Starting phenix.real_space_refine (version: dev) on Thu Feb 23 09:11:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr6_30824/02_2023/7dr6_30824.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr6_30824/02_2023/7dr6_30824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr6_30824/02_2023/7dr6_30824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr6_30824/02_2023/7dr6_30824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr6_30824/02_2023/7dr6_30824.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr6_30824/02_2023/7dr6_30824.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.108 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 Process input model Symmetric amino acids flipped Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 185": "NH1" <-> "NH2" Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 126": "NH1" <-> "NH2" Residue "1 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 242": "NH1" <-> "NH2" Residue "2 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 59957 Number of models: 1 Model: "" Number of chains: 35 Chain: "L" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1850 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain: "M" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1763 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain: "N" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1936 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain: "O" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1824 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain: "P" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1790 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Chain: "Q" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1846 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain: "R" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1879 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "A" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1684 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1720 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Chain breaks: 1 Chain: "C" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1663 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain breaks: 1 Chain: "D" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1678 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 8, 'TRANS': 198} Chain breaks: 1 Chain: "E" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Chain: "F" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1695 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 9, 'TRANS': 200} Chain breaks: 1 Chain: "G" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1654 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Chain: "a" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1824 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain: "b" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1790 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Chain: "c" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1846 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain: "d" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1879 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "e" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1856 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "f" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1793 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "g" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1936 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain: "H" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1594 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "I" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1593 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "J" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1645 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "K" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1685 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "S" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1594 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "T" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1584 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "U" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1645 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "V" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1682 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "W" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1500 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "X" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1611 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "Y" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1561 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "Z" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1500 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "1" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1611 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "2" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1561 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Time building chain proxies: 24.42, per 1000 atoms: 0.41 Number of scatterers: 59957 At special positions: 0 Unit cell: (239.876, 137.072, 216.152, 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 346 16.00 O 11349 8.00 N 10246 7.00 C 38016 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: 19.06 Conformation dependent library (CDL) restraints added in 6.7 seconds 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14226 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 72 sheets defined 46.1% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 83 through 105 removed outlier: 3.625A pdb=" N SER L 87 " --> pdb=" O MET L 83 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER L 89 " --> pdb=" O ALA L 85 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN L 90 " --> pdb=" O ASP L 86 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL L 91 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN L 100 " --> pdb=" O TYR L 96 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS L 102 " --> pdb=" O ALA L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 128 removed outlier: 3.765A pdb=" N TYR L 125 " --> pdb=" O ILE L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 185 removed outlier: 3.707A pdb=" N LYS L 185 " --> pdb=" O LYS L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 207 removed outlier: 3.686A pdb=" N LEU L 202 " --> pdb=" O ALA L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 213 No H-bonds generated for 'chain 'L' and resid 211 through 213' Processing helix chain 'L' and resid 231 through 240 Processing helix chain 'M' and resid 19 through 31 Processing helix chain 'M' and resid 79 through 102 removed outlier: 3.707A pdb=" N TYR M 83 " --> pdb=" O MET M 79 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG M 84 " --> pdb=" O GLY M 80 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL M 85 " --> pdb=" O PRO M 81 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU M 86 " --> pdb=" O ASP M 82 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS M 88 " --> pdb=" O ARG M 84 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 122 removed outlier: 3.524A pdb=" N ARG M 113 " --> pdb=" O GLN M 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET M 118 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 175 Processing helix chain 'M' and resid 183 through 199 removed outlier: 4.388A pdb=" N GLU M 197 " --> pdb=" O LEU M 193 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER M 198 " --> pdb=" O THR M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 230 removed outlier: 3.556A pdb=" N ASP M 228 " --> pdb=" O THR M 224 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 30 removed outlier: 3.764A pdb=" N GLU N 26 " --> pdb=" O GLU N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 102 removed outlier: 3.571A pdb=" N ALA N 83 " --> pdb=" O ILE N 79 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN N 84 " --> pdb=" O THR N 80 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL N 85 " --> pdb=" O SER N 81 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN N 100 " --> pdb=" O ARG N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 124 removed outlier: 3.563A pdb=" N LEU N 114 " --> pdb=" O LEU N 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP N 116 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE N 117 " --> pdb=" O ALA N 113 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR N 121 " --> pdb=" O ILE N 117 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR N 122 " --> pdb=" O LYS N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 179 removed outlier: 3.530A pdb=" N GLN N 177 " --> pdb=" O SER N 173 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP N 178 " --> pdb=" O MET N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 201 removed outlier: 4.098A pdb=" N ALA N 191 " --> pdb=" O LYS N 187 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU N 192 " --> pdb=" O SER N 188 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA N 193 " --> pdb=" O ALA N 189 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE N 194 " --> pdb=" O LEU N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 244 removed outlier: 3.677A pdb=" N HIS N 240 " --> pdb=" O LEU N 236 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU N 244 " --> pdb=" O HIS N 240 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 29 Processing helix chain 'O' and resid 56 through 60 Processing helix chain 'O' and resid 76 through 98 removed outlier: 3.837A pdb=" N ALA O 80 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG O 81 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE O 82 " --> pdb=" O ALA O 78 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL O 83 " --> pdb=" O ASP O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 121 removed outlier: 3.574A pdb=" N TYR O 110 " --> pdb=" O TYR O 106 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS O 115 " --> pdb=" O ILE O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 138 through 140 No H-bonds generated for 'chain 'O' and resid 138 through 140' Processing helix chain 'O' and resid 164 through 176 Processing helix chain 'O' and resid 183 through 195 Processing helix chain 'O' and resid 202 through 206 removed outlier: 3.638A pdb=" N ASN O 205 " --> pdb=" O GLY O 202 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE O 206 " --> pdb=" O GLY O 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 202 through 206' Processing helix chain 'O' and resid 221 through 230 removed outlier: 3.673A pdb=" N TYR O 228 " --> pdb=" O GLU O 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 31 Processing helix chain 'P' and resid 32 through 34 No H-bonds generated for 'chain 'P' and resid 32 through 34' Processing helix chain 'P' and resid 81 through 104 removed outlier: 3.886A pdb=" N ALA P 85 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS P 91 " --> pdb=" O THR P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 122 Processing helix chain 'P' and resid 173 through 185 removed outlier: 3.939A pdb=" N SER P 179 " --> pdb=" O GLU P 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU P 183 " --> pdb=" O