Starting phenix.real_space_refine on Thu Mar 21 08:19:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jco_6574/03_2024/3jco_6574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jco_6574/03_2024/3jco_6574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jco_6574/03_2024/3jco_6574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jco_6574/03_2024/3jco_6574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jco_6574/03_2024/3jco_6574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jco_6574/03_2024/3jco_6574.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 385 5.16 5 C 66043 2.51 5 N 17691 2.21 5 O 20198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 242": "OE1" <-> "OE2" Residue "L PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 414": "OE1" <-> "OE2" Residue "S GLU 22": "OE1" <-> "OE2" Residue "S GLU 455": "OE1" <-> "OE2" Residue "S ARG 464": "NH1" <-> "NH2" Residue "U GLU 141": "OE1" <-> "OE2" Residue "V GLU 258": "OE1" <-> "OE2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 104317 Number of models: 1 Model: "" Number of chains: 47 Chain: "1" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1757 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "2" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1824 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain: "3" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1574 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "4" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1684 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain: "5" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1581 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "6" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1585 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "7" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1644 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain: "8" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1757 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "9" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1824 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1921 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 232} Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1915 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain: "C" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1904 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "D" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1890 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "E" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1861 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "F" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1795 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain: "G" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1896 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 9, 'TRANS': 234} Chain: "H" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2771 Classifications: {'peptide': 356} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 333} Chain breaks: 2 Chain: "I" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2513 Classifications: {'peptide': 325} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 308} Chain breaks: 1 Chain: "J" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2928 Classifications: {'peptide': 373} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 357} Chain: "K" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2849 Classifications: {'peptide': 361} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Chain breaks: 1 Chain: "L" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2829 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Chain: "M" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2754 Classifications: {'peptide': 357} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 339} Chain breaks: 2 Chain: "N" Number of atoms: 6562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 849, 6562 Classifications: {'peptide': 849} Link IDs: {'PTRANS': 23, 'TRANS': 825} Chain breaks: 2 Chain: "O" Number of atoms: 3083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3083 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 6, 'PTRANS': 9, 'TRANS': 360} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3470 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 421} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 2, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "Q" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3471 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 7, 'TRANS': 423} Chain: "R" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3218 Classifications: {'peptide': 400} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 391} Chain: "S" Number of atoms: 3357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3357 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'CIS': 5, 'PTRANS': 8, 'TRANS': 425} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 128 Chain: "T" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2201 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain: "U" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2034 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 246} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "V" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1912 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 238} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "W" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1534 Classifications: {'peptide': 197} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 186} Chain: "X" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1032 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "Y" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 243 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 1, 'TRANS': 32} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "Z" Number of atoms: 5894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 5894 Classifications: {'peptide': 763} Link IDs: {'PTRANS': 23, 'TRANS': 739} Chain breaks: 2 Chain: "a" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1921 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 232} Chain: "b" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1915 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain: "c" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1904 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "d" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1890 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "e" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1861 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "f" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1795 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain: "g" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1896 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 9, 'TRANS': 234} Chain: "h" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1574 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "i" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1684 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain: "j" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1581 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "k" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1585 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "l" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1644 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Time building chain proxies: 41.73, per 1000 atoms: 0.40 Number of scatterers: 104317 At special positions: 0 Unit cell: (333.9, 222.6, 207.9, 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 385 16.00 O 20198 8.00 N 17691 7.00 C 66043 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: 38.62 Conformation dependent library (CDL) restraints added in 14.5 seconds 26382 Ramachandran restraints generated. 13191 Oldfield, 0 Emsley, 13191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 24892 Finding SS restraints... Secondary structure from input PDB file: 497 helices and 108 sheets defined 51.5% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.50 Creating SS restraints... Processing helix chain '1' and resid 76 through 98 removed outlier: 3.519A pdb=" N GLY 1 80 " --> pdb=" O PHE 1 76 " (cutoff:3.500A) Processing helix chain '1' and resid 104 through 119 removed outlier: 3.528A pdb=" N LYS 1 119 " --> pdb=" O LEU 1 115 " (cutoff:3.500A) Processing helix chain '1' and resid 161 through 173 Proline residue: 1 167 - end of helix Processing helix chain '1' and resid 195 through 214 Processing helix chain '2' and resid 90 through 109 removed outlier: 3.695A pdb=" N ASP 2 102 " --> pdb=" O ARG 2 98 " (cutoff:3.500A) Processing helix chain '2' and resid 111 through 115 removed outlier: 4.118A pdb=" N ASP 2 115 " --> pdb=" O PRO 2 112 " (cutoff:3.500A) Processing helix chain '2' and resid 121 through 139 removed outlier: 3.557A pdb=" N VAL 2 132 " --> pdb=" O TYR 2 128 " (cutoff:3.500A) Processing helix chain '2' and resid 177 through 192 removed outlier: 3.791A pdb=" N ASN 2 185 " --> pdb=" O ALA 2 181 " (cutoff:3.500A) Proline residue: 2 186 - end of helix Processing helix chain '2' and resid 194 through 201 Proline residue: 2 199 - end of helix Processing helix chain '2' and resid 202 through 221 removed outlier: 3.821A pdb=" N ALA 2 206 " --> pdb=" O THR 2 202 " (cutoff:3.500A) Processing helix chain '2' and resid 252 through 258 removed outlier: 3.510A pdb=" N ALA 2 255 " --> pdb=" O TRP 2 252 " (cutoff:3.500A) Processing helix chain '3' and resid 67 through 90 Processing helix chain '3' and resid 93 through 109 Processing helix chain '3' and resid 149 through 161 removed outlier: 4.816A pdb=" N GLY 3 155 " --> pdb=" O THR 3 151 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR 3 156 " --> pdb=" O PHE 3 152 " (cutoff:3.500A) Processing helix chain '3' and resid 166 through 185 Processing helix chain '3' and resid 208 through 213 Processing helix chain '4' and resid 77 through 100 Processing helix chain '4' and resid 104 through 119 removed outlier: 4.286A pdb=" N ALA 4 108 " --> pdb=" O ARG 4 104 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 171 Processing helix chain '4' and resid 176 through 195 Processing helix chain '5' and resid 3 through 9 removed outlier: 3.702A pdb=" N ASN 5 8 " --> pdb=" O PRO 5 4 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY 5 9 " --> pdb=" O SER 5 5 " (cutoff:3.500A) Processing helix chain '5' and resid 56 through 79 removed outlier: 3.594A