k' and resid 153 through 172 removed outlier: 3.517A pdb=" N GLY k 157 " --> pdb=" O THR k 153 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU k 158 " --> pdb=" O THR k 154 " (cutoff:3.500A) Processing helix chain 'l' and resid 123 through 146 removed outlier: 3.532A pdb=" N GLN l 137 " --> pdb=" O TRP l 133 " (cutoff:3.500A) Processing helix chain 'l' and resid 150 through 165 Processing helix chain 'l' and resid 207 through 219 Processing helix chain 'l' and resid 224 through 243 Processing helix chain 'l' and resid 268 through 280 Processing sheet with id= A, first strand: chain '1' and resid 155 through 158 removed outlier: 3.796A pdb=" N GLY 1 44 " --> pdb=" O GLU 1 222 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU 1 222 " --> pdb=" O GLY 1 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 48 through 50 removed outlier: 6.404A pdb=" N ASN 1 48 " --> pdb=" O ASN 1 55 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '1' and resid 62 through 66 removed outlier: 6.383A pdb=" N ILE 1 69 " --> pdb=" O CYS 1 65 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER 1 143 " --> pdb=" O GLU 1 151 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU 1 151 " --> pdb=" O SER 1 143 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 66 through 69 removed outlier: 4.746A pdb=" N LEU 2 67 " --> pdb=" O TYR 2 63 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TYR 2 63 " --> pdb=" O LEU 2 67 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '2' and resid 66 through 69 removed outlier: 4.746A pdb=" N LEU 2 67 " --> pdb=" O TYR 2 63 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TYR 2 63 " --> pdb=" O LEU 2 67 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY 2 85 " --> pdb=" O ILE 2 148 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '2' and resid 174 through 176 removed outlier: 3.595A pdb=" N ALA 2 57 " --> pdb=" O SER 2 229 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE 2 228 " --> pdb=" O ASN 2 244 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 143 through 146 Processing sheet with id= H, first strand: chain '3' and resid 39 through 41 removed outlier: 5.692A pdb=" N THR 3 41 " --> pdb=" O ILE 3 45 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE 3 45 " --> pdb=" O THR 3 41 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 53 through 55 Processing sheet with id= J, first strand: chain '4' and resid 153 through 157 removed outlier: 6.705A pdb=" N THR 4 31 " --> pdb=" O ASP 4 46 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL 4 202 " --> pdb=" O ASN 4 218 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '4' and resid 49 through 51 removed outlier: 6.433A pdb=" N SER 4 49 " --> pdb=" O ALA 4 56 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '4' and resid 63 through 67 removed outlier: 6.187A pdb=" N ILE 4 70 " --> pdb=" O ILE 4 66 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 241 through 247 removed outlier: 3.599A pdb=" N VAL 5 195 " --> pdb=" O VAL 4 247 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE 5 11 " --> pdb=" O ASP 5 26 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '5' and resid 43 through 46 Processing sheet with id= O, first strand: chain '6' and resid 130 through 131 removed outlier: 3.802A pdb=" N VAL 6 181 " --> pdb=" O VAL 6 192 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '6' and resid 22 through 23 Processing sheet with id= Q, first strand: chain '6' and resid 35 through 39 removed outlier: 6.111A pdb=" N THR 6 42 " --> pdb=" O LEU 6 38 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '7' and resid 201 through 205 removed outlier: 6.253A pdb=" N THR 7 77 " --> pdb=" O ASP 7 92 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL 7 91 " --> pdb=" O ASN 7 251 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN 7 251 " --> pdb=" O VAL 7 91 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL 7 250 " --> pdb=" O ASN 7 265 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN 7 265 " --> pdb=" O VAL 7 250 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU 7 252 " --> pdb=" O HIS 7 263 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '7' and resid 95 through 97 removed outlier: 5.016A pdb=" N ALA 7 97 " --> pdb=" O VAL 7 101 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL 7 101 " --> pdb=" O ALA 7 97 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '7' and resid 109 through 113 removed outlier: 5.179A pdb=" N GLU 7 111 " --> pdb=" O GLY 7 118 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLY 7 118 " --> pdb=" O GLU 7 111 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU 7 117 " --> pdb=" O CYS 7 177 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N CYS 7 177 " --> pdb=" O LEU 7 117 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET 7 175 " --> pdb=" O THR 7 119 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '8' and resid 155 through 159 removed outlier: 6.392A pdb=" N THR 8 30 " --> pdb=" O ASP 8 45 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY 8 44 " --> pdb=" O GLU 8 222 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU 8 222 " --> pdb=" O GLY 8 44 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '8' and resid 48 through 50 removed outlier: 6.402A pdb=" N ASN 8 48 " --> pdb=" O ASN 8 55 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '8' and resid 62 through 66 removed outlier: 6.384A pdb=" N ILE 8 69 " --> pdb=" O CYS 8 65 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER 8 143 " --> pdb=" O GLU 8 151 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU 8 151 " --> pdb=" O SER 8 143 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '9' and resid 66 through 69 removed outlier: 4.747A pdb=" N LEU 9 67 " --> pdb=" O TYR 9 63 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TYR 9 63 " --> pdb=" O LEU 9 67 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '9' and resid 66 through 69 removed outlier: 4.747A pdb=" N LEU 9 67 " --> pdb=" O TYR 9 63 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TYR 9 63 " --> pdb=" O LEU 9 67 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY 9 85 " --> pdb=" O ILE 9 148 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '9' and resid 174 through 176 removed outlier: 3.595A pdb=" N ALA 9 57 " --> pdb=" O SER 9 229 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE 9 228 " --> pdb=" O ASN 9 244 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 168 through 171 Processing sheet with id= AB, first strand: chain 'A' and resid 72 through 74 removed outlier: 3.541A pdb=" N GLY A 80 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 144 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 145 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE A 154 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 164 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY A 165 " --> pdb=" O MET B 57 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= AD, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.271A pdb=" N LEU B 66 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA B 73 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 162 through 165 Processing sheet with id= AF, first strand: chain 'C' and resid 66 through 67 removed outlier: 4.046A pdb=" N LEU C 148 " --> pdb=" O TRP C 160 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 161 through 164 removed outlier: 4.423A pdb=" N ILE D 212 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 64 through 68 removed outlier: 6.591A pdb=" N VAL D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 158 through 159 removed outlier: 4.843A pdb=" N SER D 158 " --> pdb=" O GLU E 60 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 169 through 172 removed outlier: 4.335A pdb=" N LEU E 219 " --> pdb=" O TYR E 231 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 67 through 68 Processing sheet with id= AL, first strand: chain 'F' and resid 158 through 161 Processing sheet with id= AM, first strand: chain 'F' and resid 51 through 52 removed outlier: 3.550A pdb=" N ARG F 51 " --> pdb=" O GLN F 60 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 63 through 64 removed outlier: 3.816A pdb=" N LEU F 144 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 162 through 165 Processing sheet with id= AP, first strand: chain 'G' and resid 68 through 70 Processing sheet with id= AQ, first strand: chain 'H' and resid 270 through 275 removed outlier: 6.422A pdb=" N THR H 270 " --> pdb=" O ILE H 305 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE H 307 " --> pdb=" O THR H 270 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE H 272 " --> pdb=" O PHE H 307 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP H 309 " --> pdb=" O ILE H 272 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL H 274 " --> pdb=" O ASP H 309 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'I' and resid 147 through 148 removed outlier: 6.792A pdb=" N LEU I 175 " --> pdb=" O VAL I 184 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'I' and resid 199 through 202 Processing sheet with id= AT, first strand: chain 'I' and resid 246 through 248 Processing sheet with id= AU, first strand: chain 'J' and resid 93 through 97 removed outlier: 5.407A pdb=" N LYS J 87 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL J 75 " --> pdb=" O LYS J 87 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL J 113 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG J 116 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU J 122 " --> pdb=" O ARG J 116 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 184 through 185 removed outlier: 6.893A pdb=" N SER J 243 " --> pdb=" O LYS J 289 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE J 291 " --> pdb=" O SER J 243 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE J 245 " --> pdb=" O ILE J 291 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'K' and resid 117 through 120 removed outlier: 6.964A pdb=" N THR K 107 " --> pdb=" O PRO K 102 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE K 109 " --> pdb=" O LEU K 100 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER K 136 " --> pdb=" O LEU K 150 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'K' and resid 267 through 271 removed outlier: 3.855A pdb=" N LYS K 313 " --> pdb=" O SER K 267 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY K 208 " --> pdb=" O ARG K 336 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE K 338 " --> pdb=" O GLY K 208 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU K 210 " --> pdb=" O ILE K 338 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'L' and resid 126 through 129 removed outlier: 6.336A pdb=" N LYS L 120 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL L 108 " --> pdb=" O LYS L 120 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ARG L 145 " --> pdb=" O ILE L 158 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ILE L 158 " --> pdb=" O ARG L 145 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N THR L 147 " --> pdb=" O MET L 156 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'L' and resid 126 through 129 removed outlier: 6.336A pdb=" N LYS L 120 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL L 108 " --> pdb=" O LYS L 120 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N THR M 126 " --> pdb=" O ILE L 105 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'L' and resid 171 through 174 removed outlier: 6.045A pdb=" N CYS L 276 " --> pdb=" O LYS L 322 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE L 324 " --> pdb=" O CYS L 276 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE L 278 " --> pdb=" O ILE L 324 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA L 326 " --> pdb=" O ILE L 278 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET L 280 " --> pdb=" O ALA L 326 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL L 218 " --> pdb=" O MET L 325 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU L 219 " --> pdb=" O VAL L 347 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'M' and resid 145 through 148 removed outlier: 3.890A pdb=" N LEU M 145 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'M' and resid 242 through 247 removed outlier: 5.694A pdb=" N THR M 242 " --> pdb=" O ILE M 277 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE M 279 " --> pdb=" O THR M 242 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU M 244 " --> pdb=" O PHE M 279 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASP M 281 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU M 246 " --> pdb=" O ASP M 281 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLY M 217 " --> pdb=" O ARG M 345 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ILE M 347 " --> pdb=" O GLY M 217 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU M 219 " --> pdb=" O ILE M 347 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'N' and resid 713 through 715 Processing sheet with id= BE, first strand: chain 'O' and resid 341 through 342 Processing sheet with id= BF, first strand: chain 'P' and resid 359 through 361 Processing sheet with id= BG, first strand: chain 'R' and resid 380 through 381 Processing sheet with id= BH, first strand: chain 'S' and resid 402 through 403 Processing sheet with id= BI, first strand: chain 'T' and resid 200 through 201 Processing sheet with id= BJ, first strand: chain 'U' and resid 9 through 10 Processing sheet with id= BK, first strand: chain 'U' and resid 47 through 53 removed outlier: 5.793A pdb=" N VAL U 48 " --> pdb=" O ASP U 40 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP U 40 " --> pdb=" O VAL U 48 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY U 91 " --> pdb=" O ILE U 37 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY U 39 " --> pdb=" O LEU U 89 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU U 89 " --> pdb=" O GLY U 39 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'U' and resid 56 through 58 Processing sheet with id= BM, first strand: chain 'U' and resid 122 through 123 Processing sheet with id= BN, first strand: chain 'U' and resid 137 through 139 Processing sheet with id= BO, first strand: chain 'V' and resid 26 through 29 removed outlier: 6.197A pdb=" N THR V 26 " --> pdb=" O VAL V 63 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL V 65 " --> pdb=" O THR V 26 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR V 28 " --> pdb=" O VAL V 65 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASP V 67 " --> pdb=" O TYR V 28 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL V 63 " --> pdb=" O VAL V 58 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL V 58 " --> pdb=" O VAL V 63 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL V 65 " --> pdb=" O GLU V 56 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLU V 56 " --> pdb=" O VAL V 65 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'V' and resid 107 through 108 removed outlier: 6.820A pdb=" N TRP V 107 " --> pdb=" O VAL V 139 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL V 141 " --> pdb=" O TRP V 107 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'W' and resid 4 through 5 removed outlier: 7.204A pdb=" N LEU W 8 " --> pdb=" O ILE W 52 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU W 51 " --> pdb=" O LEU W 62 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'W' and resid 4 through 5 removed outlier: 6.467A pdb=" N GLN W 108 " --> pdb=" O ALA W 138 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ASP W 140 " --> pdb=" O GLN W 108 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE W 110 " --> pdb=" O ASP W 140 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE W 142 " --> pdb=" O ILE W 110 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA W 112 " --> pdb=" O ILE W 142 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU W 172 " --> pdb=" O ILE W 141 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN W 143 " --> pdb=" O LEU W 172 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'X' and resid 32 through 34 Processing sheet with id= BT, first strand: chain 'X' and resid 74 through 75 removed outlier: 4.043A pdb=" N MET X 74 " --> pdb=" O VAL X 90 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL X 90 " --> pdb=" O MET X 74 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'Z' and resid 862 through 863 Processing sheet with id= BV, first strand: chain 'Z' and resid 915 through 916 Processing sheet with id= BW, first strand: chain 'a' and resid 168 through 171 Processing sheet with id= BX, first strand: chain 'a' and resid 72 through 74 removed outlier: 3.542A pdb=" N GLY a 80 " --> pdb=" O VAL a 144 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL a 144 " --> pdb=" O GLY a 80 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER a 145 " --> pdb=" O SER a 153 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE a 154 " --> pdb=" O TYR a 166 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL a 164 " --> pdb=" O LYS a 156 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY a 165 " --> pdb=" O MET b 57 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'b' and resid 161 through 164 Processing sheet with id= BZ, first strand: chain 'b' and resid 65 through 68 removed outlier: 5.272A pdb=" N LEU b 66 " --> pdb=" O ALA b 73 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA b 73 " --> pdb=" O LEU b 66 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'b' and resid 224 through 225 removed outlier: 4.997A pdb=" N VAL i 202 " --> pdb=" O ASN i 218 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR i 31 " --> pdb=" O ASP i 46 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'c' and resid 162 through 165 Processing sheet with id= CC, first strand: chain 'c' and resid 66 through 67 removed outlier: 4.046A pdb=" N LEU c 148 " --> pdb=" O TRP c 160 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'd' and resid 161 through 164 removed outlier: 4.423A pdb=" N ILE d 212 " --> pdb=" O LEU d 224 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'd' and resid 64 through 68 removed outlier: 6.591A pdb=" N VAL d 71 " --> pdb=" O ILE d 67 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'd' and resid 158 through 159 removed outlier: 4.713A pdb=" N SER d 158 " --> pdb=" O GLU e 60 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'e' and resid 169 through 172 removed outlier: 4.335A pdb=" N LEU e 219 " --> pdb=" O TYR e 231 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'e' and resid 67 through 68 Processing sheet with id= CI, first strand: chain 'f' and resid 158 through 161 Processing sheet with id= CJ, first strand: chain 'f' and resid 51 through 52 removed outlier: 3.550A pdb=" N ARG f 51 " --> pdb=" O GLN f 60 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'f' and resid 63 through 64 removed outlier: 3.816A pdb=" N LEU f 144 " --> pdb=" O LEU f 156 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'g' and resid 162 through 165 Processing sheet with id= CM, first strand: chain 'g' and resid 68 through 70 Processing sheet with id= CN, first strand: chain 'h' and resid 143 through 146 Processing sheet with id= CO, first strand: chain 'h' and resid 39 through 41 removed outlier: 5.692A pdb=" N THR h 41 " --> pdb=" O ILE h 45 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE h 45 " --> pdb=" O THR h 41 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'h' and resid 53 through 55 Processing sheet with id= CQ, first strand: chain 'i' and resid 49 through 51 removed outlier: 6.432A pdb=" N SER i 49 " --> pdb=" O ALA i 56 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'i' and resid 63 through 67 removed outlier: 6.188A pdb=" N ILE i 70 " --> pdb=" O ILE i 66 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'i' and resid 241 through 247 removed outlier: 3.762A pdb=" N VAL j 195 " --> pdb=" O VAL i 247 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE j 11 " --> pdb=" O ASP j 26 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'j' and resid 43 through 46 Processing sheet with id= CU, first strand: chain 'k' and resid 130 through 131 removed outlier: 3.801A pdb=" N VAL k 181 " --> pdb=" O VAL k 192 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'k' and resid 22 through 23 Processing sheet with id= CW, first strand: chain 'k' and resid 35 through 39 removed outlier: 6.111A pdb=" N THR k 42 " --> pdb=" O LEU k 38 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'l' and resid 201 through 205 removed outlier: 6.253A pdb=" N THR l 77 " --> pdb=" O ASP l 92 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL l 91 " --> pdb=" O ASN l 251 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN l 251 " --> pdb=" O VAL l 91 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL l 250 " --> pdb=" O ASN l 265 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN l 265 " --> pdb=" O VAL l 250 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU l 252 " --> pdb=" O HIS l 263 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'l' and resid 95 through 97 removed outlier: 5.017A pdb=" N ALA l 97 " --> pdb=" O VAL l 101 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL l 101 " --> pdb=" O ALA l 97 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'l' and resid 109 through 113 removed outlier: 5.178A pdb=" N GLU l 111 " --> pdb=" O GLY l 118 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY l 118 " --> pdb=" O GLU l 111 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU l 117 " --> pdb=" O CYS l 177 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS l 177 " --> pdb=" O LEU l 117 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N MET l 175 " --> pdb=" O THR l 119 " (cutoff:3.500A) 5503 hydrogen bonds defined for protein. 15894 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: 55.23 Time building geometry restraints manager: 38.