SER P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 190 through 206 removed outlier: 3.656A pdb=" N SER P 197 " --> pdb=" O GLU P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 230 through 240 removed outlier: 3.706A pdb=" N LYS P 239 " --> pdb=" O GLU P 235 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 30 removed outlier: 3.699A pdb=" N VAL Q 29 " --> pdb=" O ALA Q 25 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS Q 30 " --> pdb=" O MET Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 99 removed outlier: 4.128A pdb=" N LEU Q 83 " --> pdb=" O ALA Q 79 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU Q 84 " --> pdb=" O ASP Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 122 Proline residue: Q 119 - end of helix removed outlier: 3.950A pdb=" N ARG Q 122 " --> pdb=" O ILE Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 175 Processing helix chain 'Q' and resid 175 through 182 removed outlier: 3.896A pdb=" N MET Q 180 " --> pdb=" O MET Q 176 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU Q 181 " --> pdb=" O SER Q 177 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 196 removed outlier: 3.563A pdb=" N LEU Q 195 " --> pdb=" O GLY Q 191 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG Q 196 " --> pdb=" O LEU Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 197 through 199 No H-bonds generated for 'chain 'Q' and resid 197 through 199' Processing helix chain 'Q' and resid 228 through 234 removed outlier: 3.780A pdb=" N PHE Q 232 " --> pdb=" O ASP Q 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 32 Processing helix chain 'R' and resid 81 through 104 Processing helix chain 'R' and resid 108 through 126 removed outlier: 3.629A pdb=" N TYR R 123 " --> pdb=" O TYR R 119 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR R 124 " --> pdb=" O VAL R 120 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR R 126 " --> pdb=" O ALA R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 179 Processing helix chain 'R' and resid 186 through 202 removed outlier: 4.403A pdb=" N LYS R 192 " --> pdb=" O ARG R 188 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU R 193 " --> pdb=" O ASP R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 245 removed outlier: 3.558A pdb=" N GLU R 242 " --> pdb=" O LYS R 238 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER R 243 " --> pdb=" O TYR R 239 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU R 244 " --> pdb=" O ALA R 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 34 removed outlier: 3.699A pdb=" N ARG A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.850A pdb=" N ILE A 41 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 128 removed outlier: 3.707A pdb=" N ALA A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Proline residue: A 109 - end of helix removed outlier: 3.509A pdb=" N LEU A 128 " --> pdb=" O TRP A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 181 removed outlier: 3.800A pdb=" N GLN A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 229 removed outlier: 3.821A pdb=" N ALA A 189 " --> pdb=" O MET A 185 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLU A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LYS A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 removed outlier: 3.769A pdb=" N VAL B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 45 removed outlier: 3.563A pdb=" N SER B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 removed outlier: 3.683A pdb=" N LEU B 57 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 138 Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 147 through 191 removed outlier: 3.544A pdb=" N SER B 175 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 239 removed outlier: 4.376A pdb=" N ARG B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN B 233 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 31 Processing helix chain 'C' and resid 31 through 45 Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 107 through 137 removed outlier: 3.684A pdb=" N ARG C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Proline residue: C 119 - end of helix Processing helix chain 'C' and resid 150 through 191 removed outlier: 3.761A pdb=" N GLU C 154 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 159 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 239 removed outlier: 3.900A pdb=" N GLN C 199 " --> pdb=" O GLY C 195 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS C 236 " --> pdb=" O LYS C 232 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 16 Processing helix chain 'D' and resid 17 through 22 Processing helix chain 'D' and resid 22 through 34 removed outlier: 3.675A pdb=" N PHE D 31 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 48 removed outlier: 3.511A pdb=" N ILE D 41 " --> pdb=" O PRO D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 53 Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 98 through 127 removed outlier: 3.553A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Proline residue: D 109 - end of helix removed outlier: 3.651A pdb=" N LYS D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 180 removed outlier: 4.409A pdb=" N PHE D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER D 169 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 190 removed outlier: 4.088A pdb=" N ARG D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 229 removed outlier: 4.167A pdb=" N ARG D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR D 199 " --> pdb=" O ASP D 195 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LYS D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 31 removed outlier: 3.808A pdb=" N VAL E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 45 removed outlier: 3.514A pdb=" N SER E 38 " --> pdb=" O PRO E 34 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 40 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP E 41 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 138 Proline residue: E 119 - end of helix Processing helix chain 'E' and resid 147 through 191 removed outlier: 3.724A pdb=" N MET E 160 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR E 161 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER E 162 " --> pdb=" O GLU E 158 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU E 168 " --> pdb=" O HIS E 164 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS E 171 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE E 178 " --> pdb=" O ILE E 174 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 233 removed outlier: 3.527A pdb=" N TYR E 209 " --> pdb=" O ASP E 205 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 34 removed outlier: 3.569A pdb=" N LYS F 15 " --> pdb=" O GLY F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 48 removed outlier: 3.671A pdb=" N GLN F 38 " --> pdb=" O ARG F 34 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 41 " --> pdb=" O PRO F 37 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 128 removed outlier: 3.624A pdb=" N LEU F 106 " --> pdb=" O SER F 102 " (cutoff:3.500A) Proline residue: F 109 - end of helix removed outlier: 3.561A pdb=" N LEU F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 181 removed outlier: 3.569A pdb=" N GLN F 143 " --> pdb=" O GLY F 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE F 168 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 191 Processing helix chain 'F' and resid 192 through 223 removed outlier: 4.105A pdb=" N TYR F 213 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA F 214 " --> pdb=" O ARG F 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 228 removed outlier: 3.877A pdb=" N VAL F 228 " --> pdb=" O LEU F 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 31 Processing helix chain 'G' and resid 31 through 46 Processing helix chain 'G' and resid 107 through 139 Proline residue: G 119 - end of helix Processing helix chain 'G' and resid 147 through 191 removed outlier: 3.745A pdb=" N ALA G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL G 152 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE G 178 " --> pdb=" O ILE G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 233 removed outlier: 3.607A pdb=" N LEU G 226 " --> pdb=" O ALA G 222 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 28 removed outlier: 3.804A pdb=" N VAL a 26 " --> pdb=" O ALA a 22 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS a 27 " --> pdb=" O GLN a 23 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 98 removed outlier: 4.194A pdb=" N ALA a 80 " --> pdb=" O LEU a 76 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG a 81 " --> pdb=" O THR a 77 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE a 82 " --> pdb=" O ALA a 78 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL a 83 " --> pdb=" O ASP a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 121 removed outlier: 3.729A pdb=" N THR a 108 " --> pdb=" O VAL a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 176 removed outlier: 3.793A pdb=" N LYS a 174 " --> pdb=" O GLU a 170 " (cutoff:3.500A) Processing helix chain 'a' and resid 183 through 196 Processing helix chain 'a' and resid 221 through 230 removed outlier: 3.674A pdb=" N TYR a 228 " --> pdb=" O GLU a 224 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 32 removed outlier: 3.749A pdb=" N ILE b 28 " --> pdb=" O VAL b 24 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU b 29 " --> pdb=" O GLU b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 104 removed outlier: 4.149A pdb=" N LYS b 86 " --> pdb=" O ILE b 82 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU b 88 " --> pdb=" O ASP b 84 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP b 90 " --> pdb=" O LYS b 86 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS b 91 " --> pdb=" O THR b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 108 through 121 removed outlier: 3.783A pdb=" N THR b 113 " --> pdb=" O VAL b 109 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN b 114 " --> pdb=" O GLU b 110 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL b 116 " --> pdb=" O VAL b 112 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN b 118 " --> pdb=" O GLN b 114 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU b 119 " --> pdb=" O ALA b 115 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU b 121 " --> pdb=" O SER b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 173 through 185 removed outlier: 3.540A pdb=" N SER b 180 " --> pdb=" O GLY b 176 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU b 183 " --> pdb=" O SER b 179 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 206 removed outlier: 3.508A pdb=" N LYS b 196 " --> pdb=" O LYS b 192 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE b 201 " --> pdb=" O SER b 197 " (cutoff:3.500A) Processing helix chain 'b' and resid 230 through 240 removed outlier: 4.025A pdb=" N GLU b 236 " --> pdb=" O GLU b 232 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP b 240 " --> pdb=" O GLU b 236 " (cutoff:3.500A) Processing helix chain 'c' and resid 19 through 31 removed outlier: 4.274A pdb=" N VAL c 29 " --> pdb=" O ALA c 25 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS c 30 " --> pdb=" O MET c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 99 removed outlier: 3.928A pdb=" N LEU c 83 " --> pdb=" O ALA c 79 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE c 87 " --> pdb=" O LEU c 83 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG c 96 " --> pdb=" O CYS c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 104 through 118 removed outlier: 3.517A pdb=" N LEU c 111 " --> pdb=" O ARG c 107 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS c 115 " --> pdb=" O LEU c 111 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR c 116 " --> pdb=" O ILE c 112 " (cutoff:3.500A) Processing helix chain 'c' and resid 164 through 175 removed outlier: 3.860A pdb=" N ALA c 168 " --> pdb=" O ARG c 164 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG c 169 " --> pdb=" O SER c 165 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR c 170 " --> pdb=" O GLN c 166 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TYR c 171 " --> pdb=" O SER c 167 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU c 172 " --> pdb=" O ALA c 168 " (cutoff:3.500A) Processing helix chain 'c' and resid 175 through 182 removed outlier: 4.080A pdb=" N MET c 180 " --> pdb=" O MET c 176 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU c 181 " --> pdb=" O SER c 177 " (cutoff:3.500A) Processing helix chain 'c' and resid 183 through 197 removed outlier: 3.506A pdb=" N ARG c 193 " --> pdb=" O LYS c 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU c 195 " --> pdb=" O GLY c 191 " (cutoff:3.500A) Processing helix chain 'c' and resid 229 through 234 Processing helix chain 'd' and resid 21 through 33 removed outlier: 3.530A pdb=" N VAL d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 103 removed outlier: 3.532A pdb=" N LEU d 88 " --> pdb=" O ASP d 84 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP d 90 " --> pdb=" O ARG d 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG d 100 " --> pdb=" O ALA d 96 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 123 removed outlier: 3.640A pdb=" N ARG d 115 " --> pdb=" O HIS d 111 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR d 123 " --> pdb=" O TYR d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 180 removed outlier: 3.975A pdb=" N GLU d 176 " --> pdb=" O ALA d 172 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 202 removed outlier: 4.739A pdb=" N LYS d 192 " --> pdb=" O ARG d 188 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU d 193 " --> pdb=" O ASP d 189 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA d 195 " --> pdb=" O VAL d 191 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS d 196 " --> pdb=" O LYS d 192 " (cutoff:3.500A) Processing helix chain 'd' and resid 229 through 243 removed outlier: 3.501A pdb=" N ALA d 236 " --> pdb=" O VAL d 232 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 12 removed outlier: 3.643A pdb=" N ASP e 10 " --> pdb=" O ALA e 7 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG e 11 " --> pdb=" O GLY e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 22 through 31 Processing helix chain 'e' and resid 32 through 36 removed outlier: 3.708A pdb=" N GLY e 36 " --> pdb=" O ASN e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 83 through 105 removed outlier: 3.763A pdb=" N GLN e 92 " --> pdb=" O ARG e 88 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG e 93 " --> pdb=" O SER e 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 127 removed outlier: 3.575A pdb=" N LYS e 116 " --> pdb=" O ASP e 112 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE e 121 " --> pdb=" O ARG e 117 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL e 124 " --> pdb=" O ASP e 120 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR e 125 " --> pdb=" O ILE e 121 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR e 126 " --> pdb=" O SER e 122 " (cutoff:3.500A) Processing helix chain 'e' and resid 172 through 185 removed outlier: 4.569A pdb=" N LYS e 181 " --> pdb=" O SER e 177 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS e 182 " --> pdb=" O PHE e 178 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS e 185 " --> pdb=" O LYS e 181 " (cutoff:3.500A) Processing helix chain 'e' and resid 190 through 207 removed outlier: 3.572A pdb=" N CYS e 201 " --> pdb=" O THR e 197 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU e 202 " --> pdb=" O ALA e 198 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL e 205 " --> pdb=" O CYS e 201 " (cutoff:3.500A) Processing helix chain 'e' and resid 231 through 240 removed outlier: 3.645A pdb=" N ASP e 236 " --> pdb=" O GLU e 232 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA e 237 " --> pdb=" O ALA e 233 " (cutoff:3.500A) Processing helix chain 'f' and resid 19 through 31 removed outlier: 3.819A pdb=" N ALA f 27 " --> pdb=" O GLU f 23 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY f 31 " --> pdb=" O ALA f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 102 removed outlier: 4.385A pdb=" N LEU f 86 " --> pdb=" O ASP f 82 " (cutoff:3.500A) Processing helix chain 'f' and resid 106 through 121 removed outlier: 3.511A pdb=" N VAL f 111 " --> pdb=" O THR f 107 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN f 112 " --> pdb=" O ALA f 108 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL f 117 " --> pdb=" O ARG f 113 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR f 121 " --> pdb=" O VAL f 117 " (cutoff:3.500A) Processing helix chain 'f' and resid 166 through 178 Processing helix chain 'f' and resid 183 through 199 removed outlier: 3.557A pdb=" N HIS f 189 " --> pdb=" O GLU f 185 " (cutoff:3.500A) Processing helix chain 'f' and resid 222 through 228 removed outlier: 3.552A pdb=" N VAL f 226 " --> pdb=" O THR f 222 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS f 227 " --> pdb=" O PRO f 223 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP f 228 " --> pdb=" O THR f 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 222 through 228' Processing helix chain 'g' and resid 18 through 28 Processing helix chain 'g' and resid 29 through 31 No H-bonds generated for 'chain 'g' and resid 29 through 31' Processing helix chain 'g' and resid 79 through 102 removed outlier: 4.014A pdb=" N ALA g 83 " --> pdb=" O ILE g 79 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN g 84 " --> pdb=" O THR g 80 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL g 85 " --> pdb=" O SER g 81 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN g 88 " --> pdb=" O ASN g 84 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU g 98 " --> pdb=" O ALA g 94 " (cutoff:3.500A) Processing helix chain 'g' and resid 106 through 123 removed outlier: 3.838A pdb=" N ASP g 116 " --> pdb=" O THR g 112 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE g 117 " --> pdb=" O ALA g 113 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR g 121 " --> pdb=" O ILE g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 167 through 178 removed outlier: 3.565A pdb=" N SER g 173 " --> pdb=" O ALA g 169 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET g 174 " --> pdb=" O ALA g 170 " (cutoff:3.500A) Processing helix chain 'g' and resid 185 through 201 removed outlier: 4.016A pdb=" N ALA g 191 " --> pdb=" O LYS g 187 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS g 199 " --> pdb=" O LYS g 195 " (cutoff:3.500A) Processing helix chain 'g' and resid 229 through 244 Processing helix chain 'H' and resid 56 through 78 removed outlier: 3.701A pdb=" N VAL H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR H 62 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU H 73 " --> pdb=" O PHE H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 97 removed outlier: 4.077A pdb=" N SER H 89 " --> pdb=" O TYR H 85 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET H 90 " --> pdb=" O THR H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 154 removed outlier: 4.146A pdb=" N GLY H 148 " --> pdb=" O GLU H 144 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET H 149 " --> pdb=" O GLN H 145 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS H 150 " --> pdb=" O MET H 146 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER H 152 " --> pdb=" O GLY H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 178 removed outlier: 3.908A pdb=" N ASP H 176 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG H 177 " --> pdb=" O ASN H 173 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 72 removed outlier: 3.613A pdb=" N GLU I 58 " --> pdb=" O VAL I 54 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR I 59 " --> pdb=" O GLN I 55 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE I 60 " --> pdb=" O PHE I 56 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL I 64 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN I 65 " --> pdb=" O GLN I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 91 removed outlier: 3.553A pdb=" N ASN I 82 " --> pdb=" O THR I 78 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN I 87 " --> pdb=" O PHE I 83 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 139 removed outlier: 4.032A pdb=" N LEU I 138 " --> pdb=" O TYR I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 147 removed outlier: 3.794A pdb=" N LEU I 143 " --> pdb=" O THR I 139 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP I 144 " --> pdb=" O LEU I 140 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG I 145 " --> pdb=" O SER I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 165 Processing helix chain 'I' and resid 165 through 170 Processing helix chain 'J' and resid 85 through 107 removed outlier: 3.518A pdb=" N CYS J 89 " --> pdb=" O PHE J 85 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU J 90 " --> pdb=" O HIS J 86 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR J 91 " --> pdb=" O GLY J 87 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG J 99 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS J 101 " --> pdb=" O GLU J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 126 removed outlier: 4.193A pdb=" N ALA J 117 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA J 118 " --> pdb=" O GLY J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 181 Proline residue: J 175 - end of helix removed outlier: 3.526A pdb=" N ASP J 178 " --> pdb=" O GLN J 174 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN J 179 " --> pdb=" O PRO J 175 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN J 180 " --> pdb=" O LEU J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 214 removed outlier: 3.830A pdb=" N MET J 200 " --> pdb=" O LEU J 196 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG J 201 " --> pdb=" O ASP J 197 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU J 212 " --> pdb=" O ILE J 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 123 removed outlier: 3.709A pdb=" N PHE K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU K 119 " --> pdb=" O MET K 115 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU K 120 " --> pdb=" O VAL K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 146 removed outlier: 3.836A pdb=" N ARG K 144 " --> pdb=" O ALA K 140 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG K 145 " --> pdb=" O MET K 141 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER K 146 " --> pdb=" O TYR K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 188 removed outlier: 3.828A pdb=" N ALA K 188 " --> pdb=" O