pdb=" N GLU 5 65 " --> pdb=" O THR 5 61 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 97 Processing helix chain '5' and resid 142 through 154 removed outlier: 3.641A pdb=" N SER 5 152 " --> pdb=" O GLY 5 148 " (cutoff:3.500A) Processing helix chain '5' and resid 159 through 177 Processing helix chain '6' and resid 49 through 72 removed outlier: 3.525A pdb=" N ASN 6 63 " --> pdb=" O TYR 6 59 " (cutoff:3.500A) Processing helix chain '6' and resid 76 through 94 removed outlier: 3.522A pdb=" N GLU 6 87 " --> pdb=" O PHE 6 83 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU 6 88 " --> pdb=" O VAL 6 84 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 148 removed outlier: 4.534A pdb=" N PHE 6 138 " --> pdb=" O GLY 6 134 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR 6 139 " --> pdb=" O TYR 6 135 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR 6 140 " --> pdb=" O SER 6 136 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER 6 142 " --> pdb=" O PHE 6 138 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU 6 143 " --> pdb=" O TYR 6 139 " (cutoff:3.500A) Processing helix chain '6' and resid 153 through 172 removed outlier: 3.749A pdb=" N GLY 6 157 " --> pdb=" O THR 6 153 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU 6 158 " --> pdb=" O THR 6 154 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP 6 159 " --> pdb=" O GLU 6 155 " (cutoff:3.500A) Processing helix chain '7' and resid 123 through 146 removed outlier: 3.553A pdb=" N SER 7 136 " --> pdb=" O THR 7 132 " (cutoff:3.500A) Processing helix chain '7' and resid 150 through 166 removed outlier: 3.541A pdb=" N TYR 7 165 " --> pdb=" O LEU 7 161 " (cutoff:3.500A) Processing helix chain '7' and resid 207 through 219 removed outlier: 3.534A pdb=" N ALA 7 211 " --> pdb=" O GLY 7 207 " (cutoff:3.500A) Processing helix chain '7' and resid 224 through 243 removed outlier: 3.591A pdb=" N ALA 7 239 " --> pdb=" O SER 7 235 " (cutoff:3.500A) Processing helix chain '7' and resid 268 through 280 Processing helix chain '8' and resid 76 through 98 removed outlier: 3.517A pdb=" N GLY 8 80 " --> pdb=" O PHE 8 76 " (cutoff:3.500A) Processing helix chain '8' and resid 104 through 119 removed outlier: 3.528A pdb=" N LYS 8 119 " --> pdb=" O LEU 8 115 " (cutoff:3.500A) Processing helix chain '8' and resid 161 through 173 Proline residue: 8 167 - end of helix Processing helix chain '8' and resid 195 through 214 Processing helix chain '9' and resid 90 through 109 removed outlier: 3.694A pdb=" N ASP 9 102 " --> pdb=" O ARG 9 98 " (cutoff:3.500A) Processing helix chain '9' and resid 111 through 115 removed outlier: 4.117A pdb=" N ASP 9 115 " --> pdb=" O PRO 9 112 " (cutoff:3.500A) Processing helix chain '9' and resid 121 through 139 removed outlier: 3.557A pdb=" N VAL 9 132 " --> pdb=" O TYR 9 128 " (cutoff:3.500A) Processing helix chain '9' and resid 177 through 192 removed outlier: 3.791A pdb=" N ASN 9 185 " --> pdb=" O ALA 9 181 " (cutoff:3.500A) Proline residue: 9 186 - end of helix Processing helix chain '9' and resid 194 through 201 Proline residue: 9 199 - end of helix Processing helix chain '9' and resid 202 through 221 removed outlier: 3.822A pdb=" N ALA 9 206 " --> pdb=" O THR 9 202 " (cutoff:3.500A) Processing helix chain '9' and resid 252 through 258 removed outlier: 3.509A pdb=" N ALA 9 255 " --> pdb=" O TRP 9 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 16 removed outlier: 4.038A pdb=" N HIS A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 38 removed outlier: 3.979A pdb=" N ASN A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 69 Processing helix chain 'A' and resid 86 through 109 removed outlier: 3.509A pdb=" N ALA A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 131 removed outlier: 3.701A pdb=" N SER A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 190 Processing helix chain 'A' and resid 198 through 215 Processing helix chain 'A' and resid 237 through 252 Processing helix chain 'B' and resid 18 through 31 removed outlier: 3.663A pdb=" N THR B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 78 through 97 removed outlier: 4.214A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.621A pdb=" N VAL B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 184 through 200 Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.991A pdb=" N HIS C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 103 removed outlier: 3.790A pdb=" N GLU C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 125 removed outlier: 3.885A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'D' and resid 17 through 30 removed outlier: 3.585A pdb=" N GLU D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 101 removed outlier: 3.503A pdb=" N ARG D 83 " --> pdb=" O ASN D 79 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 123 removed outlier: 3.515A pdb=" N GLY D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 116 " --> pdb=" O TYR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 179 Processing helix chain 'D' and resid 187 through 204 removed outlier: 3.958A pdb=" N VAL D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 242 removed outlier: 3.510A pdb=" N GLU D 239 " --> pdb=" O GLN D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.638A pdb=" N LYS E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 