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.53: 102401 1.53 - 1.86: 3492 1.86 - 2.19: 0 2.19 - 2.52: 1 2.52 - 2.85: 1 Bond restraints: 105895 Sorted by residual: bond pdb=" C ASP M 38 " pdb=" N LYS M 70 " ideal model delta sigma weight residual 1.334 2.853 -1.520 1.30e-02 5.92e+03 1.37e+04 bond pdb=" C GLY I 239 " pdb=" N PRO I 242 " ideal model delta sigma weight residual 1.329 2.329 -1.000 1.18e-02 7.18e+03 7.19e+03 bond pdb=" C VAL R 330 " pdb=" N ARG R 331 " ideal model delta sigma weight residual 1.334 1.694 -0.360 1.38e-02 5.25e+03 6.81e+02 bond pdb=" C GLU O 34 " pdb=" N GLU O 35 " ideal model delta sigma weight residual 1.332 1.453 -0.120 1.29e-02 6.01e+03 8.68e+01 bond pdb=" C ALA K 363 " pdb=" N PRO K 364 " ideal model delta sigma weight residual 1.333 1.405 -0.072 7.80e-03 1.64e+04 8.61e+01 ... (remaining 105890 not shown) Histogram of bond angle deviations from ideal: 67.67 - 87.38: 4 87.38 - 107.09: 3291 107.09 - 126.80: 138915 126.80 - 146.51: 908 146.51 - 166.22: 1 Bond angle restraints: 143119 Sorted by residual: angle pdb=" O VAL R 330 " pdb=" C VAL R 330 " pdb=" N ARG R 331 " ideal model delta sigma weight residual 122.57 166.22 -43.65 1.25e+00 6.40e-01 1.22e+03 angle pdb=" O ASP M 38 " pdb=" C ASP M 38 " pdb=" N LYS M 70 " ideal model delta sigma weight residual 122.46 77.40 45.06 1.38e+00 5.25e-01 1.07e+03 angle pdb=" CA VAL R 330 " pdb=" C VAL R 330 " pdb=" N ARG R 331 " ideal model delta sigma weight residual 116.60 70.15 46.45 1.45e+00 4.76e-01 1.03e+03 angle pdb=" C VAL R 330 " pdb=" N ARG R 331 " pdb=" CA ARG R 331 " ideal model delta sigma weight residual 121.18 72.53 48.65 1.98e+00 2.55e-01 6.04e+02 angle pdb=" CA ASP M 38 " pdb=" C ASP M 38 " pdb=" N LYS M 70 " ideal model delta sigma weight residual 118.43 98.22 20.21 1.33e+00 5.65e-01 2.31e+02 ... (remaining 143114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 61783 17.89 - 35.79: 1996 35.79 - 53.68: 396 53.68 - 71.58: 112 71.58 - 89.47: 52 Dihedral angle restraints: 64339 sinusoidal: 25548 harmonic: 38791 Sorted by residual: dihedral pdb=" CA ARG S 298 " pdb=" C ARG S 298 " pdb=" N LYS S 299 " pdb=" CA LYS S 299 " ideal model delta harmonic sigma weight residual 180.00 104.54 75.46 0 5.00e+00 4.00e-02 2.28e+02 dihedral pdb=" CA ARG V 273 " pdb=" C ARG V 273 " pdb=" N GLN V 274 " pdb=" CA GLN V 274 " ideal model delta harmonic sigma weight residual -180.00 -112.20 -67.80 0 5.00e+00 4.00e-02 1.84e+02 dihedral pdb=" CA SER P 106 " pdb=" C SER P 106 " pdb=" N SER P 107 " pdb=" CA SER P 107 " ideal model delta harmonic sigma weight residual 180.00 114.47 65.53 0 5.00e+00 4.00e-02 1.72e+02 ... (remaining 64336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 16278 0.197 - 0.393: 79 0.393 - 0.590: 3 0.590 - 0.786: 0 0.786 - 0.983: 2 Chirality restraints: 16362 Sorted by residual: chirality pdb=" CA TYR R 338 " pdb=" N TYR R 338 " pdb=" C TYR R 338 " pdb=" CB TYR R 338 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" CB ILE I 146 " pdb=" CA ILE I 146 " pdb=" CG1 ILE I 146 " pdb=" CG2 ILE I 146 " both_signs ideal model delta sigma weight residual False 2.64 1.75 0.90 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" CA PRO H 380 " pdb=" N PRO H 380 " pdb=" C PRO H 380 " pdb=" CB PRO H 380 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.34e+00 ... (remaining 16359 not shown) Planarity restraints: 18444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP M 38 " -0.187 2.00e-02 2.50e+03 2.72e-01 7.39e+02 pdb=" C ASP M 38 " 0.445 2.00e-02 2.50e+03 pdb=" O ASP M 38 " -0.251 2.00e-02 2.50e+03 pdb=" N LYS M 70 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY I 239 " 0.092 2.00e-02 2.50e+03 1.44e-01 2.07e+02 pdb=" C GLY I 239 " -0.246 2.00e-02 2.50e+03 pdb=" O GLY I 239 " 0.105 2.00e-02 2.50e+03 pdb=" N PRO I 242 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY I 239 " -0.110 5.00e-02 4.00e+02 2.58e-01 1.06e+02 pdb=" N PRO I 242 " 0.435 5.00e-02 4.00e+02 pdb=" CA PRO I 242 " -0.238 5.00e-02 4.00e+02 pdb=" CD PRO I 242 " -0.087 5.00e-02 4.00e+02 ... (remaining 18441 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.87: 50 1.87 - 2.63: 4526 2.63 - 3.39: 179361 3.39 - 4.14: 305618 4.14 - 4.90: 515469 Nonbonded interactions: 1005024 Sorted by model distance: nonbonded pdb=" O GLN I 281 " pdb=" O LYS J 221 " model vdw 1.114 3.040 nonbonded pdb=" O ASN Q 308 " pdb=" CE LYS Q 349 " model vdw 1.135 3.440 nonbonded pdb=" OH TYR Q 400 " pdb=" N ARG R 392 " model vdw 1.142 2.520 nonbonded pdb=" OH TYR Q 400 " pdb=" C ASN R 391 " model vdw 1.187 3.270 nonbonded pdb=" O SER Z 365 " pdb=" NH2 ARG Z 962 " model vdw 1.281 2.520 ... (remaining 1005019 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 '1' selection = chain '8' } ncs_group { reference = chain '2' selection = chain '9' } ncs_group { reference = chain '3' selection = (chain 'h' and ((resid 11 and (name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2)) or resid 12 through 215)) } ncs_group { reference = chain '4' selection = chain 'i' } ncs_group { reference = (chain '5' and (resid 2 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 33 through 205)) selection = chain 'j' } ncs_group { reference = chain '6' selection = chain 'k' } ncs_group { reference = chain '7' selection = chain 'l' } ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 8.770 Check model and map are aligned: 1.090 Set scattering table: 0.680 Process input model: 228.500 Find NCS groups from input model: 6.250 Set up NCS constraints: 0.720 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 251.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 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 : 0.011 1.520 105895 Z= 0.652 Angle : 1.304 57.332 143119 Z= 0.744 Chirality : 0.058 0.983 16362 Planarity : 0.007 0.272 18444 Dihedral : 10.564 89.470 39373 Min Nonbonded Distance : 1.114 Molprobity Statistics. All-atom Clashscore : 72.15 Ramachandran Plot: Outliers : 1.68 % Allowed : 11.67 % Favored : 86.65 % Rotamer: Outliers : 0.76 % Allowed : 1.07 % Favored : 98.18 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 1.20 % Twisted General : 0.98 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.05), residues: 13225 helix: -4.40 (0.04), residues: 4898 sheet: -1.77 (0.10), residues: 1848 loop : -2.84 (0.06), residues: 6479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.005 TRP P 257 HIS 0.027 0.004 HIS P 348 PHE 0.052 0.004 PHE O 310 TYR 0.051 0.004 TYR S 259 ARG 0.042 0.002 ARG L 303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26450 Ramachandran restraints generated. 13225 Oldfield, 0 Emsley, 13225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26450 Ramachandran restraints generated. 13225 Oldfield, 0 Emsley, 13225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1405 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1320 time to evaluate : 9.417 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 102 ASP cc_start: 0.8560 (m-30) cc_final: 0.8119 (m-30) REVERT: 2 204 GLN cc_start: 0.8650 (mp10) cc_final: 0.8075 (pm20) REVERT: 2 214 MET cc_start: 0.9210 (mmm) cc_final: 0.8606 (mmt) REVERT: 3 165 MET cc_start: 0.8838 (mtp) cc_final: 0.8463 (mtp) REVERT: 4 119 TYR cc_start: 0.7655 (m-80) cc_final: 0.7378 (m-80) REVERT: 4 126 TYR cc_start: 0.7854 (m-80) cc_final: 0.7519 (m-10) REVERT: 4 127 LEU cc_start: 0.8885 (mt) cc_final: 0.8409 (pp) REVERT: 4 164 MET cc_start: 0.8835 (tpp) cc_final: 0.7943 (tpp) REVERT: 5 149 MET cc_start: 0.8200 (mmm) cc_final: 0.7952 (mmm) REVERT: 5 150 CYS cc_start: 0.7684 (m) cc_final: 0.7150 (m) REVERT: 9 93 MET cc_start: 0.8658 (ttp) cc_final: 0.8273 (ttp) REVERT: A 81 MET cc_start: 0.6475 (ttp) cc_final: 0.6142 (ptm) REVERT: B 110 LEU cc_start: 0.8804 (tp) cc_final: 0.8345 (tp) REVERT: C 46 LEU cc_start: 0.8831 (mt) cc_final: 0.8327 (mp) REVERT: E 134 MET cc_start: 0.7637 (ttp) cc_final: 0.7078 (ttp) REVERT: E 208 MET cc_start: 0.7713 (mtp) cc_final: 0.7340 (ttm) REVERT: F 88 LEU cc_start: 0.9397 (tp) cc_final: 0.9076 (tt) REVERT: F 132 LEU cc_start: 0.8639 (mt) cc_final: 0.7922 (mt) REVERT: H 172 MET cc_start: 0.8038 (mmm) cc_final: 0.7770 (mmm) REVERT: H 330 GLN cc_start: 0.7480 (tp40) cc_final: 0.7193 (tp40) REVERT: H 337 ILE cc_start: 0.8869 (mt) cc_final: 0.8320 (mm) REVERT: J 40 ASN cc_start: 0.7635 (m-40) cc_final: 0.7054 (t0) REVERT: J 154 THR cc_start: 0.8074 (m) cc_final: 0.6794 (t) REVERT: J 229 MET cc_start: 0.7529 (mtp) cc_final: 0.6404 (mtp) REVERT: J 304 LEU cc_start: 0.6182 (tp) cc_final: 0.5952 (tp) REVERT: K 131 LEU cc_start: 0.7645 (tp) cc_final: 0.7342 (tp) REVERT: K 210 LEU cc_start: 0.8361 (tp) cc_final: 0.6851 (tt) REVERT: K 245 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7366 (mmtm) REVERT: K 253 MET cc_start: 0.7406 (mmm) cc_final: 0.6762 (mmt) REVERT: L 140 LEU cc_start: 0.7619 (mt) cc_final: 0.7029 (mt) REVERT: L 256 ILE cc_start: 0.5564 (mm) cc_final: 0.5218 (mm) REVERT: N 64 ILE cc_start: 0.7580 (mt) cc_final: 0.7357 (mt) REVERT: N 543 ASP cc_start: 0.7938 (p0) cc_final: 0.7621 (p0) REVERT: N 773 MET cc_start: 0.8261 (mmt) cc_final: 0.7658 (mpp) REVERT: O 223 LEU cc_start: 0.7582 (mt) cc_final: 0.7355 (mm) REVERT: P 131 PHE cc_start: 0.4283 (t80) cc_final: 0.3164 (t80) REVERT: Q 413 LEU cc_start: 0.9343 (tp) cc_final: 0.8883 (pp) REVERT: U 76 MET cc_start: 0.8234 (ttm) cc_final: 0.7176 (tpp) REVERT: U 79 MET cc_start: 0.8853 (mtm) cc_final: 0.7325 (mtm) REVERT: U 275 VAL cc_start: 0.6730 (t) cc_final: 0.6127 (t) REVERT: V 290 ASN cc_start: 0.9485 (m-40) cc_final: 0.8771 (p0) REVERT: Z 124 MET cc_start: 0.2804 (tpp) cc_final: 0.0935 (tmm) REVERT: Z 277 GLU cc_start: 0.0673 (OUTLIER) cc_final: 0.0287 (pt0) REVERT: Z 415 MET cc_start: -0.0079 (tpp) cc_final: -0.0282 (tpt) REVERT: Z 583 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7594 (m-30) REVERT: Z 756 MET cc_start: 0.9019 (tpt) cc_final: 0.8235 (tpp) REVERT: Z 757 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.5735 (p) REVERT: Z 775 MET cc_start: 0.4610 (tpt) cc_final: 0.2757 (tpt) REVERT: b 87 ASP cc_start: 0.8628 (m-30) cc_final: 0.7698 (t0) REVERT: b 199 SER cc_start: 0.8905 (m) cc_final: 0.8406 (t) REVERT: b 209 ILE cc_start: 0.9684 (mm) cc_final: 0.9327 (mt) REVERT: c 19 LEU cc_start: 0.7377 (mt) cc_final: 0.7157 (mp) REVERT: e 40 ILE cc_start: 0.8386 (mt) cc_final: 0.8160 (mt) REVERT: e 78 MET cc_start: 0.6848 (ptp) cc_final: 0.6563 (ptm) REVERT: f 64 ILE cc_start: 0.9024 (mt) cc_final: 0.8550 (mm) REVERT: f 111 LEU cc_start: 0.9222 (mt) cc_final: 0.9018 (mm) REVERT: f 132 LEU cc_start: 0.8688 (mt) cc_final: 0.8430 (mt) REVERT: i 142 ILE cc_start: 0.9248 (mt) cc_final: 0.8675 (mt) REVERT: i 164 MET cc_start: 0.8858 (tpp) cc_final: 0.8655 (tpp) REVERT: j 149 MET cc_start: 0.8931 (mmm) cc_final: 0.7827 (mmm) REVERT: k 5 LEU cc_start: 0.8411 (mt) cc_final: 0.8058 (mt) REVERT: k 104 ILE cc_start: 0.8437 (mt) cc_final: 0.8159 (mt) outliers start: 85 outliers final: 33 residues processed: 1388 average time/residue: 1.0854 time to fit residues: 2463.9113 Evaluate side-chains 728 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 691 time to evaluate : 9.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 1114 optimal weight: 5.9990 chunk 1000 optimal weight: 6.9990 chunk 555 optimal weight: 5.9990 chunk 341 optimal weight: 3.9990 chunk 674 optimal weight: 2.9990 chunk 534 optimal weight: 10.0000 chunk 1034 optimal weight: 10.0000 chunk 400 optimal weight: 7.9990 chunk 629 optimal weight: 1.9990 chunk 770 optimal weight: 1.9990 chunk 1198 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 51 ASN 2 70 ASN 2 246 GLN ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 51 GLN ** 4 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 122 HIS 4 143 HIS ** 4 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 32 GLN ** 5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 89 GLN 6 55 GLN ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 251 ASN 9 70 ASN 9 246 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS C 21 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 HIS D 19 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN E 91 HIS E 114 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN E 215 ASN E 233 ASN F 60 GLN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN F 199 GLN G 23 GLN ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 HIS ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS G 195 GLN G 237 GLN H 98 GLN ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 301 ASN ** I 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 437 GLN J 103 ASN ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN K 285 GLN ** K 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 311 ASN ** L 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 ASN M 250 GLN ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 359 GLN ** M 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 216 ASN ** N 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN N 306 ASN ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 378 ASN ** N 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 870 ASN ** N 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 64 ASN O 75 GLN O 169 ASN O 236 HIS O 244 ASN ** O 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 349 ASN P 410 GLN P 