GLY K 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 185 through 188' Processing helix chain 'K' and resid 191 through 202 removed outlier: 3.996A pdb=" N GLU K 200 " --> pdb=" O ARG K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 225 Processing helix chain 'K' and resid 254 through 259 removed outlier: 3.940A pdb=" N HIS K 258 " --> pdb=" O TRP K 254 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 6 Processing helix chain 'S' and resid 56 through 78 removed outlier: 3.648A pdb=" N ALA S 64 " --> pdb=" O VAL S 60 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN S 65 " --> pdb=" O GLN S 61 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS S 68 " --> pdb=" O ALA S 64 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE S 69 " --> pdb=" O GLN S 65 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU S 73 " --> pdb=" O PHE S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 98 removed outlier: 3.914A pdb=" N SER S 89 " --> pdb=" O TYR S 85 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS S 98 " --> pdb=" O LEU S 94 " (cutoff:3.500A) Processing helix chain 'S' and resid 142 through 154 removed outlier: 4.564A pdb=" N GLY S 148 " --> pdb=" O GLU S 144 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET S 149 " --> pdb=" O GLN S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 177 removed outlier: 3.746A pdb=" N GLU S 165 " --> pdb=" O GLU S 161 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN S 173 " --> pdb=" O GLN S 169 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG S 177 " --> pdb=" O ASN S 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.789A pdb=" N VAL T 54 " --> pdb=" O ALA T 50 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU T 58 " --> pdb=" O VAL T 54 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR T 59 " --> pdb=" O GLN T 55 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE T 60 " --> pdb=" O PHE T 56 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET T 69 " --> pdb=" O GLN T 65 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG T 70 " --> pdb=" O LEU T 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 91 removed outlier: 3.616A pdb=" N ASN T 87 " --> pdb=" O PHE T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 147 removed outlier: 4.442A pdb=" N SER T 141 " --> pdb=" O PHE T 137 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE T 142 " --> pdb=" O LEU T 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG T 145 " --> pdb=" O SER T 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 170 removed outlier: 3.730A pdb=" N VAL T 157 " --> pdb=" O ARG T 153 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS T 162 " --> pdb=" O GLU T 158 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS T 163 " --> pdb=" O LEU T 159 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU T 166 " --> pdb=" O LYS T 162 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU T 167 " --> pdb=" O CYS T 163 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN T 168 " --> pdb=" O LEU T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 108 removed outlier: 3.586A pdb=" N CYS U 89 " --> pdb=" O PHE U 85 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU U 90 " --> pdb=" O HIS U 86 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR U 91 " --> pdb=" O GLY U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 127 removed outlier: 3.804A pdb=" N ALA U 117 " --> pdb=" O THR U 113 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA U 118 " --> pdb=" O GLY U 114 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG U 127 " --> pdb=" O ILE U 123 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 181 removed outlier: 3.882A pdb=" N GLN U 174 " --> pdb=" O SER U 170 " (cutoff:3.500A) Proline residue: U 175 - end of helix Processing helix chain 'U' and resid 195 through 214 removed outlier: 3.576A pdb=" N LYS U 204 " --> pdb=" O MET U 200 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU U 212 " --> pdb=" O ILE U 208 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG U 213 " --> pdb=" O SER U 209 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 123 removed outlier: 3.509A pdb=" N PHE V 105 " --> pdb=" O ASP V 101 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR V 107 " --> pdb=" O ALA V 103 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY V 113 " --> pdb=" O LYS V 109 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP V 118 " --> pdb=" O GLN V 114 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU V 119 " --> pdb=" O MET V 115 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU V 122 " --> pdb=" O ASP V 118 " (cutoff:3.500A) Processing helix chain 'V' and resid 129 through 147 removed outlier: 3.930A pdb=" N ARG V 144 " --> pdb=" O ALA V 140 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG V 145 " --> pdb=" O MET V 141 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER V 146 " --> pdb=" O TYR V 142 " (cutoff:3.500A) Processing helix chain 'V' and resid 184 through 189 Processing helix chain 'V' and resid 190 through 202 removed outlier: 3.795A pdb=" N LEU V 194 " --> pdb=" O LEU V 190 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS V 201 " --> pdb=" O GLU V 197 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 224 removed outlier: 3.660A pdb=" N VAL V 220 " --> pdb=" O ARG V 216 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU V 221 " --> pdb=" O CYS V 217 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR V 223 " --> pdb=" O ARG V 219 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 91 removed outlier: 3.702A pdb=" N LEU W 90 " --> pdb=" O HIS W 86 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU W 91 " --> pdb=" O GLY W 87 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 111 removed outlier: 3.501A pdb=" N LYS W 109 " --> pdb=" O ASN W 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 135 through 138 removed outlier: 3.501A pdb=" N MET W 138 " --> pdb=" O MET W 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 135 through 138' Processing helix chain 'W' and resid 154 through 162 removed outlier: 3.593A pdb=" N ALA W 161 " --> pdb=" O TYR W 157 " (cutoff:3.500A) Processing helix chain 'W' and resid 167 through 186 removed outlier: 3.526A pdb=" N LYS W 184 " --> pdb=" O ALA W 180 " (cutoff:3.500A) Processing helix chain 'W' and resid 209 through 213 removed outlier: 3.557A pdb=" N LEU W 213 " --> pdb=" O GLY W 210 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 110 removed outlier: 3.624A pdb=" N ALA X 91 " --> pdb=" O VAL X 87 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR X 94 " --> pdb=" O ASP X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 128 removed outlier: 3.608A pdb=" N VAL X 118 " --> pdb=" O ARG X 114 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG X 128 " --> pdb=" O GLN X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 169 through 180 removed outlier: 3.927A pdb=" N VAL X 176 " --> pdb=" O ALA X 172 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU X 177 " --> pdb=" O ALA X 173 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP X 179 " --> pdb=" O ALA X 175 " (cutoff:3.500A) Processing helix chain 'X' and resid 186 through 205 removed outlier: 3.730A pdb=" N ALA X 200 " --> pdb=" O GLU X 196 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY X 201 " --> pdb=" O ALA X 197 " (cutoff:3.500A) Processing helix chain 'Y' and resid 120 through 140 removed outlier: 3.665A pdb=" N CYS Y 124 " --> pdb=" O CYS Y 120 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU Y 134 " --> pdb=" O LEU Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 162 removed outlier: 3.525A pdb=" N MET Y 158 " --> pdb=" O LEU Y 154 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN Y 161 " --> pdb=" O ASN Y 157 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR Y 162 " --> pdb=" O MET Y 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 203 through 213 removed outlier: 4.468A pdb=" N GLY Y 209 " --> pdb=" O SER Y 205 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL Y 210 " --> pdb=" O HIS Y 206 " (cutoff:3.500A) Processing helix chain 'Y' and resid 220 through 238 removed outlier: 3.552A pdb=" N ILE Y 232 " --> pdb=" O GLY Y 228 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL Y 233 " --> pdb=" O ARG Y 229 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS Y 234 " --> pdb=" O ARG Y 230 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG Y 238 " --> pdb=" O HIS Y 234 " (cutoff:3.500A) Processing helix chain 'Y' and resid 264 through 273 removed outlier: 3.660A pdb=" N HIS Y 269 " --> pdb=" O SER Y 265 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU Y 273 " --> pdb=" O HIS Y 269 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 91 removed outlier: 3.569A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE Z 75 " --> pdb=" O ASP Z 71 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU Z 90 " --> pdb=" O HIS Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 111 Processing helix chain 'Z' and resid 135 through 138 Processing helix chain 'Z' and resid 150 through 153 removed outlier: 3.683A pdb=" N TYR Z 153 " --> pdb=" O GLY Z 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 150 through 153' Processing helix chain 'Z' and resid 154 through 162 removed outlier: 3.837A pdb=" N ASP Z 159 " --> pdb=" O TYR Z 155 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA Z 160 " --> pdb=" O GLY Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 167 through 186 removed outlier: 4.114A pdb=" N LYS Z 184 " --> pdb=" O ALA Z 180 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG Z 185 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) Processing helix chain '1' and resid 87 through 110 removed outlier: 3.556A pdb=" N THR 1 94 " --> pdb=" O ASP 1 90 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN 1 101 " --> pdb=" O MET 1 97 " (cutoff:3.500A) Processing helix chain '1' and resid 114 through 129 removed outlier: 3.908A pdb=" N VAL 1 118 " --> pdb=" O ARG 1 114 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR 1 119 " --> pdb=" O VAL 1 115 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG 1 120 " --> pdb=" O ALA 1 116 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET 1 121 " --> pdb=" O THR 1 117 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN 1 124 " --> pdb=" O ARG 1 120 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR 1 129 " --> pdb=" O THR 1 125 " (cutoff:3.500A) Processing helix chain '1' and resid 169 through 181 removed outlier: 4.128A pdb=" N VAL 1 176 " --> pdb=" O ALA 1 172 " (cutoff:3.500A) Processing helix chain '1' and resid 186 through 205 removed outlier: 3.769A pdb=" N LEU 1 203 " --> pdb=" O THR 1 199 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY 1 204 " --> pdb=" O ALA 1 200 " (cutoff:3.500A) Processing helix chain '2' and resid 120 through 142 removed outlier: 3.630A pdb=" N CYS 2 124 " --> pdb=" O CYS 2 120 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 162 removed outlier: 4.200A pdb=" N TYR 2 162 " --> pdb=" O MET 2 158 " (cutoff:3.500A) Processing helix chain '2' and resid 204 through 212 removed outlier: 4.083A pdb=" N GLY 2 209 " --> pdb=" O SER 2 205 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL 2 210 " --> pdb=" O HIS 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 