81 through 104 removed outlier: 4.417A pdb=" N ALA E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG E 86 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 119 through 123 removed outlier: 4.168A pdb=" N PHE E 123 " --> pdb=" O ALA E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 187 Processing helix chain 'E' and resid 192 through 208 Processing helix chain 'E' and resid 232 through 248 Processing helix chain 'F' and resid 3 through 7 Processing helix chain 'F' and resid 19 through 32 removed outlier: 3.875A pdb=" N LYS F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 99 removed outlier: 3.830A pdb=" N ALA F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.655A pdb=" N LEU F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP F 114 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 182 removed outlier: 5.713A pdb=" N ASP F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE F 179 " --> pdb=" O THR F 175 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 201 Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.652A pdb=" N LYS F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'G' and resid 81 through 104 removed outlier: 3.903A pdb=" N ALA G 97 " --> pdb=" O ARG G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.597A pdb=" N LEU G 116 " --> pdb=" O PHE G 112 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.577A pdb=" N GLU G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 207 removed outlier: 3.676A pdb=" N ASP G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN G 207 " --> pdb=" O ALA G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 247 removed outlier: 3.589A pdb=" N LEU G 236 " --> pdb=" O LYS G 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 73 removed outlier: 4.190A pdb=" N LEU H 56 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY H 68 " --> pdb=" O LYS H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 77 Processing helix chain 'H' and resid 214 through 225 Processing helix chain 'H' and resid 225 through 231 Processing helix chain 'H' and resid 231 through 239 removed outlier: 4.254A pdb=" N PHE H 235 " --> pdb=" O SER H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 267 Processing helix chain 'H' and resid 276 through 280 Processing helix chain 'H' and resid 285 through 302 removed outlier: 3.525A pdb=" N MET H 290 " --> pdb=" O GLU H 286 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG H 299 " --> pdb=" O PHE H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 324 Processing helix chain 'H' and resid 325 through 344 removed outlier: 4.041A pdb=" N VAL H 329 " --> pdb=" O GLY H 325 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY H 342 " --> pdb=" O THR H 338 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE H 343 " --> pdb=" O GLN H 339 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP H 344 " --> pdb=" O LEU H 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 367 removed outlier: 3.830A pdb=" N LEU H 366 " --> pdb=" O ASP H 362 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG H 367 " --> pdb=" O PRO H 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 362 through 367' Processing helix chain 'H' and resid 381 through 396 removed outlier: 3.535A pdb=" N ALA H 386 " --> pdb=" O LEU H 382 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER H 395 " --> pdb=" O ILE H 391 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET H 396 " --> pdb=" O HIS H 392 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 411 removed outlier: 3.631A pdb=" N LEU H 410 " --> pdb=" O LEU H 406 " (cutoff:3.500A) Processing helix chain 'H' and resid 418 through 423 removed outlier: 3.516A pdb=" N VAL H 422 " --> pdb=" O GLU H 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 425 through 433 removed outlier: 3.806A pdb=" N PHE H 429 " --> pdb=" O GLU H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 455 removed outlier: 3.851A pdb=" N LYS H 455 " --> pdb=" O ILE H 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 101 removed outlier: 4.078A pdb=" N ARG I 100 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY I 101 " --> pdb=" O GLU I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 141 Processing helix chain 'I' and resid 187 through 198 removed outlier: 3.942A pdb=" N GLU I 193 " --> pdb=" O SER I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 203 removed outlier: 3.800A pdb=" N THR I 203 " --> pdb=" O LEU I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 241 removed outlier: 3.624A pdb=" N LYS I 234 " --> pdb=" O THR I 230 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL I 236 " --> pdb=" O LEU I 232 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA I 237 " --> pdb=" O ALA I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 253 Processing helix chain 'I' and resid 258 through 274 Processing helix chain 'I' and resid 299 through 314 removed outlier: 3.847A pdb=" N GLN I 303 " --> pdb=" O GLU I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 340 Processing helix chain 'I' and resid 354 through 368 removed outlier: 3.647A pdb=" N SER I 367 " --> pdb=" O GLY I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 376 through 383 removed outlier: 3.820A pdb=" N THR I 383 " --> pdb=" O THR I 379 