440 HIS ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 HIS ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 226 HIS Q 252 HIS ** Q 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 404 ASN Q 418 GLN ** R 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 397 ASN ** S 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 458 GLN S 459 GLN T 37 ASN ** T 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 204 ASN ** T 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 71 ASN ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 192 ASN ** U 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 223 HIS ** U 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 184 ASN V 190 HIS W 18 ASN ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 38 GLN W 44 ASN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 149 GLN ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 ASN X 105 ASN Y 89 GLN Z 132 HIS Z 168 GLN ** Z 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 435 GLN ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 549 ASN Z 618 GLN Z 763 HIS Z 789 GLN ** Z 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 130 GLN ** b 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 GLN ** c 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 ASN d 16 HIS ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 122 GLN ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 23 GLN e 91 HIS ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 215 ASN e 233 ASN f 5 ASN ** f 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 148 GLN f 199 GLN g 23 GLN g 62 GLN ** g 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 195 GLN g 237 GLN ** h 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 143 HIS i 194 ASN ** i 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 89 GLN ** k 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 141 HIS l 251 ASN Total number of N/Q/H flips: 105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.153 105895 Z= 0.362 Angle : 0.984 17.157 143119 Z= 0.525 Chirality : 0.052 0.437 16362 Planarity : 0.007 0.102 18444 Dihedral : 8.376 74.350 14437 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 38.93 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.00 % Favored : 90.48 % Rotamer: Outliers : 0.35 % Allowed : 2.40 % Favored : 97.25 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.28 % Twisted Proline : 0.48 % Twisted General : 0.61 % 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: -3.37 (0.06), residues: 13229 helix: -2.36 (0.05), residues: 5937 sheet: -1.59 (0.10), residues: 1872 loop : -2.13 (0.08), residues: 5420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP Q 396 HIS 0.021 0.003 HIS P 348 PHE 0.058 0.003 PHE O 310 TYR 0.043 0.003 TYR B 104 ARG 0.026 0.001 ARG M 299 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 994 time to evaluate : 9.414 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 166 MET cc_start: 0.8731 (mmm) cc_final: 0.8346 (mmm) REVERT: 2 100 LEU cc_start: 0.9235 (mt) cc_final: 0.9000 (mm) REVERT: 2 102 ASP cc_start: 0.7879 (m-30) cc_final: 0.7444 (m-30) REVERT: 2 214 MET cc_start: 0.9027 (mmm) cc_final: 0.8547 (mmt) REVERT: 5 149 MET cc_start: 0.7948 (mmm) cc_final: 0.7638 (mmm) REVERT: 7 175 MET cc_start: 0.6998 (mpp) cc_final: 0.6736 (mpp) REVERT: 9 101 LYS cc_start: 0.9059 (ptpt) cc_final: 0.8811 (pttm) REVERT: 9 250 MET cc_start: 0.7584 (pmm) cc_final: 0.7352 (pmm) REVERT: A 81 MET cc_start: 0.6188 (ttp) cc_final: 0.5527 (ptm) REVERT: C 135 PHE cc_start: 0.8842 (m-80) cc_final: 0.7805 (m-80) REVERT: H 352 MET cc_start: 0.5231 (mtp) cc_final: 0.4857 (mtm) REVERT: I 189 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.6198 (t0) REVERT: I 266 GLN cc_start: 0.5397 (tp40) cc_final: 0.4893 (tm-30) REVERT: J 40 ASN cc_start: 0.7698 (m-40) cc_final: 0.7102 (t0) REVERT: J 138 MET cc_start: 0.0029 (ppp) cc_final: -0.0650 (ttt) REVERT: J 292 MET cc_start: 0.6777 (mmp) cc_final: 0.6343 (tpp) REVERT: K 131 LEU cc_start: 0.7495 (tp) cc_final: 0.7151 (mt) REVERT: L 112 LEU cc_start: 0.7221 (tt) cc_final: 0.6912 (tt) REVERT: L 192 GLU cc_start: 0.5337 (mp0) cc_final: 0.4969 (pt0) REVERT: L 309 LEU cc_start: 0.8144 (tp) cc_final: 0.7289 (tp) REVERT: L 343 LEU cc_start: 0.8705 (tp) cc_final: 0.8449 (tp) REVERT: M 235 CYS cc_start: 0.8378 (p) cc_final: 0.7600 (t) REVERT: M 254 MET cc_start: 0.8941 (pmm) cc_final: 0.8411 (pmm) REVERT: N 217 MET cc_start: 0.7309 (tpt) cc_final: 0.5256 (mmm) REVERT: N 489 MET cc_start: 0.7974 (mpp) cc_final: 0.7749 (mpp) REVERT: N 543 ASP cc_start: 0.7575 (p0) cc_final: 0.7247 (p0) REVERT: O 223 LEU cc_start: 0.8198 (mt) cc_final: 0.7648 (mm) REVERT: P 131 PHE cc_start: 0.5360 (t80) cc_final: 0.4959 (t80) REVERT: Q 68 MET cc_start: 0.1399 (mtt) cc_final: 0.1034 (mtt) REVERT: Q 413 LEU cc_start: 0.9359 (tp) cc_final: 0.8998 (pp) REVERT: R 404 VAL cc_start: 0.8258 (m) cc_final: 0.8033 (m) REVERT: S 1 MET cc_start: 0.6816 (ppp) cc_final: 0.6412 (ppp) REVERT: S 232 MET cc_start: 0.6820 (tmm) cc_final: 0.5935 (tmm) REVERT: U 76 MET cc_start: 0.7984 (ttm) cc_final: 0.7545 (tpp) REVERT: V 290 ASN cc_start: 0.8789 (m-40) cc_final: 0.8506 (p0) REVERT: X 9 LYS cc_start: 0.7331 (mttt) cc_final: 0.6835 (mtpt) REVERT: Y 77 LEU cc_start: 0.6994 (tt) cc_final: 0.6725 (tt) REVERT: Z 124 MET cc_start: 0.3994 (tpp) cc_final: 0.2526 (tmm) REVERT: Z 601 VAL cc_start: 0.4143 (OUTLIER) cc_final: 0.3919 (m) REVERT: Z 756 MET cc_start: 0.8102 (tpt) cc_final: 0.7695 (tpp) REVERT: Z 759 ARG cc_start: 0.5588 (ttt180) cc_final: 0.5321 (mtp180) REVERT: Z 775 MET cc_start: 0.4614 (tpt) cc_final: 0.3704 (tpt) REVERT: Z 788 PRO cc_start: 0.1047 (Cg_endo) cc_final: 0.0626 (Cg_exo) REVERT: Z 862 MET cc_start: 0.4995 (mmt) cc_final: 0.4310 (mmm) REVERT: a 81 MET cc_start: 0.6013 (ttp) cc_final: 0.5172 (ttp) REVERT: a 112 MET cc_start: 0.6473 (ptm) cc_final: 0.6273 (ptp) REVERT: a 121 MET cc_start: 0.7560 (mmm) cc_final: 0.7202 (mmt) REVERT: a 210 MET cc_start: 0.6912 (ttm) cc_final: 0.6625 (ttm) REVERT: b 209 ILE cc_start: 0.9481 (mm) cc_final: 0.9274 (mt) REVERT: c 135 PHE cc_start: 0.8410 (m-80) cc_final: 0.7999 (m-80) REVERT: e 102 TYR cc_start: 0.7074 (m-10) cc_final: 0.6586 (m-10) REVERT: f 234 ILE cc_start: 0.5065 (mt) cc_final: 0.4811 (mt) REVERT: g 150 MET cc_start: 0.6297 (tpt) cc_final: 0.5833 (tpt) REVERT: h 101 PHE cc_start: 0.8779 (m-80) cc_final: 0.8407 (m-80) REVERT: h 194 MET cc_start: 0.6563 (mtt) cc_final: 0.6219 (mtt) REVERT: i 218 ASN cc_start: 0.6893 (m-40) cc_final: 0.6444 (m-40) REVERT: j 149 MET cc_start: 0.8278 (mmm) cc_final: 0.7660 (mmm) REVERT: j 190 ILE cc_start: 0.9376 (mt) cc_final: 0.9058 (mt) REVERT: k 172 MET cc_start: 0.7805 (tmm) cc_final: 0.7046 (tmm) outliers start: 39 outliers final: 12 residues processed: 1030 average time/residue: 1.1297 time to fit residues: 1950.6003 Evaluate side-chains 648 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 634 time to evaluate : 9.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 666 optimal weight: 0.0020 chunk 372 optimal weight: 6.9990 chunk 997 optimal weight: 7.9990 chunk 816 optimal weight: 6.9990 chunk 330 optimal weight: 5.9990 chunk 1200 optimal weight: 2.9990 chunk 1297 optimal weight: 0.0470 chunk 1069 optimal weight: 0.6980 chunk 1190 optimal weight: 1.9990 chunk 409 optimal weight: 0.8980 chunk 963 optimal weight: 30.0000 overall best weight: 0.7288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 111 ASN ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 55 GLN 6 63 ASN ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 160 ASN 8 99 ASN 8 111 ASN C 96 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 HIS ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 330 GLN ** I 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 HIS ** K 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 ASN ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 226 ASN N 306 ASN ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 878 GLN O 169 ASN ** O 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 210 ASN ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 410 GLN ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 404 ASN ** R 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 195 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 366 ASN R 397 ASN R 401 HIS ** S 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 177 ASN ** S 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 HIS ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 258 ASN ** U 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 ASN ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 149 GLN ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN ** Z 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 123 ASN b 139 HIS b 190 HIS c 96 GLN ** c 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 ASN ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 154 GLN ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 HIS g 182 HIS ** h 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 63 ASN k 99 GLN ** k 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 160 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 105895 Z= 0.264 Angle : 0.814 14.424 143119 Z= 0.434 Chirality : 0.048 0.466 16362 Planarity : 0.006 0.208 18444 Dihedral : 7.448 71.634 14437 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 29.85 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.88 % Favored : 91.73 % Rotamer: Outliers : 0.12 % Allowed : 3.36 % Favored : 96.52 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -2.20 (0.07), residues: 13229 helix: -1.10 (0.06), residues: 6032 sheet: -1.31 (0.11), residues: 1870 loop : -1.78 (0.08), residues: 5327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Z 428 HIS 0.018 0.002 HIS Q 361 PHE 0.055 0.002 PHE O 310 TYR 0.046 0.002 TYR B 104 ARG 0.030 0.001 ARG M 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 949 time to evaluate : 9.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 71 MET cc_start: 0.7550 (ttm) cc_final: 0.7204 (ttm) REVERT: 2 93 MET cc_start: 0.8159 (ppp) cc_final: 0.6712 (ppp) REVERT: 2 214 MET cc_start: 0.8822 (mmm) cc_final: 0.8603 (mmt) REVERT: 3 101 PHE cc_start: 0.8338 (m-10) cc_final: 0.7766 (m-10) REVERT: 3 165 MET cc_start: 0.8699 (ttt) cc_final: 0.7941 (ttt) REVERT: 4 164 MET cc_start: 0.8275 (tpt) cc_final: 0.7318 (tpp) REVERT: 5 63 LEU cc_start: 0.9322 (mt) cc_final: 0.8895 (mt) REVERT: 5 149 MET cc_start: 0.7656 (mmm) cc_final: 0.7418 (mmm) REVERT: 5 193 ASP cc_start: 0.8857 (p0) cc_final: 0.8428 (p0) REVERT: 6 152 MET cc_start: 0.8281 (mtp) cc_final: 0.7416 (mtt) REVERT: B 130 PHE cc_start: 0.7232 (m-80) cc_final: 0.6546 (m-80) REVERT: C 135 PHE cc_start: 0.8748 (m-80) cc_final: 0.7052 (m-80) REVERT: D 74 SER cc_start: 0.7395 (p) cc_final: 0.6834 (t) REVERT: H 191 ILE cc_start: 0.7228 (pt) cc_final: 0.6943 (pt) REVERT: H 352 MET cc_start: 0.5271 (mtp) cc_final: 0.4867 (mtm) REVERT: I 396 MET cc_start: 0.6698 (mmt) cc_final: 0.6340 (mmm) REVERT: J 40 ASN cc_start: 0.7827 (m-40) cc_final: 0.7606 (t0) REVERT: J 138 MET cc_start: 0.0495 (ppp) cc_final: -0.1847 (tpp) REVERT: J 292 MET cc_start: 0.6021 (mmp) cc_final: 0.5808 (mmm) REVERT: K 314 VAL cc_start: 0.8437 (t) cc_final: 0.7741 (t) REVERT: L 127 TYR cc_start: 0.5743 (m-80) cc_final: 0.5525 (m-80) REVERT: L 140 LEU cc_start: 0.7853 (mt) cc_final: 0.7211 (mt) REVERT: L 181 ASP cc_start: 0.7403 (p0) cc_final: 0.7190 (p0) REVERT: M 31 GLN cc_start: 0.7743 (mt0) cc_final: 0.7515 (mp10) REVERT: M 254 MET cc_start: 0.8986 (pmm) cc_final: 0.8734 (pmm) REVERT: M 308 LEU cc_start: 0.9515 (tp) cc_final: 0.9198 (tt) REVERT: N 64 ILE cc_start: 0.6820 (mt) cc_final: 0.6611 (mt) REVERT: N 217 MET cc_start: 0.6734 (tpt) cc_final: 0.6219 (tpt) REVERT: N 731 VAL cc_start: 0.8743 (t) cc_final: 0.8541 (t) REVERT: O 223 LEU cc_start: 0.7178 (mt) cc_final: 0.6902 (mt) REVERT: P 131 PHE cc_start: 0.4844 (t80) cc_final: 0.4588 (t80) REVERT: Q 68 MET cc_start: 0.2622 (mtt) cc_final: 0.2135 (mtt) REVERT: Q 266 LEU cc_start: 0.7864 (mt) cc_final: 0.7597 (mp) REVERT: R 404 VAL cc_start: 0.7820 (m) cc_final: 0.7331 (m) REVERT: S 136 CYS cc_start: 0.7209 (t) cc_final: 0.6856 (t) REVERT: T 255 GLN cc_start: 0.8607 (mp10) cc_final: 0.8098 (mp10) REVERT: U 79 MET cc_start: 0.7781 (mtt) cc_final: 0.6956 (mtm) REVERT: V 37 MET cc_start: 0.7797 (tmm) cc_final: 0.7175 (tmm) REVERT: V 290 ASN cc_start: 0.8809 (m-40) cc_final: 0.8403 (p0) REVERT: Z 124 MET cc_start: 0.3095 (tpp) cc_final: 0.1579 (tmm) REVERT: Z 788 PRO cc_start: 0.1533 (Cg_endo) cc_final: 0.1055 (Cg_exo) REVERT: Z 862 MET cc_start: 0.4476 (mmt) cc_final: 0.2882 (mmt) REVERT: a 112 MET cc_start: 0.6272 (ptm) cc_final: 0.5338 (ptm) REVERT: a 117 LEU cc_start: 0.8569 (tt) cc_final: 0.8218 (tp) REVERT: a 143 PHE cc_start: 0.8346 (m-80) cc_final: 0.7407 (m-80) REVERT: c 39 MET cc_start: 0.8600 (tmm) cc_final: 0.8348 (tmm) REVERT: c 115 LEU cc_start: 0.8430 (tt) cc_final: 0.7767 (tt) REVERT: c 135 PHE cc_start: 0.8110 (m-80) cc_final: 0.7643 (m-80) REVERT: e 102 TYR cc_start: 0.7453 (m-10) cc_final: 0.6901 (m-10) REVERT: e 157 HIS cc_start: 0.7938 (t70) cc_final: 0.6936 (t70) REVERT: f 219 ASP cc_start: 0.6416 (p0) cc_final: 0.6182 (p0) REVERT: g 150 MET cc_start: 0.6265 (tpt) cc_final: 0.5828 (tpt) REVERT: h 101 PHE cc_start: 0.8698 (m-80) cc_final: 0.8414 (m-80) REVERT: h 164 ASN cc_start: 0.6649 (t0) cc_final: 0.6030 (t0) REVERT: i 110 GLN cc_start: 0.9340 (mp10) cc_final: 0.8792 (mp10) REVERT: i 117 PHE cc_start: 0.7508 (t80) cc_final: 0.7305 (t80) REVERT: i 218 ASN cc_start: 0.7512 (m-40) cc_final: 0.6955 (m-40) REVERT: j 15 MET cc_start: 0.7693 (ttp) cc_final: 0.7058 (ttp) REVERT: j 149 MET cc_start: 0.8268 (mmm) cc_final: 0.6753 (mmp) REVERT: k 90 LYS cc_start: 0.9215 (mtmm) cc_final: 0.8966 (pttt) outliers start: 13 outliers final: 2 residues processed: 960 average time/residue: 1.0206 time to fit residues: 1651.7013 Evaluate side-chains 625 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 623 time to evaluate : 9.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 1186 optimal weight: 1.9990 chunk 902 optimal weight: 30.0000 chunk 623 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 573 optimal weight: 6.9990 chunk 806 optimal weight: 20.0000 chunk 1205 optimal weight: 5.9990 chunk 1275 optimal weight: 0.3980 chunk 629 optimal weight: 9.9990 chunk 1142 optimal weight: 0.0470 chunk 343 optimal weight: 0.9980 overall best weight: 1.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 111 ASN ** 1 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 115 HIS 6 63 ASN 6 146 HIS 8 111 ASN A 123 ASN C 103 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 ASN ** K 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 302 GLN M 253 GLN ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 374 ASN ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 296 GLN ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 145 HIS ** R 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 401 HIS ** S 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 177 ASN S 458 GLN ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 71 ASN ** U 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 279 HIS W 18 ASN ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 ASN Y 89 GLN Z 338 HIS ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 801 HIS ** Z 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 926 ASN a 123 ASN c 94 HIS ** c 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 ASN ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 154 GLN f 4 ASN f 5 ASN ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 146 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 105895 Z= 0.238 Angle : 0.759 13.909 143119 Z= 0.402 Chirality : 0.046 0.524 16362 Planarity : 0.005 0.159 18444 Dihedral : 6.988 70.864 14437 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 28.49 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.46 % Favored : 92.18 % Rotamer: Outliers : 0.11 % Allowed : 2.60 % Favored : 97.30 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.70 (0.07), residues: 13229 helix: -0.54 (0.06), residues: 6064 sheet: -1.08 (0.11), residues: 1872 loop : -1.71 (0.09), residues: 5293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP P 257 HIS 0.013 0.002 HIS P 348 PHE 0.052 0.002 PHE O 310 TYR 0.042 0.002 TYR K 48 ARG 0.014 0.001 ARG O 369 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 818 time to evaluate : 9.655 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 71 MET cc_start: 0.7838 (ttm) cc_final: 0.7627 (ttm) REVERT: 1 166 MET cc_start: 0.8855 (mmm) cc_final: 0.7829 (mmm) REVERT: 2 183 MET cc_start: 0.7715 (mmm) cc_final: 0.7189 (mmm) REVERT: 2 214 MET cc_start: 0.8714 (mmm) cc_final: 0.8468 (mmm) REVERT: 3 101 PHE cc_start: 0.8332 (m-10) cc_final: 0.8090 (m-10) REVERT: 4 126 TYR cc_start: 0.7474 (m-10) cc_final: 0.7255 (m-10) REVERT: 4 127 LEU cc_start: 0.9017 (mt) cc_final: 0.8519 (pp) REVERT: 4 164 MET cc_start: 0.8088 (tpt) cc_final: 0.7066 (tpp) REVERT: 5 15 MET cc_start: 0.7500 (tpp) cc_final: 0.6437 (tpp) REVERT: 5 69 TYR cc_start: 0.8821 (t80) cc_final: 0.7896 (t80) REVERT: 5 149 MET cc_start: 0.7678 (mmm) cc_final: 0.7359 (mmm) REVERT: 5 193 ASP cc_start: 0.8893 (p0) cc_final: 0.8605 (p0) REVERT: 9 93 MET cc_start: 0.8817 (ptt) cc_final: 0.8292 (ttp) REVERT: A 81 MET cc_start: 0.7379 (ppp) cc_final: 0.6865 (ppp) REVERT: B 130 PHE cc_start: 0.7214 (m-80) cc_final: 0.6560 (m-80) REVERT: C 117 ASP cc_start: 0.8519 (m-30) cc_final: 0.8268 (m-30) REVERT: C 135 PHE cc_start: 0.8525 (m-80) cc_final: 0.7274 (m-80) REVERT: D 74 SER cc_start: 0.6882 (p) cc_final: 0.6228 (t) REVERT: G 126 TYR cc_start: 0.7608 (m-80) cc_final: 0.6480 (m-80) REVERT: I 333 MET cc_start: 0.6795 (ptt) cc_final: 0.4926 (ppp) REVERT: I 334 LEU cc_start: 0.8585 (mt) cc_final: 0.7707 (mt) REVERT: I 396 MET cc_start: 0.6840 (mmt) cc_final: 0.6486 (mmm) REVERT: J 40 ASN cc_start: 0.8039 (m-40) cc_final: 0.7545 (t0) REVERT: J 138 MET cc_start: 0.0224 (ppp) cc_final: -0.0789 (tpp) REVERT: J 247 MET cc_start: 0.5498 (mtm) cc_final: 0.4690 (mtp) REVERT: K 314 VAL cc_start: 0.8283 (t) cc_final: 0.7919 (p) REVERT: L 170 MET cc_start: 0.4498 (ptp) cc_final: 0.4250 (ptt) REVERT: L 309 LEU cc_start: 0.8200 (tp) cc_final: 0.7894 (tp) REVERT: M 254 MET cc_start: 0.9004 (pmm) cc_final: 0.8729 (pmm) REVERT: N 217 MET cc_start: 0.7008 (tpt) cc_final: 0.6597 (tpt) REVERT: N 489 MET cc_start: 0.7810 (mpp) cc_final: 0.7496 (mpp) REVERT: Q 68 MET cc_start: 0.2533 (mtt) cc_final: 0.2007 (mtt) REVERT: Q 85 MET cc_start: 0.5749 (mtm) cc_final: 0.5470 (mtm) REVERT: Q 409 TYR cc_start: 0.7372 (t80) cc_final: 0.5320 (t80) REVERT: R 404 VAL cc_start: 0.7802 (m) cc_final: 0.7259 (m) REVERT: S 1 MET cc_start: 0.6243 (ppp) cc_final: 0.5978 (ppp) REVERT: S 136 CYS cc_start: 0.7135 (t) cc_final: 0.6856 (t) REVERT: S 232 MET cc_start: 0.7432 (tmm) cc_final: 0.7038 (tmm) REVERT: T 255 GLN cc_start: 0.8809 (mp10) cc_final: 0.8216 (mp10) REVERT: U 79 MET cc_start: 0.6705 (mtt) cc_final: 0.5766 (mtt) REVERT: V 37 MET cc_start: 0.7713 (tmm) cc_final: 0.7413 (tmm) REVERT: V 290 ASN cc_start: 0.8670 (m-40) cc_final: 0.8306 (p0) REVERT: W 69 PHE cc_start: 0.7054 (t80) cc_final: 0.6613 (t80) REVERT: W 123 ASP cc_start: 0.6182 (p0) cc_final: 0.5881 (p0) REVERT: Z 124 MET cc_start: 0.3106 (tpp) cc_final: 0.1639 (tmm) REVERT: Z 788 PRO cc_start: 0.1962 (Cg_endo) cc_final: 0.1071 (Cg_exo) REVERT: Z 862 MET cc_start: 0.4279 (mmt) cc_final: 0.3096 (mmt) REVERT: a 141 LEU cc_start: 0.9013 (mp) cc_final: 0.8728 (mt) REVERT: c 39 MET cc_start: 0.8647 (tmm) cc_final: 0.8337 (tmm) REVERT: c 115 LEU cc_start: 0.8461 (tt) cc_final: 0.7705 (tt) REVERT: e 102 TYR cc_start: 0.7518 (m-10) cc_final: 0.7293 (m-10) REVERT: e 122 ARG cc_start: 0.8305 (mmp80) cc_final: 0.7901 (mmm-85) REVERT: e 157 HIS cc_start: 0.8280 (t70) cc_final: 0.6603 (t-170) REVERT: h 80 TYR cc_start: 0.7284 (t80) cc_final: 0.7057 (t80) REVERT: h 164 ASN cc_start: 0.6471 (t0) cc_final: 0.6084 (t0) REVERT: i 110 GLN cc_start: 0.9251 (mp10) cc_final: 0.8475 (mt0) REVERT: i 218 ASN cc_start: 0.7252 (m-40) cc_final: 0.6721 (m-40) REVERT: j 149 MET cc_start: 0.8181 (mmm) cc_final: 0.7482 (mmp) REVERT: l 120 MET cc_start: 0.4912 (tpt) cc_final: 0.4372 (tpt) outliers start: 12 outliers final: 2 residues processed: 829 average time/residue: 0.9845 time to fit residues: 1394.9429 Evaluate side-chains 587 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 585 time to evaluate : 9.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 1062 optimal weight: 9.9990 chunk 724 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 950 optimal weight: 30.0000 chunk 526 optimal weight: 0.4980 chunk 1088 optimal weight: 9.9990 chunk 881 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 651 optimal weight: 10.0000 chunk 1145 optimal weight: 8.9990 chunk 321 optimal weight: 7.9990 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 111 ASN ** 1 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 227 ASN ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 63 ASN 7 283 ASN 8 111 ASN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 ASN ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 240 HIS ** J 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 HIS ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 306 ASN ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 374 ASN P 242 GLN ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN ** S 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 458 GLN ** T 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 201 GLN W 18 ASN ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 38 GLN W 149 GLN ** Z 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 823 ASN ** a 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 31 HIS ** c 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 ASN ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 204 GLN ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 5 ASN ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 123 HIS ** g 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 HIS ** h 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 115 HIS k 63 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 105895 Z= 0.302 Angle : 0.774 22.722 143119 Z= 0.411 Chirality : 0.046 0.328 16362 Planarity : 0.005 0.130 18444 Dihedral : 6.837 71.927 14437 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 31.93 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.01 % Favored : 91.65 % Rotamer: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.52 (0.07), residues: 13229 helix: -0.34 (0.06), residues: 6112 sheet: -1.03 (0.11), residues: 1895 loop : -1.69 (0.09), residues: 5222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP O 373 HIS 0.014 0.002 HIS P 348 PHE 0.051 0.002 PHE O 310 TYR 0.047 0.002 TYR Z 358 ARG 0.011 0.001 ARG b 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 732 time to evaluate : 9.248 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 166 MET cc_start: 0.8712 (mmm) cc_final: 0.7408 (mmm) REVERT: 2 183 MET cc_start: 0.7769 (mmm) cc_final: 0.7513 (mmm) REVERT: 3 101 PHE cc_start: 0.8097 (m-80) cc_final: 0.7515 (m-80) REVERT: 4 111 MET cc_start: 0.8206 (ptp) cc_final: 0.7982 (ptm) REVERT: 4 127 LEU cc_start: 0.9085 (mt) cc_final: 0.8537 (pp) REVERT: 4 164 MET cc_start: 0.7979 (tpt) cc_final: 0.6986 (tpp) REVERT: 5 193 ASP cc_start: 0.8821 (p0) cc_final: 0.8472 (p0) REVERT: 8 166 MET cc_start: 0.9051 (tpt) cc_final: 0.8456 (tpt) REVERT: A 81 MET cc_start: 0.7438 (ppp) cc_final: 0.6692 (ppp) REVERT: B 130 PHE cc_start: 0.7338 (m-80) cc_final: 0.7083 (m-10) REVERT: I 333 MET cc_start: 0.7075 (ptt) cc_final: 0.6181 (ptp) REVERT: I 396 MET cc_start: 0.6986 (mmt) cc_final: 0.6622 (mmm) REVERT: J 40 ASN cc_start: 0.8254 (m-40) cc_final: 0.7590 (t0) REVERT: J 138 MET cc_start: 0.1254 (ppp) cc_final: -0.0404 (tpp) REVERT: K 212 TYR cc_start: 0.5234 (t80) cc_final: 0.4730 (t80) REVERT: L 170 MET cc_start: 0.6414 (ptp) cc_final: 0.5520 (ptt) REVERT: L 309 LEU cc_start: 0.8257 (tp) cc_final: 0.7893 (tp) REVERT: M 254 MET cc_start: 0.9178 (pmm) cc_final: 0.8636 (pmm) REVERT: M 343 LEU cc_start: 0.6819 (mt) cc_final: 0.6500 (mt) REVERT: N 217 MET cc_start: 0.7040 (tpt) cc_final: 0.6405 (tpt) REVERT: O 366 MET cc_start: 0.8386 (ppp) cc_final: 0.7996 (ppp) REVERT: O 373 TRP cc_start: 0.3011 (m-10) cc_final: 0.2110 (m-10) REVERT: Q 68 MET cc_start: 0.3189 (mtt) cc_final: 0.1692 (mtt) REVERT: Q 429 LYS cc_start: 0.8413 (mttt) cc_final: 0.8083 (mtpp) REVERT: R 404 VAL cc_start: 0.7946 (m) cc_final: 0.7203 (m) REVERT: S 136 CYS cc_start: 0.7223 (t) cc_final: 0.6964 (t) REVERT: T 255 GLN cc_start: 0.8905 (mp10) cc_final: 0.8349 (mp10) REVERT: U 76 MET cc_start: 0.7738 (mmp) cc_final: 0.7264 (mmp) REVERT: V 290 ASN cc_start: 0.8399 (m-40) cc_final: 0.8094 (p0) REVERT: W 123 ASP cc_start: 0.6445 (p0) cc_final: 0.6140 (p0) REVERT: Z 124 MET cc_start: 0.0279 (tpp) cc_final: -0.1608 (tmm) REVERT: Z 775 MET cc_start: 0.5998 (ttp) cc_final: 0.4106 (ptt) REVERT: Z 788 PRO cc_start: 0.2400 (Cg_endo) cc_final: 0.1574 (Cg_exo) REVERT: Z 862 MET cc_start: 0.2990 (mmt) cc_final: 0.2130 (mmt) REVERT: a 81 MET cc_start: 0.4347 (ttp) cc_final: 0.3792 (ttp) REVERT: a 112 MET cc_start: 0.6907 (ptm) cc_final: 0.5528 (ptm) REVERT: a 134 MET cc_start: 0.8107 (mmm) cc_final: 0.7667 (mmm) REVERT: a 141 LEU cc_start: 0.9231 (mp) cc_final: 0.8946 (mt) REVERT: c 39 MET cc_start: 0.8616 (tmm) cc_final: 0.8176 (tmm) REVERT: c 115 LEU cc_start: 0.8441 (tt) cc_final: 0.8027 (tt) REVERT: e 78 MET cc_start: 0.6188 (ppp) cc_final: 0.5852 (ppp) REVERT: e 81 LEU cc_start: 0.7244 (tp) cc_final: 0.6846 (tt) REVERT: e 122 ARG cc_start: 0.8682 (mmp80) cc_final: 0.8372 (mmm-85) REVERT: h 164 ASN cc_start: 0.6609 (t0) cc_final: 0.6274 (t0) REVERT: i 110 GLN cc_start: 0.9177 (mp10) cc_final: 0.8548 (mt0) REVERT: i 111 MET cc_start: 0.7235 (mmt) cc_final: 0.6972 (mmt) REVERT: i 218 ASN cc_start: 0.7290 (m-40) cc_final: 0.6996 (m-40) REVERT: j 149 MET cc_start: 0.8152 (mmm) cc_final: 0.7692 (mmp) REVERT: j 202 MET cc_start: 0.8556 (ppp) cc_final: 0.8034 (ppp) REVERT: l 158 LEU cc_start: 0.8862 (pp) cc_final: 0.8275 (pp) outliers start: 4 outliers final: 1 residues processed: 734 average time/residue: 0.9841 time to fit residues: 1240.4536 Evaluate side-chains 549 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 548 time to evaluate : 9.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 429 optimal weight: 20.0000 chunk 1149 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 749 optimal weight: 2.9990 chunk 314 optimal weight: 1.9990 chunk 1277 optimal weight: 20.0000 chunk 1060 optimal weight: 5.9990 chunk 591 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 422 optimal weight: 10.0000 chunk 670 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 111 ASN ** 1 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 55 GLN 6 63 ASN 7 160 ASN 7 283 ASN ** 8 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 111 ASN ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 GLN ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 269 GLN ** J 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 364 HIS ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 306 ASN ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN ** S 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 159 ASN ** S 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 240 ASN ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 103 ASN ** c 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 ASN ** c 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 5 ASN ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 157 ASN k 63 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 105895 Z= 0.268 Angle : 0.742 14.441 143119 Z= 0.392 Chirality : 0.045 0.592 16362 Planarity : 0.005 0.115 18444 Dihedral : 6.722 72.422 14437 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 30.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.79 % Favored : 91.90 % Rotamer: Outliers : 0.04 % Allowed : 1.68 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.39 (0.07), residues: 13229 helix: -0.17 (0.06), residues: 6162 sheet: -0.98 (0.11), residues: 1881 loop : -1.72 (0.09), residues: 5186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP O 373 HIS 0.012 0.002 HIS P 348 PHE 0.051 0.002 PHE N 302 TYR 0.028 0.002 TYR P 168 ARG 0.011 0.001 ARG H 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 728 time to evaluate : 9.241 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 166 MET cc_start: 0.8765 (mmm) cc_final: 0.7930 (mmm) REVERT: 1 207 PHE cc_start: 0.7881 (m-10) cc_final: 0.7599 (m-10) REVERT: 2 183 MET cc_start: 0.7739 (mmm) cc_final: 0.7453 (mmm) REVERT: 3 101 PHE cc_start: 0.8058 (m-80) cc_final: 0.7637 (m-80) REVERT: 4 164 MET cc_start: 0.7968 (tpt) cc_final: 0.7366 (tpp) REVERT: 5 193 ASP cc_start: 0.8958 (p0) cc_final: 0.8667 (p0) REVERT: 8 166 MET cc_start: 0.8895 (tpt) cc_final: 0.8274 (mmm) REVERT: 9 93 MET cc_start: 0.8182 (ppp) cc_final: 0.7362 (ppp) REVERT: B 99 ARG cc_start: 0.8771 (mtt180) cc_final: 0.8319 (mtt-85) REVERT: B 104 TYR cc_start: 0.7625 (m-80) cc_final: 0.7209 (m-80) REVERT: B 130 PHE cc_start: 0.7347 (m-80) cc_final: 0.7137 (m-80) REVERT: I 333 MET cc_start: 0.6901 (ptt) cc_final: 0.6322 (ptp) REVERT: I 396 MET cc_start: 0.7007 (mmt) cc_final: 0.6675 (mmm) REVERT: J 138 MET cc_start: 0.1662 (ppp) cc_final: 0.0612 (tpt) REVERT: J 229 MET cc_start: 0.4593 (ptm) cc_final: 0.4336 (ptm) REVERT: J 292 MET cc_start: 0.7264 (tpt) cc_final: 0.7036 (tpt) REVERT: K 161 MET cc_start: 0.1027 (ptt) cc_final: 0.0802 (ptt) REVERT: K 212 TYR cc_start: 0.5308 (t80) cc_final: 0.4703 (t80) REVERT: L 309 LEU cc_start: 0.8221 (tp) cc_final: 0.7936 (tp) REVERT: M 254 MET cc_start: 0.9092 (pmm) cc_final: 0.8602 (pmm) REVERT: N 731 VAL cc_start: 0.8665 (t) cc_final: 0.8400 (t) REVERT: O 366 MET cc_start: 0.8428 (ppp) cc_final: 0.8213 (ppp) REVERT: P 184 MET cc_start: 0.7921 (mtm) cc_final: 0.7716 (mtm) REVERT: P 306 ASN cc_start: 0.5071 (OUTLIER) cc_final: 0.4746 (t0) REVERT: Q 68 MET cc_start: 0.2817 (mtt) cc_final: 0.1382 (mtt) REVERT: Q 409 TYR cc_start: 0.7823 (t80) cc_final: 0.6591 (t80) REVERT: Q 429 LYS cc_start: 0.8442 (mttt) cc_final: 0.8162 (mtpp) REVERT: R 171 MET cc_start: 0.7074 (tmm) cc_final: 0.6869 (tmm) REVERT: S 136 CYS cc_start: 0.7244 (t) cc_final: 0.6938 (t) REVERT: S 232 MET cc_start: 0.7310 (tmm) cc_final: 0.7047 (tmm) REVERT: T 255 GLN cc_start: 0.8894 (mp10) cc_final: 0.8338 (mp10) REVERT: U 76 MET cc_start: 0.6830 (mmp) cc_final: 0.5967 (mmm) REVERT: V 290 ASN cc_start: 0.8323 (m-40) cc_final: 0.8107 (p0) REVERT: W 123 ASP cc_start: 0.6406 (p0) cc_final: 0.6094 (p0) REVERT: Z 124 MET cc_start: 0.0178 (tpp) cc_final: -0.1644 (tmm) REVERT: Z 756 MET cc_start: 0.6907 (mtm) cc_final: 0.6692 (mtp) REVERT: Z 775 MET cc_start: 0.5970 (ttp) cc_final: 0.3636 (ptt) REVERT: Z 788 PRO cc_start: 0.2786 (Cg_endo) cc_final: 0.1739 (Cg_exo) REVERT: Z 862 MET cc_start: 0.3818 (mmt) cc_final: 0.2817 (mmt) REVERT: a 112 MET cc_start: 0.6553 (ptm) cc_final: 0.6257 (ptm) REVERT: c 39 MET cc_start: 0.8624 (tmm) cc_final: 0.8135 (tmm) REVERT: c 115 LEU cc_start: 0.8447 (tt) cc_final: 0.8020 (tt) REVERT: d 173 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8119 (tp30) REVERT: e 81 LEU cc_start: 0.7327 (tp) cc_final: 0.7041 (tt) REVERT: e 102 TYR cc_start: 0.7935 (m-10) cc_final: 0.7475 (m-10) REVERT: e 123 PHE cc_start: 0.8463 (p90) cc_final: 0.8204 (p90) REVERT: h 134 LEU cc_start: 0.8313 (mp) cc_final: 0.8071 (mp) REVERT: h 164 ASN cc_start: 0.6803 (t0) cc_final: 0.6413 (t0) REVERT: i 110 GLN cc_start: 0.9190 (mp10) cc_final: 0.8683 (mt0) REVERT: i 218 ASN cc_start: 0.7190 (m-40) cc_final: 0.6962 (m-40) REVERT: j 149 MET cc_start: 0.8136 (mmm) cc_final: 0.7686 (mmp) outliers start: 4 outliers final: 0 residues processed: 732 average time/residue: 0.9781 time to fit residues: 1233.7637 Evaluate side-chains 537 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 536 time to evaluate : 9.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 1231 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 727 optimal weight: 3.9990 chunk 932 optimal weight: 0.0470 chunk 722 optimal weight: 0.9990 chunk 1075 optimal weight: 1.9990 chunk 713 optimal weight: 0.5980 chunk 1272 optimal weight: 10.0000 chunk 796 optimal weight: 20.0000 chunk 775 optimal weight: 9.9990 chunk 587 optimal weight: 0.2980 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 111 ASN 1 171 ASN 1 172 GLN ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 55 GLN 6 63 ASN 7 160 ASN ** 8 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 111 ASN 9 227 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 397 ASN ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 302 GLN ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 374 ASN P 277 GLN ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 397 ASN ** S 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 135 ASN ** S 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 458 GLN ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 192 ASN ** U 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 40 HIS V 184 ASN ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 240 ASN Z 338 HIS ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 766 HIS ** Z 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 958 ASN ** c 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 ASN ** c 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 19 GLN ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 5 ASN ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.5964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 105895 Z= 0.199 Angle : 0.713 15.949 143119 Z= 0.374 Chirality : 0.045 0.401 16362 Planarity : 0.005 0.103 18444 Dihedral : 6.392 74.357 14437 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.98 % Favored : 92.73 % Rotamer: Outliers : 0.01 % Allowed : 1.26 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.30 % Twisted Proline : 0.00 % 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: -1.15 (0.07), residues: 13229 helix: 0.06 (0.06), residues: 6192 sheet: -0.83 (0.11), residues: 1872 loop : -1.66 (0.09), residues: 5165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP O 373 HIS 0.026 0.001 HIS P 348 PHE 0.038 0.002 PHE N 399 TYR 0.031 0.002 TYR P 168 ARG 0.028 0.001 ARG S 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 796 time to evaluate : 9.207 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 166 MET cc_start: 0.8702 (mmm) cc_final: 0.8036 (mmm) REVERT: 2 183 MET cc_start: 0.7815 (mmm) cc_final: 0.7436 (mmm) REVERT: 2 214 MET cc_start: 0.8400 (mmm) cc_final: 0.8124 (mmm) REVERT: 3 101 PHE cc_start: 0.7973 (m-80) cc_final: 0.7599 (m-80) REVERT: 3 165 MET cc_start: 0.7857 (ttt) cc_final: 0.7441 (ttt) REVERT: 4 164 MET cc_start: 0.7729 (tpt) cc_final: 0.7142 (tpp) REVERT: 5 193 ASP cc_start: 0.8724 (p0) cc_final: 0.8407 (p0) REVERT: 8 166 MET cc_start: 0.8876 (tpt) cc_final: 