220 through 239 Processing helix chain '2' and resid 267 through 273 removed outlier: 3.672A pdb=" N TYR 2 271 " --> pdb=" O LEU 2 267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 165 through 168 Processing sheet with id=AA2, first strand: chain 'L' and resid 69 through 71 removed outlier: 3.895A pdb=" N GLY L 77 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS L 153 " --> pdb=" O CYS L 161 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS L 161 " --> pdb=" O LYS L 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 160 through 163 Processing sheet with id=AA4, first strand: chain 'M' and resid 66 through 69 removed outlier: 6.646A pdb=" N ILE M 72 " --> pdb=" O ILE M 68 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL M 75 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER M 133 " --> pdb=" O SER M 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 161 through 164 removed outlier: 3.696A pdb=" N LEU N 216 " --> pdb=" O VAL N 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 65 through 66 removed outlier: 4.052A pdb=" N LEU N 134 " --> pdb=" O SER N 150 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY N 138 " --> pdb=" O GLN N 146 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU N 147 " --> pdb=" O TRP N 159 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY N 158 " --> pdb=" O ASP O 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 158 through 161 removed outlier: 3.668A pdb=" N VAL O 42 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL O 45 " --> pdb=" O GLU O 207 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU O 207 " --> pdb=" O VAL O 45 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 62 through 64 Processing sheet with id=AA9, first strand: chain 'P' and resid 169 through 170 removed outlier: 3.838A pdb=" N THR P 219 " --> pdb=" O HIS P 227 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 141 through 147 removed outlier: 3.556A pdb=" N VAL P 163 " --> pdb=" O HIS P 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 158 through 161 Processing sheet with id=AB3, first strand: chain 'Q' and resid 63 through 65 removed outlier: 3.587A pdb=" N ILE Q 72 " --> pdb=" O LEU Q 64 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 163 through 166 removed outlier: 4.792A pdb=" N ALA R 209 " --> pdb=" O VAL R 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 67 through 69 Processing sheet with id=AB6, first strand: chain 'a' and resid 158 through 161 removed outlier: 3.953A pdb=" N THR a 31 " --> pdb=" O GLU a 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL a 42 " --> pdb=" O VAL a 35 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET a 211 " --> pdb=" O VAL a 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'a' and resid 54 through 55 removed outlier: 4.244A pdb=" N GLY g 158 " --> pdb=" O ASP a 55 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LEU g 147 " --> pdb=" O TRP g 159 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU g 135 " --> pdb=" O SER g 75 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE g 137 " --> pdb=" O ALA g 73 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS g 74 " --> pdb=" O TYR g 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'a' and resid 63 through 64 removed outlier: 3.837A pdb=" N THR a 141 " --> pdb=" O ASP a 137 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 167 through 170 removed outlier: 3.667A pdb=" N ALA b 49 " --> pdb=" O ILE b 38 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL b 46 " --> pdb=" O VAL b 220 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL b 220 " --> pdb=" O VAL b 46 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA b 218 " --> pdb=" O LEU b 48 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL b 50 " --> pdb=" O GLU b 216 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU b 217 " --> pdb=" O PHE b 229 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR b 219 " --> pdb=" O HIS b 227 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN b 221 " --> pdb=" O ASN b 225 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASN b 225 " --> pdb=" O GLN b 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 67 through 69 Processing sheet with id=AC2, first strand: chain 'b' and resid 79 through 80 removed outlier: 4.104A pdb=" N LEU b 141 " --> pdb=" O MET b 156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'c' and resid 158 through 161 removed outlier: 3.783A pdb=" N SER c 211 " --> pdb=" O ALA c 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 63 through 65 Processing sheet with id=AC5, first strand: chain 'd' and resid 163 through 166 removed outlier: 4.005A pdb=" N CYS d 164 " --> pdb=" O GLY d 39 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY d 39 " --> pdb=" O CYS d 164 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE d 38 " --> pdb=" O GLY d 49 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE d 48 " --> pdb=" O SER d 215 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'd' and resid 68 through 69 removed outlier: 4.313A pdb=" N GLY d 75 " --> pdb=" O GLY d 139 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY d 139 " --> pdb=" O GLY d 75 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA d 77 " --> pdb=" O MET d 137 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER d 140 " --> pdb=" O GLN d 148 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN d 148 " --> pdb=" O SER d 140 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET d 151 " --> pdb=" O TYR d 159 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR d 159 " --> pdb=" O MET d 151 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'e' and resid 168 through 169 removed outlier: 3.539A pdb=" N SER e 39 " --> pdb=" O ALA e 168 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR e 38 " --> pdb=" O GLN e 53 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL e 220 " --> pdb=" O ALA e 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 70 through 71 removed outlier: 4.150A pdb=" N GLY e 77 " --> pdb=" O ILE e 141 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE e 141 " --> pdb=" O GLY e 77 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY e 142 " --> pdb=" O GLN e 150 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN e 150 " --> pdb=" O GLY e 142 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'f' and resid 160 through 163 removed outlier: 3.669A pdb=" N GLY f 37 " --> pdb=" O THR f 161 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL f 44 " --> pdb=" O CYS f 213 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'f' and resid 66 through 67 removed outlier: 3.550A pdb=" N VAL f 75 " --> pdb=" O LEU f 135 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER f 77 " --> pdb=" O SER f 133 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN f 140 " --> pdb=" O ARG f 143 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'g' and resid 161 through 164 removed outlier: 3.501A pdb=" N ILE g 37 " --> pdb=" O LEU g 44 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU g 44 " --> pdb=" O ILE g 37 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL g 43 " --> pdb=" O LEU g 216 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA g 47 " --> pdb=" O GLU g 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 136 through 140 removed outlier: 5.549A pdb=" N ALA H 10 " --> pdb=" O ASP H 25 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL H 20 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL H 185 " --> pdb=" O LEU H 200 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 28 through 30 removed outlier: 6.751A pdb=" N PHE H 28 " --> pdb=" O VAL H 35 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 42 through 44 removed outlier: 3.620A pdb=" N ILE H 51 " --> pdb=" O PHE H 43 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 129 through 131 Processing sheet with id=AD7, first strand: chain 'I' and resid 21 through 23 removed outlier: 6.613A pdb=" N SER I 23 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLN I 27 " --> pdb=" O SER I 23 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 36 through 37 removed outlier: 3.516A pdb=" N LEU I 102 " --> pdb=" O MET I 118 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET I 118 " --> pdb=" O LEU I 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 163 through 167 removed outlier: 6.018A pdb=" N THR J 39 " --> pdb=" O ASP J 54 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP J 54 " --> pdb=" O THR J 39 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.681A pdb=" N LEU J 57 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR J 65 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLU J 59 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE J 63 " --> pdb=" O GLU J 59 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 72 through 75 removed outlier: 6.597A pdb=" N THR J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY J 139 " --> pdb=" O VAL J 79 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE J 137 " --> pdb=" O GLY J 81 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL J 149 " --> pdb=" O ASP J 161 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER J 151 " --> pdb=" O GLN J 159 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN J 159 " --> pdb=" O SER J 151 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 181 through 183 removed outlier: 6.394A pdb=" N PHE K 232 " --> pdb=" O PRO K 247 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE K 234 " --> pdb=" O GLU K 245 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR K 238 " --> pdb=" O GLY K 241 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 73 through 75 removed outlier: 6.108A pdb=" N TYR K 75 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA K 79 " --> pdb=" O TYR K 75 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 87 through 90 removed outlier: 4.157A pdb=" N MET K 155 " --> pdb=" O VAL K 170 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL K 170 " --> pdb=" O MET K 155 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 136 through 140 removed outlier: 5.408A pdb=" N ALA S 10 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL S 185 " --> pdb=" O LEU S 200 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER 1 252 " --> pdb=" O THR S 199 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 28 through 30 removed outlier: 5.761A pdb=" N ILE S 30 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N MET S 34 " --> pdb=" O ILE S 30 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 42 through 44 removed outlier: 3.601A pdb=" N ILE S 51 " --> pdb=" O PHE S 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA S 110 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 129 through 131 Processing sheet with id=AF1, first strand: chain 'T' and resid 21 through 23 removed outlier: 6.169A pdb=" N SER T 23 " --> pdb=" O GLN T 27 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN T 27 " --> pdb=" O SER T 23 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 35 through 37 removed outlier: 3.713A pdb=" N ALA T 105 " --> pdb=" O LEU T 43 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 163 through 164 removed outlier: 4.214A pdb=" N SER U 49 " --> pdb=" O VAL U 226 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL U 226 " --> pdb=" O SER U 49 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 57 through 59 removed outlier: 7.102A pdb=" N LEU U 57 " --> pdb=" O HIS U 64 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 72 through 73 removed outlier: 3.670A pdb=" N GLY U 81 " --> pdb=" O ILE U 137 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN U 136 " --> pdb=" O PHE U 152 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 181 through 182 removed outlier: 3.534A pdb=" N GLY V 64 " --> pdb=" O PHE V 61 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 74 through 75 Processing sheet with id=AF8, first strand: chain 'V' and resid 88 through 90 removed outlier: 3.546A pdb=" N GLY V 158 " --> pdb=" O MET V 95 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 144 through 148 removed outlier: 5.821A pdb=" N THR W 22 " --> pdb=" O ASP W 37 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL W 32 " --> pdb=" O ILE W 198 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE W 198 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 40 through 42 removed outlier: 6.992A pdb=" N VAL W 40 " --> pdb=" O VAL W 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 54 through 56 removed outlier: 3.682A pdb=" N SER W 55 " --> pdb=" O CYS W 63 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 164 through 167 removed outlier: 3.618A pdb=" N THR X 164 " --> pdb=" O GLY X 44 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE X 42 " --> pdb=" O LEU X 166 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS X 215 " --> pdb=" O LEU X 53 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL X 216 " --> pdb=" O LYS X 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR X 218 " --> pdb=" O GLY X 221 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY X 221 " --> pdb=" O THR X 218 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 59 through 60 removed outlier: 6.742A pdb=" N ALA X 59 " --> pdb=" O ALA X 66 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 74 through 77 removed outlier: 3.991A pdb=" N CYS X 82 " --> pdb=" O HIS X 74 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE X 76 " --> pdb=" O ILE X 80 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE X 80 " --> pdb=" O ILE X 76 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 197 through 200 removed outlier: 3.683A pdb=" N VAL Y 84 " --> pdb=" O MET Y 251 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N HIS Y 250 " --> pdb=" O LYS Y 258 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS Y 258 " --> pdb=" O HIS Y 250 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 92 through 94 removed outlier: 7.220A pdb=" N ALA Y 92 " --> pdb=" O ALA Y 99 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 114 through 115 removed outlier: 3.670A pdb=" N LEU Y 114 " --> pdb=" O CYS Y 174 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS Y 174 " --> pdb=" O LEU Y 114 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 144 through 147 removed outlier: 3.784A pdb=" N VAL Z 32 " --> pdb=" O ILE Z 198 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE Z 198 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 40 through 41 Processing sheet with id=AH2, first strand: chain 'Z' and resid 54 through 56 removed outlier: 3.522A pdb=" N SER Z 55 " --> pdb=" O CYS Z 63 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS Z 117 " --> pdb=" O SER Z 66 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '1' and resid 164 through 167 removed outlier: 6.639A pdb=" N THR 1 41 " --> pdb=" O ASP 1 56 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP 1 56 " --> pdb=" O THR 1 41 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ALA 1 214 " --> pdb=" O ALA 1 227 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA 1 227 " --> pdb=" O ALA 1 214 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL 1 216 " --> pdb=" O LEU 1 225 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU 1 225 " --> pdb=" O VAL 1 216 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR 1 218 " --> pdb=" O LYS 1 223 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS 1 223 " --> pdb=" O THR 1 218 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain '1' and resid 59 through 60 Processing sheet with id=AH5, first strand: chain '1' and resid 73 through 77 removed outlier: 6.587A pdb=" N ILE 1 80 " --> pdb=" O ILE 1 76 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR 1 81 " --> pdb=" O GLY 1 140 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY 1 140 " --> pdb=" O TYR 1 81 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '2' and resid 200 through 201 removed outlier: 5.976A pdb=" N THR 2 74 " --> pdb=" O ASP 2 89 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP 2 89 " --> pdb=" O THR 2 74 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE 2 78 " --> pdb=" O ILE 2 85 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU 2 260 " --> pdb=" O MET 2 248 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS 2 250 " --> pdb=" O LYS 2 258 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LYS 2 258 " --> pdb=" O HIS 2 250 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '2' and resid 92 through 94 removed outlier: 7.580A pdb=" N ALA 2 92 " --> pdb=" O ALA 2 99 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 2 99 " --> pdb=" O ALA 2 92 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '2' and resid 107 through 110 removed outlier: 6.423A pdb=" N LEU 2 113 " --> pdb=" O ILE 2 109 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY 2 170 " --> pdb=" O SER 2 118 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '2' and resid 107 through 110 removed outlier: 6.423A pdb=" N LEU 2 113 " --> pdb=" O ILE 2 109 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER 2 171 " --> pdb=" O VAL 2 186 " (cutoff:3.500A) 3138 hydrogen bonds defined for protein. 9033 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: 20.63 Time building geometry restraints manager: 20.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 19668 1.34 - 1.46: 8870 1.46 - 1.58: 31935 1.58 - 1.70: 0 1.70 - 1.82: 569 Bond restraints: 61042 Sorted by residual: bond pdb=" C GLY Y 180 " pdb=" N PRO Y 181 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.41e+00 bond pdb=" C GLN B 191 " pdb=" N PRO B 192 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.78e+00 bond pdb=" C GLN E 191 " pdb=" N PRO E 192 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.15e+00 bond pdb=" CA SER X 63 " pdb=" C SER X 63 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.34e-02 5.57e+03 4.06e+00 bond pdb=" N GLY F 232 " pdb=" CA GLY F 232 " ideal model delta sigma weight residual 1.449 1.474 -0.025 1.45e-02 4.76e+03 3.02e+00 ... (remaining 61037 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.36: 1496 106.36 - 113.28: 33148 113.28 - 120.21: 21276 120.21 - 127.14: 26077 127.14 - 134.06: 483 Bond angle restraints: 82480 Sorted by residual: angle pdb=" N THR c 78 " pdb=" CA THR c 78 " pdb=" C THR c 78 " ideal model delta sigma weight residual 111.82 120.13 -8.31 1.16e+00 7.43e-01 5.13e+01 angle pdb=" C LYS b 187 " pdb=" CA LYS b 187 " pdb=" CB LYS b 187 " ideal model delta sigma weight residual 116.54 109.13 7.41 1.15e+00 7.56e-01 4.15e+01 angle pdb=" C ARG a 213 " pdb=" CA ARG a 213 " pdb=" CB ARG a 213 " ideal model delta sigma weight residual 116.54 110.17 6.37 1.15e+00 7.56e-01 3.07e+01 angle pdb=" C ALA f 41 " pdb=" CA ALA f 41 " pdb=" CB ALA f 41 " ideal model delta sigma weight residual 117.23 109.79 7.44 1.36e+00 5.41e-01 3.00e+01 angle pdb=" C ASN I 24 " pdb=" CA ASN I 24 " pdb=" CB ASN I 24 " ideal model delta sigma weight residual 116.63 110.52 6.11 1.16e+00 7.43e-01 2.77e+01 ... (remaining 82475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 36229 16.80 - 33.59: 515 33.59 - 50.39: 201 50.39 - 67.18: 39 67.18 - 83.98: 12 Dihedral angle restraints: 36996 sinusoidal: 14812 harmonic: 22184 Sorted by residual: dihedral pdb=" CA GLY S 101 " pdb=" C GLY S 101 " pdb=" N PRO S 102 " pdb=" CA PRO S 102 " ideal model delta harmonic sigma weight residual 180.00 -150.11 -29.89 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA GLN a 200 " pdb=" C GLN a 200 " pdb=" N SER a 201 " pdb=" CA SER a 201 " ideal model delta harmonic sigma weight residual -180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLY H 101 " pdb=" C GLY H 101 " pdb=" N PRO H 102 " pdb=" CA PRO H 102 " ideal model delta harmonic sigma weight residual -180.00 -154.41 -25.59 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 36993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 7813 0.055 - 0.110: 1295 0.110 - 0.164: 170 0.164 - 0.219: 6 0.219 - 0.274: 5 Chirality restraints: 9289 Sorted by residual: chirality pdb=" CA VAL V 51 " pdb=" N VAL V 51 " pdb=" C VAL V 51 " pdb=" CB VAL V 51 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA THR c 78 " pdb=" N THR c 78 " pdb=" C THR c 78 " pdb=" CB THR c 78 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ASP 1 62 " pdb=" N ASP 1 62 " pdb=" C ASP 1 62 " pdb=" CB ASP 1 62 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 9286 not shown) Planarity restraints: 10629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 235 " 0.061 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO D 236 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO D 236 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 236 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 231 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LYS F 231 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS F 231 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY F 232 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR 1 232 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C THR 1 232 " 0.049 2.00e-02 2.50e+03 pdb=" O THR 1 232 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS 1 233 " -0.017 2.00e-02 2.50e+03 ... (remaining 10626 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4148 2.74 - 3.28: 60683 3.28 - 3.82: 96288 3.82 - 4.36: 118302 4.36 - 4.90: 200658 Nonbonded interactions: 480079 Sorted by model distance: nonbonded pdb=" OG SER N 62 " pdb=" O ILE N 65 " model vdw 2.196 2.440 nonbonded pdb=" OG1 THR b 161 " pdb=" OG1 THR c 78 " model vdw 2.197 2.440 nonbonded pdb=" NZ LYS U 164 " pdb=" OG1 THR 2 100 " model vdw 2.208 2.520 nonbonded pdb=" O LEU C 49 " pdb=" OH TYR C 209 " model vdw 2.213 2.440 nonbonded pdb=" OG1 THR O 31 " pdb=" O ARG O 163 " model vdw 2.215 2.440 ... (remaining 480074 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 'X' } ncs_group { reference = chain '2' selection = chain 'Y' } ncs_group { reference = (chain 'A' and (resid 7 through 67 or resid 94 through 237)) selection = (chain 'D' and (resid 7 through 200 or (resid 201 and (name N or name CA or name \ C or name O or name CB )) or resid 202 through 237)) selection = (chain 'F' and (resid 7 through 67 or resid 94 through 200 or (resid 201 and (na \ me N or name CA or name C or name O or name CB )) or resid 202 through 237)) } ncs_group { reference = (chain 'B' and (resid 4 through 63 or resid 102 through 242)) selection = (chain 'C' and (resid 4 through 63 or resid 102 through 242)) selection = (chain 'E' and resid 4 through 242) selection = (chain 'G' and (resid 4 through 63 or resid 102 through 