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 406 removed outlier: 3.515A pdb=" N GLY I 400 " --> pdb=" O CYS I 396 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU I 401 " --> pdb=" O THR I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 423 removed outlier: 3.853A pdb=" N PHE I 416 " --> pdb=" O THR I 412 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 65 removed outlier: 3.960A pdb=" N THR J 30 " --> pdb=" O LYS J 26 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU J 31 " --> pdb=" O ILE J 27 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU J 32 " --> pdb=" O GLN J 28 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS J 33 " --> pdb=" O GLU J 29 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE J 34 " --> pdb=" O THR J 30 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLU J 39 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN J 40 " --> pdb=" O SER J 36 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL J 41 " --> pdb=" O LYS J 37 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG J 42 " --> pdb=" O THR J 38 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU J 62 " --> pdb=" O ILE J 58 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 150 removed outlier: 3.702A pdb=" N MET J 149 " --> pdb=" O THR J 146 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL J 150 " --> pdb=" O TYR J 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 146 through 150' Processing helix chain 'J' and resid 153 through 164 Processing helix chain 'J' and resid 164 through 170 Processing helix chain 'J' and resid 170 through 177 removed outlier: 4.331A pdb=" N PHE J 174 " --> pdb=" O HIS J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 206 removed outlier: 3.693A pdb=" N LEU J 198 " --> pdb=" O GLY J 194 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL J 202 " --> pdb=" O LEU J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 219 removed outlier: 3.940A pdb=" N VAL J 219 " --> pdb=" O ALA J 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 216 through 219' Processing helix chain 'J' and resid 224 through 240 removed outlier: 3.667A pdb=" N MET J 229 " --> pdb=" O GLU J 225 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL J 230 " --> pdb=" O GLY J 226 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG J 238 " --> pdb=" O PHE J 234 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS J 240 " --> pdb=" O MET J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 279 removed outlier: 3.730A pdb=" N GLU J 267 " --> pdb=" O GLY J 263 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL J 268 " --> pdb=" O GLY J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 306 removed outlier: 4.386A pdb=" N LEU J 305 " --> pdb=" O ASP J 301 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 335 removed outlier: 3.645A pdb=" N MET J 335 " --> pdb=" O HIS J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 350 Processing helix chain 'J' and resid 354 through 372 removed outlier: 3.566A pdb=" N LYS J 359 " --> pdb=" O GLY J 355 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY J 360 " --> pdb=" O ALA J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 395 removed outlier: 4.274A pdb=" N PHE J 382 " --> pdb=" O THR J 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 54 removed outlier: 3.560A pdb=" N LYS K 53 " --> pdb=" O PHE K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 89 removed outlier: 4.001A pdb=" N LEU K 61 " --> pdb=" O GLU K 57 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE K 68 " --> pdb=" O GLN K 64 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LYS K 69 " --> pdb=" O GLU K 65 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASP K 70 " --> pdb=" O ASP K 66 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU K 71 " --> pdb=" O TYR K 67 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU K 84 " --> pdb=" O LYS K 80 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU K 85 " --> pdb=" O ARG K 81 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL K 86 " --> pdb=" O ALA K 82 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS K 87 " --> pdb=" O GLN K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 188 Processing helix chain 'K' and resid 188 through 194 Processing helix chain 'K' and resid 218 through 231 Processing helix chain 'K' and resid 250 through 264 removed outlier: 4.149A pdb=" N VAL K 254 " --> pdb=" O GLY K 250 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE K 258 " --> pdb=" O VAL K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 274 through 279 removed outlier: 3.556A pdb=" N THR K 279 " --> pdb=" O ASP K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 305 removed outlier: 4.829A pdb=" N VAL K 292 " --> pdb=" O SER K 288 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN K 293 " --> pdb=" O ASP K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 330 Processing helix chain 'K' and resid 345 through 360 removed outlier: 4.693A pdb=" N SER K 358 " --> pdb=" O GLY K 354 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS K 359 " --> pdb=" O THR K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 375 removed outlier: 4.233A pdb=" N ILE K 373 " --> pdb=" O ASP K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 379 through 397 removed