0.8145 (mmm) REVERT: 9 93 MET cc_start: 0.8169 (ppp) cc_final: 0.7212 (ppp) REVERT: A 81 MET cc_start: 0.7965 (ppp) cc_final: 0.7320 (ppp) REVERT: B 130 PHE cc_start: 0.7300 (m-80) cc_final: 0.7090 (m-10) REVERT: C 135 PHE cc_start: 0.8492 (m-80) cc_final: 0.7403 (m-80) REVERT: E 225 GLN cc_start: 0.8902 (pm20) cc_final: 0.8375 (pm20) REVERT: I 333 MET cc_start: 0.7160 (ptt) cc_final: 0.6929 (ptp) REVERT: I 396 MET cc_start: 0.6905 (mmt) cc_final: 0.6640 (mmm) REVERT: J 138 MET cc_start: 0.1411 (ppp) cc_final: 0.0669 (tpt) REVERT: J 247 MET cc_start: 0.6735 (mpp) cc_final: 0.6412 (mpp) REVERT: K 328 LEU cc_start: 0.7634 (tp) cc_final: 0.7433 (tp) REVERT: K 360 MET cc_start: 0.5195 (mmm) cc_final: 0.4850 (mmp) REVERT: M 254 MET cc_start: 0.9147 (pmm) cc_final: 0.8697 (pmm) REVERT: N 217 MET cc_start: 0.4809 (tpt) cc_final: 0.3182 (mmm) REVERT: N 223 LEU cc_start: 0.7775 (tp) cc_final: 0.7528 (tp) REVERT: N 731 VAL cc_start: 0.8475 (t) cc_final: 0.8268 (t) REVERT: Q 68 MET cc_start: 0.2601 (mtt) cc_final: 0.1267 (mtt) REVERT: Q 429 LYS cc_start: 0.8113 (mttt) cc_final: 0.7689 (mtpp) REVERT: R 171 MET cc_start: 0.6977 (tmm) cc_final: 0.6766 (tmm) REVERT: R 271 ILE cc_start: 0.7471 (tt) cc_final: 0.6273 (tp) REVERT: S 1 MET cc_start: 0.7029 (ppp) cc_final: 0.6118 (ppp) REVERT: S 136 CYS cc_start: 0.7098 (t) cc_final: 0.6660 (t) REVERT: T 250 MET cc_start: 0.0545 (mpp) cc_final: -0.0263 (mpp) REVERT: T 255 GLN cc_start: 0.8492 (mp10) cc_final: 0.8048 (mt0) REVERT: U 76 MET cc_start: 0.7263 (mmp) cc_final: 0.6913 (mmm) REVERT: V 214 MET cc_start: 0.6311 (mmt) cc_final: 0.6104 (mmt) REVERT: W 123 ASP cc_start: 0.6325 (p0) cc_final: 0.6021 (p0) REVERT: Z 124 MET cc_start: 0.1364 (tpp) cc_final: 0.0351 (tmm) REVERT: Z 756 MET cc_start: 0.7014 (mtm) cc_final: 0.6713 (mtm) REVERT: Z 775 MET cc_start: 0.1716 (ttp) cc_final: 0.1143 (ptm) REVERT: Z 862 MET cc_start: 0.3498 (mmt) cc_final: 0.2726 (mmt) REVERT: a 112 MET cc_start: 0.6455 (ptm) cc_final: 0.5676 (ptm) REVERT: a 141 LEU cc_start: 0.9126 (mp) cc_final: 0.8895 (tp) REVERT: c 39 MET cc_start: 0.8550 (tmm) cc_final: 0.8125 (tmm) REVERT: c 115 LEU cc_start: 0.8392 (tt) cc_final: 0.8000 (tt) REVERT: e 78 MET cc_start: 0.6779 (ppp) cc_final: 0.6239 (ppp) REVERT: e 81 LEU cc_start: 0.7144 (tp) cc_final: 0.6731 (tt) REVERT: e 102 TYR cc_start: 0.7728 (m-10) cc_final: 0.7489 (m-10) REVERT: e 123 PHE cc_start: 0.8325 (p90) cc_final: 0.7576 (p90) REVERT: e 157 HIS cc_start: 0.8390 (t70) cc_final: 0.6438 (t-170) REVERT: f 219 ASP cc_start: 0.6721 (p0) cc_final: 0.6257 (p0) REVERT: g 24 VAL cc_start: 0.8969 (t) cc_final: 0.8751 (p) REVERT: g 151 LEU cc_start: 0.8054 (pp) cc_final: 0.7816 (pp) REVERT: i 110 GLN cc_start: 0.8938 (mp10) cc_final: 0.8600 (mt0) REVERT: i 117 PHE cc_start: 0.7939 (t80) cc_final: 0.7536 (t80) REVERT: i 218 ASN cc_start: 0.7018 (m-40) cc_final: 0.6736 (m-40) REVERT: j 202 MET cc_start: 0.8258 (ppp) cc_final: 0.7704 (ppp) REVERT: l 158 LEU cc_start: 0.8723 (pp) cc_final: 0.8182 (pp) outliers start: 1 outliers final: 0 residues processed: 797 average time/residue: 0.9889 time to fit residues: 1356.1188 Evaluate side-chains 566 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 566 time to evaluate : 9.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 787 optimal weight: 9.9990 chunk 508 optimal weight: 10.0000 chunk 759 optimal weight: 9.9990 chunk 383 optimal weight: 5.9990 chunk 249 optimal weight: 8.9990 chunk 246 optimal weight: 4.9990 chunk 808 optimal weight: 0.5980 chunk 866 optimal weight: 5.9990 chunk 629 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 1000 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 111 ASN 1 171 ASN ** 2 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 55 GLN 7 160 ASN 7 283 ASN ** 8 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 111 ASN 9 35 GLN 9 246 GLN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 293 GLN ** I 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 393 ASN ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 607 GLN ** N 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 141 ASN O 326 HIS O 374 ASN P 113 ASN ** P 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 296 GLN ** P 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 GLN ** S 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 317 HIS ** S 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 240 ASN Z 338 HIS ** Z 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 766 HIS ** Z 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 926 ASN a 92 ASN a 251 GLN ** c 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 ASN ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 157 HIS f 5 ASN ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 210 ASN ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 79 GLN ** h 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 89 GLN k 99 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 105895 Z= 0.285 Angle : 0.739 12.904 143119 Z= 0.391 Chirality : 0.045 0.299 16362 Planarity : 0.005 0.097 18444 Dihedral : 6.417 77.466 14437 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 29.94 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.70 % Favored : 92.00 % Rotamer: Outliers : 0.01 % Allowed : 1.08 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.07), residues: 13229 helix: 0.10 (0.06), residues: 6209 sheet: -0.81 (0.11), residues: 1882 loop : -1.68 (0.09), residues: 5138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP O 373 HIS 0.022 0.002 HIS P 348 PHE 0.045 0.002 PHE W 69 TYR 0.047 0.002 TYR R 70 ARG 0.017 0.001 ARG V 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 684 time to evaluate : 9.771 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: 1 166 MET cc_start: 0.8664 (mmm) cc_final: 0.8030 (mmm) REVERT: 2 183 MET cc_start: 0.7723 (mmm) cc_final: 0.7441 (mmm) REVERT: 2 214 MET cc_start: 0.8440 (mmm) cc_final: 0.8220 (mmm) REVERT: 3 101 PHE cc_start: 0.8006 (m-80) cc_final: 0.7661 (m-80) REVERT: 4 127 LEU cc_start: 0.9064 (mt) cc_final: 0.8603 (mp) REVERT: 4 164 MET cc_start: 0.7800 (tpt) cc_final: 0.7174 (tpp) REVERT: 5 69 TYR cc_start: 0.7940 (t80) cc_final: 0.7684 (t80) REVERT: 5 193 ASP cc_start: 0.8927 (p0) cc_final: 0.8664 (p0) REVERT: 6 1 MET cc_start: 0.5736 (tmm) cc_final: 0.5512 (tmm) REVERT: 8 166 MET cc_start: 0.8934 (tpt) cc_final: 0.8173 (tpt) REVERT: 9 93 MET cc_start: 0.8616 (ppp) cc_final: 0.8408 (ppp) REVERT: 9 214 MET cc_start: 0.8335 (ttp) cc_final: 0.8118 (ttt) REVERT: A 81 MET cc_start: 0.8052 (ppp) cc_final: 0.7318 (ppp) REVERT: B 130 PHE cc_start: 0.7350 (m-80) cc_final: 0.7115 (m-80) REVERT: H 333 MET cc_start: 0.7821 (tmm) cc_final: 0.7495 (tmm) REVERT: H 352 MET cc_start: 0.4736 (ptp) cc_final: 0.4498 (ptp) REVERT: I 396 MET cc_start: 0.7053 (mmt) cc_final: 0.6740 (mmm) REVERT: J 138 MET cc_start: 0.2723 (ppp) cc_final: 0.1280 (tpt) REVERT: J 229 MET cc_start: 0.5996 (ptp) cc_final: 0.5609 (ptp) REVERT: J 247 MET cc_start: 0.7336 (mpp) cc_final: 0.6891 (mpp) REVERT: L 253 ASP cc_start: 0.4898 (t0) cc_final: 0.4643 (t0) REVERT: M 254 MET cc_start: 0.9199 (pmm) cc_final: 0.8754 (pmm) REVERT: M 343 LEU cc_start: 0.6835 (mt) cc_final: 0.6626 (mt) REVERT: O 373 TRP cc_start: 0.4017 (m-10) cc_final: 0.2420 (m-10) REVERT: Q 68 MET cc_start: 0.3739 (mtt) cc_final: 0.1796 (mtt) REVERT: Q 174 LEU cc_start: 0.8592 (tt) cc_final: 0.8349 (tp) REVERT: Q 409 TYR cc_start: 0.7699 (t80) cc_final: 0.6218 (t80) REVERT: R 171 MET cc_start: 0.7157 (tmm) cc_final: 0.6915 (tmm) REVERT: S 1 MET cc_start: 0.7001 (ppp) cc_final: 0.6127 (ppp) REVERT: S 136 CYS cc_start: 0.7140 (t) cc_final: 0.6798 (t) REVERT: T 255 GLN cc_start: 0.8855 (mp10) cc_final: 0.8477 (mp10) REVERT: V 73 GLN cc_start: 0.7522 (pm20) cc_final: 0.7127 (mp10) REVERT: V 94 MET cc_start: 0.6194 (tpt) cc_final: 0.5787 (tpt) REVERT: V 244 MET cc_start: 0.5261 (pmm) cc_final: 0.5055 (pmm) REVERT: W 123 ASP cc_start: 0.6499 (p0) cc_final: 0.6153 (p0) REVERT: Z 124 MET cc_start: 0.1309 (tpp) cc_final: 0.0300 (tmm) REVERT: Z 780 MET cc_start: 0.7657 (mpp) cc_final: 0.6571 (mpp) REVERT: a 112 MET cc_start: 0.6580 (ptm) cc_final: 0.6161 (ptp) REVERT: b 2 THR cc_start: 0.7115 (p) cc_final: 0.6626 (p) REVERT: b 118 MET cc_start: 0.7335 (ppp) cc_final: 0.7125 (ppp) REVERT: c 39 MET cc_start: 0.8565 (tmm) cc_final: 0.8138 (tmm) REVERT: c 115 LEU cc_start: 0.8528 (tt) cc_final: 0.8151 (tt) REVERT: e 81 LEU cc_start: 0.7840 (tp) cc_final: 0.7309 (tt) REVERT: e 102 TYR cc_start: 0.7842 (m-10) cc_final: 0.7629 (m-10) REVERT: e 123 PHE cc_start: 0.8428 (p90) cc_final: 0.8151 (p90) REVERT: f 219 ASP cc_start: 0.6156 (p0) cc_final: 0.5687 (p0) REVERT: i 186 ASP cc_start: 0.8393 (m-30) cc_final: 0.8066 (m-30) REVERT: j 149 MET cc_start: 0.6749 (mmp) cc_final: 0.6300 (mmt) REVERT: j 202 MET cc_start: 0.8630 (ppp) cc_final: 0.7943 (ppp) outliers start: 1 outliers final: 0 residues processed: 685 average time/residue: 1.0023 time to fit residues: 1196.0483 Evaluate side-chains 521 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 521 time to evaluate : 9.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 1157 optimal weight: 0.9980 chunk 1218 optimal weight: 7.9990 chunk 1112 optimal weight: 9.9990 chunk 1185 optimal weight: 10.0000 chunk 713 optimal weight: 20.0000 chunk 516 optimal weight: 8.9990 chunk 930 optimal weight: 3.9990 chunk 363 optimal weight: 1.9990 chunk 1071 optimal weight: 20.0000 chunk 1121 optimal weight: 8.9990 chunk 1181 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 111 ASN ** 1 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 81 HIS ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 55 GLN 6 63 ASN 7 160 ASN 7 283 ASN ** 8 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 111 ASN 9 35 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 305 ASN ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 16 ASN ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 GLN ** S 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 458 GLN ** T 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 192 ASN ** U 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 823 ASN ** Z 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 ASN ** c 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 5 ASN ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 63 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 105895 Z= 0.297 Angle : 0.757 14.822 143119 Z= 0.402 Chirality : 0.046 0.568 16362 Planarity : 0.005 0.101 18444 Dihedral : 6.504 76.459 14437 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 31.53 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.25 % Favored : 91.43 % Rotamer: Outliers : 0.01 % Allowed : 0.61 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.30 % Twisted Proline : 0.00 % 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: -1.15 (0.07), residues: 13229 helix: 0.09 (0.06), residues: 6190 sheet: -0.89 (0.11), residues: 1860 loop : -1.69 (0.09), residues: 5179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP X 100 HIS 0.023 0.002 HIS P 348 PHE 0.038 0.002 PHE O 310 TYR 0.035 0.002 TYR R 70 ARG 0.020 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 661 time to evaluate : 9.330 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: 1 166 MET cc_start: 0.8820 (mmm) cc_final: 0.8344 (mmm) REVERT: 1 216 GLN cc_start: 0.9031 (mp10) cc_final: 0.8828 (mp10) REVERT: 2 183 MET cc_start: 0.7758 (mmm) cc_final: 0.7453 (mmm) REVERT: 2 214 MET cc_start: 0.8458 (mmm) cc_final: 0.8182 (mmm) REVERT: 3 101 PHE cc_start: 0.7894 (m-80) cc_final: 0.7608 (m-80) REVERT: 3 165 MET cc_start: 0.6372 (ttt) cc_final: 0.6107 (ttt) REVERT: 4 127 LEU cc_start: 0.9039 (mt) cc_final: 0.8476 (pp) REVERT: 