242)) } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = (chain 'I' and resid 1 through 197) selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'U' } ncs_group { reference = (chain 'K' and resid 47 through 261) selection = (chain 'V' and resid 47 through 261) } ncs_group { reference = (chain 'L' and resid 9 through 243) selection = (chain 'e' and resid 9 through 243) } ncs_group { reference = chain 'M' selection = (chain 'f' and resid 7 through 232) } ncs_group { reference = chain 'N' selection = chain 'g' } ncs_group { reference = chain 'O' selection = chain 'a' } ncs_group { reference = chain 'P' selection = chain 'b' } ncs_group { reference = chain 'Q' selection = chain 'c' } ncs_group { reference = chain 'R' selection = chain 'd' } ncs_group { reference = chain 'W' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 346 5.16 5 C 38016 2.51 5 N 10246 2.21 5 O 11349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 7.530 Check model and map are aligned: 0.660 Process input model: 117.740 Find NCS groups from input model: 4.930 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Set scattering table: 0.410 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 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 : 0.002 0.064 61042 Z= 0.127 Angle : 0.548 8.309 82480 Z= 0.349 Chirality : 0.041 0.274 9289 Planarity : 0.004 0.094 10629 Dihedral : 7.814 83.979 22770 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.91 % Favored : 94.95 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.08), residues: 7577 helix: -2.80 (0.06), residues: 3115 sheet: -0.71 (0.13), residues: 1293 loop : -0.99 (0.10), residues: 3169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3302 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 3294 time to evaluate : 5.174 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 outliers start: 8 outliers final: 2 residues processed: 3299 average time/residue: 0.6158 time to fit residues: 3289.3760 Evaluate side-chains 1790 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1788 time to evaluate : 5.194 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4211 time to fit residues: 8.7377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 632 optimal weight: 9.9990 chunk 567 optimal weight: 2.9990 chunk 315 optimal weight: 0.9990 chunk 193 optimal weight: 0.2980 chunk 382 optimal weight: 7.9990 chunk 303 optimal weight: 2.9990 chunk 587 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 356 optimal weight: 3.9990 chunk 436 optimal weight: 8.9990 chunk 680 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 ASN M 148 GLN M 179 ASN M 207 ASN N 100 GLN ** N 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 146 GLN ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 GLN ** Q 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 90 GLN Q 143 HIS B 138 GLN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS E 233 ASN F 192 HIS F 218 HIS G 7 GLN G 115 GLN ** G 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 94 HIS a 116 GLN b 41 GLN b 99 HIS c 68 ASN d 144 ASN ** e 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 146 GLN H 7 ASN I 71 ASN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 HIS J 107 ASN J 136 ASN ** J 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN K 126 HIS ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 ASN S 145 GLN ** S 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 ASN T 168 GLN T 189 HIS T 193 ASN U 64 HIS U 107 ASN ** U 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 126 HIS W 82 GLN ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 61 ASN X 105 HIS ** Y 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 237 HIS ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 142 ASN 2 206 HIS 2 234 HIS 2 247 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 61042 Z= 0.286 Angle : 0.708 10.528 82480 Z= 0.375 Chirality : 0.046 0.277 9289 Planarity : 0.006 0.090 10629 Dihedral : 4.871 54.684 8371 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.47 % Favored : 97.52 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.01 % 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: -1.07 (0.09), residues: 7577 helix: -0.58 (0.08), residues: 3216 sheet: -0.39 (0.13), residues: 1372 loop : -0.80 (0.10), residues: 2989 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2255 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 2246 time to evaluate : 5.348 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 outliers start: 9 outliers final: 0 residues processed: 2250 average time/residue: 0.5961 time to fit residues: 2232.8851 Evaluate side-chains 1633 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1633 time to evaluate : 5.197 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 378 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 566 optimal weight: 0.9990 chunk 463 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 681 optimal weight: 2.9990 chunk 736 optimal weight: 0.6980 chunk 606 optimal weight: 2.9990 chunk 675 optimal weight: 8.9990 chunk 232 optimal weight: 7.9990 chunk 546 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN L 90 GLN ** L 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN M 140 ASN ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 GLN O 154 HIS O 175 ASN ** P 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 186 HIS Q 190 HIS ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 153 GLN C 136 GLN D 127 HIS D 136 ASN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 23 GLN ** b 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 ASN e 24 GLN ** e 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 172 GLN e 238 HIS f 140 ASN ** g 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 146 GLN H 7 ASN H 162 HIS H 188 HIS I 63 ASN I 168 GLN ** J 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 GLN K 207 GLN S 7 ASN S 61 GLN S 169 GLN ** T 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 193 ASN U 64 HIS ** U 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 GLN W 101 ASN ** Y 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 247 ASN Z 73 GLN ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 142 ASN 2 269 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 61042 Z= 0.230 Angle : 0.664 12.152 82480 Z= 0.347 Chirality : 0.045 0.208 9289 Planarity : 0.005 0.079 10629 Dihedral : 4.857 48.603 8371 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.67 % Favored : 97.32 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.09), residues: 7577 helix: 0.20 (0.09), residues: 3200 sheet: -0.11 (0.13), residues: 1386 loop : -0.66 (0.11), residues: 2991 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2138 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 2125 time to evaluate : 5.382 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 outliers start: 13 outliers final: 0 residues processed: 2129 average time/residue: 0.5940 time to fit residues: 2099.3269 Evaluate side-chains 1566 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1566 time to evaluate : 5.278 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 673 optimal weight: 0.3980 chunk 512 optimal weight: 1.9990 chunk 353 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 325 optimal weight: 3.9990 chunk 457 optimal weight: 0.0970 chunk 683 optimal weight: 0.0270 chunk 723 optimal weight: 6.9990 chunk 357 optimal weight: 0.9990 chunk 648 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN ** L 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 172 GLN ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 182 GLN Q 143 HIS Q 190 HIS ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN C 107 ASN C 136 GLN C 171 HIS D 143 GLN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 60 GLN c 121 GLN d 144 ASN ** e 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 172 GLN f 140 ASN f 189 HIS g 88 ASN ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS H 7 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 ASN I 71 ASN ** J 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 ASN T 61 GLN T 87 ASN ** T 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 101 ASN X 105 HIS ** X 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 269 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 61042 Z= 0.178 Angle : 0.619 11.884 82480 Z= 0.320 Chirality : 0.044 0.356 9289 Planarity : 0.004 0.097 10629 Dihedral : 4.711 48.655 8371 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.53 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.09), residues: 7577 helix: 0.44 (0.09), residues: 3207 sheet: 0.03 (0.13), residues: 1419 loop : -0.56 (0.11), residues: 2951 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2040 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2036 time to evaluate : 5.214 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 outliers start: 4 outliers final: 0 residues processed: 2038 average time/residue: 0.5791 time to fit residues: 1971.1438 Evaluate side-chains 1577 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1577 time to evaluate : 5.246 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 602 optimal weight: 8.9990 chunk 410 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 539 optimal weight: 0.9980 chunk 298 optimal weight: 10.0000 chunk 617 optimal weight: 1.9990 chunk 500 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 369 optimal weight: 10.0000 chunk 649 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 HIS ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN O 18 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 99 HIS P 155 HIS P 182 GLN Q 190 HIS B 153 GLN C 56 ASN C 107 ASN D 143 GLN E 164 HIS a 120 GLN ** e 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 172 GLN e 238 HIS f 189 HIS g 88 ASN ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS H 7 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN I 71 ASN ** J 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN K 110 GLN K 114 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 GLN S 7 ASN S 173 ASN T 61 GLN T 87 ASN ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 64 HIS W 101 ASN ** Y 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 153 HIS ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 206 HIS 2 269 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.6908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 61042 Z= 0.244 Angle : 0.659 10.813 82480 Z= 0.344 Chirality : 0.045 0.344 9289 Planarity : 0.005 0.064 10629 Dihedral : 4.840 48.007 8371 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.09), residues: 7577 helix: 0.57 (0.09), residues: 3230 sheet: 0.06 (0.13), residues: 1419 loop : -0.55 (0.11), residues: 2928 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1962 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1959 time to evaluate : 5.390 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 outliers start: 3 outliers final: 0 residues processed: 1960 average time/residue: 0.5974 time to fit residues: 1950.8139 Evaluate side-chains 1530 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1530 time to evaluate : 5.358 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 243 optimal weight: 7.9990 chunk 651 optimal weight: 0.1980 chunk 143 optimal weight: 8.9990 chunk 425 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 724 optimal weight: 0.4980 chunk 601 optimal weight: 0.5980 chunk 335 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 380 optimal weight: 10.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 221 GLN Q 143 HIS Q 190 HIS B 191 GLN C 107 ASN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN E 164 HIS E 233 ASN G 127 GLN d 73 HIS ** e 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 53 HIS ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN H 93 ASN ** J 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN K 114 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 ASN S 173 ASN T 61 GLN T 87 ASN ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 174 ASN W 73 GLN W 101 ASN W 142 GLN X 105 HIS ** Y 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 86 HIS 1 48 GLN ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.7286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 61042 Z= 0.203 Angle : 0.642 10.704 82480 Z= 0.332 Chirality : 0.044 0.290 9289 Planarity : 0.005 0.093 10629 Dihedral : 4.793 45.895 8371 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.02 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.09), residues: 7577 helix: 0.69 (0.09), residues: 3234 sheet: 0.16 (0.13), residues: 1403 loop : -0.50 (0.11), residues: 2940 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1930 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1926 time to evaluate : 5.376 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 outliers start: 4 outliers final: 0 residues processed: 1928 average time/residue: 0.5826 time to fit residues: 1887.7020 Evaluate side-chains 1521 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1521 time to evaluate : 5.294 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 698 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 412 optimal weight: 0.9980 chunk 529 optimal weight: 5.9990 chunk 410 optimal weight: 9.9990 chunk 610 optimal weight: 6.9990 chunk 404 optimal weight: 1.9990 chunk 721 optimal weight: 10.0000 chunk 451 optimal weight: 10.0000 chunk 440 optimal weight: 2.9990 chunk 333 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 172 GLN ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN O 18 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 155 HIS P 221 GLN B 153 GLN C 7 GLN C 107 ASN C 136 GLN D 143 GLN E 164 HIS F 143 GLN ** e 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN ** J 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 ASN K 114 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 GLN S 7 ASN T 61 GLN T 63 ASN T 87 ASN ** T 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 174 ASN V 258 HIS ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 101 ASN W 142 GLN ** Y 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 206 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.7715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 61042 Z= 0.238 Angle : 0.670 10.674 82480 Z= 0.348 Chirality : 0.045 0.232 9289 Planarity : 0.005 0.129 10629 Dihedral : 4.867 40.370 8371 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.53 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.09), residues: 7577 helix: 0.72 (0.09), residues: 3233 sheet: 0.15 (0.13), residues: 1392 loop : -0.54 (0.11), residues: 2952 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1917 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1913 time to evaluate : 5.308 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 outliers start: 4 outliers final: 0 residues processed: 1915 average time/residue: 0.6094 time to fit residues: 1970.5234 Evaluate side-chains 1534 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1534 time to evaluate : 5.392 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 446 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 431 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 458 optimal weight: 8.9990 chunk 491 optimal weight: 3.9990 chunk 356 optimal weight: 8.9990 chunk 67 optimal weight: 0.3980 chunk 567 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 54 GLN Q 60 GLN Q 121 GLN R 121 HIS B 115 GLN B 153 GLN E 164 HIS a 122 ASN e 24 GLN ** e 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 123 GLN g 142 HIS H 7 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN I 168 GLN ** J 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN T 87 ASN T 174 ASN ** U 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 126 HIS V 258 HIS W 101 ASN W 142 GLN ** X 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 HIS ** Y 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 153 HIS ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.7987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 61042 Z= 0.206 Angle : 0.653 12.267 82480 Z= 0.338 Chirality : 0.044 0.213 9289 Planarity : 0.004 0.072 10629 Dihedral : 4.819 40.343 8371 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.10), residues: 7577 helix: 0.80 (0.09), residues: 3226 sheet: 0.09 (0.14), residues: 1384 loop : -0.53 (0.11), residues: 2967 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1909 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1907 time to evaluate : 5.813 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 outliers start: 2 outliers final: 0 residues processed: 1908 average time/residue: 0.5928 time to fit residues: 1901.1805 Evaluate side-chains 1514 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1514 time to evaluate : 5.410 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 656 optimal weight: 0.7980 chunk 691 optimal weight: 3.9990 chunk 631 optimal weight: 0.0980 chunk 672 optimal weight: 3.9990 chunk 404 optimal weight: 7.9990 chunk 293 optimal weight: 0.8980 chunk 528 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 607 optimal weight: 6.9990 chunk 636 optimal weight: 2.9990 chunk 670 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 54 GLN P 221 GLN Q 121 GLN ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN D 45 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS E 202 HIS ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS H 7 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN I 168 GLN J 64 HIS J 174 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 ASN K 192 GLN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN T 87 ASN ** U 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 ASN V 258 HIS W 101 ASN ** W 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 101 ASN 1 153 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.8187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 61042 Z= 0.200 Angle : 0.656 13.348 82480 Z= 0.339 Chirality : 0.044 0.221 9289 Planarity : 0.005 0.143 10629 Dihedral : 4.805 37.837 8371 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.56 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.10), residues: 7577 helix: 0.83 (0.09), residues: 3231 sheet: 0.12 (0.14), residues: 1396 loop : -0.51 (0.12), residues: 2950 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1893 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1890 time to evaluate : 5.427 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 outliers start: 3 outliers final: 0 residues processed: 1891 average time/residue: 0.5974 time to fit residues: 1907.2323 Evaluate side-chains 1498 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1498 time to evaluate : 5.356 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 441 optimal weight: 0.0020 chunk 711 optimal weight: 5.9990 chunk 434 optimal weight: 0.9990 chunk 337 optimal weight: 0.9990 chunk 494 optimal weight: 0.7980 chunk 746 optimal weight: 10.0000 chunk 686 optimal weight: 9.9990 chunk 594 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 458 optimal weight: 0.0980 chunk 364 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 54 GLN O 215 GLN Q 60 GLN ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 16 GLN B 115 GLN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN D 97 ASN D 143 GLN E 164 HIS ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 97 GLN e 12 HIS ** e 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 ASN ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 ASN K 114 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 ASN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN T 87 ASN ** T 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 258 HIS W 101 ASN ** W 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 101 ASN 1 153 HIS ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.8290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 61042 Z= 0.190 Angle : 0.666 14.604 82480 Z= 0.342 Chirality : 0.044 0.255 9289 Planarity : 0.004 0.084 10629 Dihedral : 4.767 37.099 8371 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.10), residues: 7577 helix: 0.87 (0.09), residues: 3243 sheet: 0.07 (0.13), residues: 1410 loop : -0.53 (0.12), residues: 2924 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1891 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1888 time to evaluate : 5.278 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 outliers start: 3 outliers final: 0 residues processed: 1890 average time/residue: 0.5906 time to fit residues: 1887.7493 Evaluate side-chains 1491 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1491 time to evaluate : 5.258 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 471 optimal weight: 5.9990 chunk 632 optimal weight: 0.0970 chunk 182 optimal weight: 7.9990 chunk 547 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 595 optimal weight: 6.9990 chunk 249 optimal weight: 0.7980 chunk 611 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 172 GLN M 52 GLN ** N 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 240 HIS O 54 GLN O 215 GLN ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 GLN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS E 202 HIS ** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 97 GLN ** e 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 ASN J 179 ASN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 ASN K 192 GLN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN T 87 ASN V 258 HIS W 101 ASN ** W 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 101 ASN 1 153 HIS ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.152621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.133654 restraints weight = 137514.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.137198 restraints weight = 77850.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.138652 restraints weight = 49795.232| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.8594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 61042 Z= 0.231 Angle : 0.692 11.842 82480 Z= 0.357 Chirality : 0.045 0.263 9289 Planarity : 0.005 0.076 10629 Dihedral : 4.866 34.266 8371 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.76 % Favored : 96.23 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.10), residues: 7577 helix: 0.83 (0.09), residues: 3253 sheet: 0.09 (0.14), residues: 1413 loop : -0.54 (0.12), residues: 2911 =============================================================================== Job complete usr+sys time: 24906.83 seconds wall clock time: 431 minutes 27.85 seconds (25887.85 seconds total)