4 164 MET cc_start: 0.7778 (tpt) cc_final: 0.7002 (tpp) REVERT: 5 69 TYR cc_start: 0.7938 (t80) cc_final: 0.7645 (t80) REVERT: 5 193 ASP cc_start: 0.8967 (p0) cc_final: 0.8673 (p0) REVERT: 7 120 MET cc_start: 0.7420 (mmp) cc_final: 0.7148 (mmm) REVERT: 7 175 MET cc_start: 0.7822 (mpp) cc_final: 0.7593 (mpp) REVERT: 8 166 MET cc_start: 0.8947 (tpt) cc_final: 0.8099 (tpt) REVERT: 9 63 TYR cc_start: 0.7684 (t80) cc_final: 0.7391 (t80) REVERT: 9 179 PHE cc_start: 0.7439 (t80) cc_final: 0.5622 (t80) REVERT: A 81 MET cc_start: 0.8041 (ppp) cc_final: 0.7329 (ppp) REVERT: B 130 PHE cc_start: 0.7431 (m-80) cc_final: 0.7119 (m-80) REVERT: C 135 PHE cc_start: 0.9045 (m-80) cc_final: 0.7758 (m-80) REVERT: F 228 GLU cc_start: 0.8124 (mp0) cc_final: 0.7788 (mp0) REVERT: F 234 ILE cc_start: 0.7345 (mm) cc_final: 0.6988 (mm) REVERT: J 118 ASP cc_start: 0.6577 (t0) cc_final: 0.6160 (t0) REVERT: J 138 MET cc_start: 0.2701 (ppp) cc_final: 0.1101 (tpt) REVERT: L 309 LEU cc_start: 0.7710 (tp) cc_final: 0.7248 (tp) REVERT: M 235 CYS cc_start: 0.8252 (p) cc_final: 0.7675 (m) REVERT: M 254 MET cc_start: 0.9140 (pmm) cc_final: 0.8677 (pmm) REVERT: M 255 TYR cc_start: 0.4056 (m-10) cc_final: 0.3705 (m-80) REVERT: M 343 LEU cc_start: 0.6946 (mt) cc_final: 0.6730 (mt) REVERT: N 657 MET cc_start: 0.7499 (ptt) cc_final: 0.6690 (ptt) REVERT: O 373 TRP cc_start: 0.3638 (m-10) cc_final: 0.2543 (m-10) REVERT: Q 68 MET cc_start: 0.3674 (mtt) cc_final: 0.1882 (mtt) REVERT: Q 85 MET cc_start: 0.5460 (ttp) cc_final: 0.5159 (ptm) REVERT: Q 174 LEU cc_start: 0.8560 (tt) cc_final: 0.8163 (tp) REVERT: Q 409 TYR cc_start: 0.7324 (t80) cc_final: 0.7120 (t80) REVERT: R 225 LYS cc_start: 0.8228 (tppt) cc_final: 0.7999 (mmmt) REVERT: R 401 HIS cc_start: 0.6388 (t70) cc_final: 0.5963 (t70) REVERT: S 1 MET cc_start: 0.6899 (ppp) cc_final: 0.6063 (ppp) REVERT: S 136 CYS cc_start: 0.7237 (t) cc_final: 0.6864 (t) REVERT: T 255 GLN cc_start: 0.8862 (mp10) cc_final: 0.8426 (mp10) REVERT: V 71 MET cc_start: 0.8540 (tpt) cc_final: 0.8304 (tpp) REVERT: V 244 MET cc_start: 0.5768 (pmm) cc_final: 0.5402 (pmm) REVERT: W 69 PHE cc_start: 0.7813 (t80) cc_final: 0.7479 (t80) REVERT: Z 124 MET cc_start: 0.1188 (tpp) cc_final: 0.0267 (tmm) REVERT: Z 775 MET cc_start: 0.3978 (ttt) cc_final: 0.2642 (tpp) REVERT: Z 780 MET cc_start: 0.8210 (mpp) cc_final: 0.7148 (mpp) REVERT: Z 788 PRO cc_start: 0.3074 (Cg_endo) cc_final: 0.2238 (Cg_exo) REVERT: c 39 MET cc_start: 0.8294 (tmm) cc_final: 0.7842 (tmm) REVERT: c 115 LEU cc_start: 0.8661 (tt) cc_final: 0.8268 (tt) REVERT: e 78 MET cc_start: 0.6785 (ppp) cc_final: 0.6043 (ppp) REVERT: e 123 PHE cc_start: 0.8509 (p90) cc_final: 0.7958 (p90) REVERT: f 219 ASP cc_start: 0.6336 (p0) cc_final: 0.5936 (p0) REVERT: g 81 LEU cc_start: 0.6702 (tt) cc_final: 0.4980 (mm) REVERT: i 110 GLN cc_start: 0.9004 (mp10) cc_final: 0.8494 (mp10) REVERT: j 202 MET cc_start: 0.8739 (ppp) cc_final: 0.8067 (ppp) outliers start: 1 outliers final: 0 residues processed: 662 average time/residue: 0.9647 time to fit residues: 1108.2012 Evaluate side-chains 505 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 9.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 778 optimal weight: 0.0970 chunk 1253 optimal weight: 6.9990 chunk 765 optimal weight: 10.0000 chunk 594 optimal weight: 4.9990 chunk 871 optimal weight: 5.9990 chunk 1315 optimal weight: 20.0000 chunk 1210 optimal weight: 0.9980 chunk 1047 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 808 optimal weight: 7.9990 chunk 642 optimal weight: 9.9990 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 111 ASN ** 1 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 180 GLN ** 4 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 55 GLN 6 63 ASN 7 160 ASN 7 283 ASN ** 8 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 111 ASN 9 35 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 394 GLN ** K 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 242 ASN L 353 ASN ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 374 ASN ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 401 ASN ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 387 ASN ** Z 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 766 HIS ** Z 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 123 ASN ** c 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 ASN ** c 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 5 ASN ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 63 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 105895 Z= 0.244 Angle : 0.725 14.765 143119 Z= 0.383 Chirality : 0.045 0.617 16362 Planarity : 0.005 0.082 18444 Dihedral : 6.388 75.074 14437 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 28.78 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.82 % Favored : 91.88 % Rotamer: Outliers : 0.01 % Allowed : 0.31 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.31 % Twisted Proline : 0.00 % 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: -1.05 (0.07), residues: 13229 helix: 0.17 (0.06), residues: 6214 sheet: -0.87 (0.11), residues: 1853 loop : -1.63 (0.09), residues: 5162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP O 373 HIS 0.021 0.002 HIS P 348 PHE 0.032 0.002 PHE I 271 TYR 0.052 0.002 TYR h 89 ARG 0.012 0.001 ARG l 181 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26458 Ramachandran restraints generated. 13229 Oldfield, 0 Emsley, 13229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 648 time to evaluate : 9.406 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: 1 166 MET cc_start: 0.8360 (mmm) cc_final: 0.7764 (mmm) REVERT: 2 183 MET cc_start: 0.7709 (mmm) cc_final: 0.7405 (mmm) REVERT: 2 214 MET cc_start: 0.8416 (mmm) cc_final: 0.8131 (mmm) REVERT: 3 101 PHE cc_start: 0.7900 (m-80) cc_final: 0.7610 (m-80) REVERT: 3 165 MET cc_start: 0.7192 (ttt) cc_final: 0.6881 (ttt) REVERT: 4 164 MET cc_start: 0.7721 (tpt) cc_final: 0.7241 (tpp) REVERT: 5 149 MET cc_start: 0.7260 (mmm) cc_final: 0.6719 (mmp) REVERT: 5 193 ASP cc_start: 0.8967 (p0) cc_final: 0.8604 (p0) REVERT: 7 120 MET cc_start: 0.7609 (mmp) cc_final: 0.6864 (mmm) REVERT: 8 166 MET cc_start: 0.8925 (tpt) cc_final: 0.8316 (tpt) REVERT: 9 63 TYR cc_start: 0.7623 (t80) cc_final: 0.7329 (t80) REVERT: 9 93 MET cc_start: 0.8293 (ppp) cc_final: 0.7957 (ppp) REVERT: 9 179 PHE cc_start: 0.7713 (t80) cc_final: 0.7380 (t80) REVERT: A 81 MET cc_start: 0.8087 (ppp) cc_final: 0.7363 (ppp) REVERT: B 130 PHE cc_start: 0.7382 (m-80) cc_final: 0.7091 (m-80) REVERT: C 135 PHE cc_start: 0.8630 (m-80) cc_final: 0.7529 (m-80) REVERT: E 225 GLN cc_start: 0.8996 (pm20) cc_final: 0.8413 (pm20) REVERT: F 228 GLU cc_start: 0.7934 (mp0) cc_final: 0.7729 (mp0) REVERT: F 234 ILE cc_start: 0.7460 (mm) cc_final: 0.7069 (mm) REVERT: I 194 MET cc_start: 0.6444 (mmm) cc_final: 0.5690 (mmm) REVERT: I 333 MET cc_start: 0.7126 (ptt) cc_final: 0.6748 (ptp) REVERT: J 138 MET cc_start: 0.1700 (ppp) cc_final: 0.0551 (tpt) REVERT: J 229 MET cc_start: 0.6168 (ptm) cc_final: 0.5239 (ptm) REVERT: J 236 MET cc_start: 0.7508 (ttm) cc_final: 0.6301 (ttt) REVERT: K 253 MET cc_start: 0.7704 (tpt) cc_final: 0.7292 (tpp) REVERT: L 309 LEU cc_start: 0.7791 (tp) cc_final: 0.7151 (tp) REVERT: M 254 MET cc_start: 0.9087 (pmm) cc_final: 0.8710 (pmm) REVERT: M 343 LEU cc_start: 0.6915 (mt) cc_final: 0.6625 (mt) REVERT: N 657 MET cc_start: 0.7418 (ptt) cc_final: 0.6196 (ptt) REVERT: O 373 TRP cc_start: 0.2857 (m-10) cc_final: 0.1358 (m-10) REVERT: Q 68 MET cc_start: 0.3546 (mtt) cc_final: 0.1906 (mtt) REVERT: Q 174 LEU cc_start: 0.8540 (tt) cc_final: 0.8177 (tp) REVERT: Q 409 TYR cc_start: 0.7692 (t80) cc_final: 0.6405 (t80) REVERT: R 401 HIS cc_start: 0.6065 (t70) cc_final: 0.5842 (t70) REVERT: S 1 MET cc_start: 0.6741 (ppp) cc_final: 0.5896 (ppp) REVERT: S 136 CYS cc_start: 0.7187 (t) cc_final: 0.6744 (t) REVERT: T 106 ILE cc_start: 0.7752 (tp) cc_final: 0.7206 (tt) REVERT: T 255 GLN cc_start: 0.8680 (mp10) cc_final: 0.8138 (mt0) REVERT: V 91 MET cc_start: 0.7415 (mmp) cc_final: 0.7214 (mmm) REVERT: V 94 MET cc_start: 0.6354 (tpt) cc_final: 0.5949 (tpt) REVERT: V 244 MET cc_start: 0.5839 (pmm) cc_final: 0.5507 (pmm) REVERT: W 69 PHE cc_start: 0.8336 (t80) cc_final: 0.7884 (t80) REVERT: Z 124 MET cc_start: 0.1124 (tpp) cc_final: 0.0242 (tmm) REVERT: Z 788 PRO cc_start: 0.2865 (Cg_endo) cc_final: 0.2356 (Cg_exo) REVERT: Z 865 ASP cc_start: 0.7524 (m-30) cc_final: 0.7290 (m-30) REVERT: b 2 THR cc_start: 0.8009 (p) cc_final: 0.7576 (p) REVERT: c 39 MET cc_start: 0.8315 (tmm) cc_final: 0.7855 (tmm) REVERT: c 115 LEU cc_start: 0.8604 (tt) cc_final: 0.8161 (tt) REVERT: e 78 MET cc_start: 0.6864 (ppp) cc_final: 0.5824 (ppp) REVERT: e 88 MET cc_start: 0.7809 (mpp) cc_final: 0.7232 (mtm) REVERT: e 123 PHE cc_start: 0.8349 (p90) cc_final: 0.7196 (p90) REVERT: f 219 ASP cc_start: 0.6257 (p0) cc_final: 0.5803 (p0) REVERT: h 134 LEU cc_start: 0.8509 (mp) cc_final: 0.8290 (mp) REVERT: i 110 GLN cc_start: 0.9182 (mp10) cc_final: 0.8714 (mp10) REVERT: j 149 MET cc_start: 0.7804 (mmm) cc_final: 0.7389 (mmp) REVERT: j 202 MET cc_start: 0.8736 (ppp) cc_final: 0.8082 (ppp) REVERT: l 158 LEU cc_start: 0.8688 (pp) cc_final: 0.8310 (pp) outliers start: 1 outliers final: 0 residues processed: 649 average time/residue: 1.0060 time to fit residues: 1136.7442 Evaluate side-chains 511 residues out of total 11498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 511 time to evaluate : 9.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 831 optimal weight: 30.0000 chunk 1115 optimal weight: 10.0000 chunk 320 optimal weight: 10.0000 chunk 965 optimal weight: 9.9990 chunk 154 optimal weight: 0.8980 chunk 291 optimal weight: 8.9990 chunk 1048 optimal weight: 8.9990 chunk 438 optimal weight: 7.9990 chunk 1077 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 193 optimal weight: 0.0980 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 111 ASN ** 1 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 55 GLN 6 63 ASN 7 160 ASN 7 283 ASN ** 8 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 111 ASN 8 177 ASN 9 35 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 242 ASN ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 379 GLN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 766 HIS ** Z 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 123 ASN ** a 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 177 GLN c 221 ASN ** c 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 5 ASN ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 283 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.046001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.038059 restraints weight = 1055760.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.039317 restraints weight = 691593.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.039913 restraints weight = 487363.971| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 105895 Z= 0.298 Angle : 0.753 14.288 143119 Z= 0.399 Chirality : 0.045 0.515 16362 Planarity : 0.005 0.080 18444 Dihedral : 6.447 73.657 14437 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 31.90 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.60 % Favored : 91.08 % Rotamer: Outliers : 0.01 % Allowed : 0.29 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.07), residues: 13229 helix: 0.13 (0.06), residues: 6219 sheet: -0.91 (0.11), residues: 1850 loop : -1.69 (0.09), residues: 5160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP O 373 HIS 0.021 0.002 HIS P 348 PHE 0.027 0.002 PHE O 310 TYR 0.036 0.002 TYR h 89 ARG 0.037 0.001 ARG e 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22365.02 seconds wall clock time: 400 minutes 44.86 seconds (24044.86 seconds total)