outlier: 4.137A pdb=" N VAL K 395 " --> pdb=" O GLY K 391 " (cutoff:3.500A) Processing helix chain 'K' and resid 403 through 416 removed outlier: 4.450A pdb=" N LYS K 416 " --> pdb=" O ALA K 412 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 98 removed outlier: 3.770A pdb=" N ARG L 69 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP L 83 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU L 87 " --> pdb=" O ASP L 83 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR L 88 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP L 89 " --> pdb=" O GLU L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 184 removed outlier: 3.871A pdb=" N ILE L 183 " --> pdb=" O PHE L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 197 removed outlier: 3.522A pdb=" N ILE L 190 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU L 192 " --> pdb=" O GLU L 188 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU L 193 " --> pdb=" O GLN L 189 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG L 194 " --> pdb=" O ILE L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 203 Processing helix chain 'L' and resid 227 through 240 removed outlier: 4.178A pdb=" N LYS L 233 " --> pdb=" O THR L 229 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY L 240 " --> pdb=" O ALA L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 252 Processing helix chain 'L' and resid 257 through 274 removed outlier: 3.656A pdb=" N ALA L 270 " --> pdb=" O MET L 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 313 Processing helix chain 'L' and resid 329 through 333 removed outlier: 3.817A pdb=" N THR L 332 " --> pdb=" O ARG L 329 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 339 Processing helix chain 'L' and resid 353 through 365 Processing helix chain 'L' and resid 375 through 383 Processing helix chain 'L' and resid 387 through 405 removed outlier: 3.649A pdb=" N ALA L 398 " --> pdb=" O CYS L 394 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 425 removed outlier: 3.777A pdb=" N LYS L 417 " --> pdb=" O ASP L 413 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL L 425 " --> pdb=" O LYS L 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 38 Proline residue: M 13 - end of helix removed outlier: 3.995A pdb=" N LEU M 18 " --> pdb=" O GLY M 14 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP M 19 " --> pdb=" O ASP M 15 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR M 27 " --> pdb=" O LEU M 23 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN M 28 " --> pdb=" O ASN M 24 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU M 29 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR M 32 " --> pdb=" O GLN M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 72 No H-bonds generated for 'chain 'M' and resid 71 through 72' Processing helix chain 'M' and resid 186 through 197 removed outlier: 3.700A pdb=" N GLU M 192 " --> pdb=" O LYS M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 203 Processing helix chain 'M' and resid 227 through 239 Processing helix chain 'M' and resid 248 through 252 Processing helix chain 'M' and resid 257 through 273 Processing helix chain 'M' and resid 283 through 286 Processing helix chain 'M' and resid 299 through 313 Processing helix chain 'M' and resid 353 through 367 removed outlier: 4.446A pdb=" N LYS M 367 " --> pdb=" O ILE M 363 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 383 Processing helix chain 'M' and resid 387 through 405 removed outlier: 4.040A pdb=" N LEU M 391 " --> pdb=" O ASN M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 411 through 421 Processing helix chain 'N' and resid 6 through 15 removed outlier: 4.233A pdb=" N ARG N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU N 15 " --> pdb=" O ALA N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 41 removed outlier: 4.561A pdb=" N ASP N 33 " --> pdb=" O ASN N 29 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLN N 34 " --> pdb=" O ASN N 30 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER N 37 " --> pdb=" O ASP N 33 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU N 38 " --> pdb=" O GLN N 34 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN N 41 " --> pdb=" O SER N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 52 Processing helix chain 'N' and resid 58 through 72 Processing helix chain 'N' and resid 75 through 86 Processing helix chain 'N' and resid 95 through 120 removed outlier: 3.678A pdb=" N MET N 108 " --> pdb=" O LYS N 104 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL N 110 " --> pdb=" O ILE N 106 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN N 111 " --> pdb=" O GLU N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 126 Processing helix chain 'N' and resid 130 through 148 Processing helix chain 'N' and resid 149 through 161 removed outlier: 3.809A pdb=" N ALA N 153 " --> pdb=" O GLU N 149 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 174 Processing helix chain 'N' and resid 179 through 197 removed outlier: 3.929A pdb=" N ILE N 186 " --> pdb=" O ASN N 182 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 216 Processing helix chain 'N' and resid 221 through 233 Processing helix chain 'N' and resid 234 through 249 Processing helix chain 'N' and resid 250 through 263 Processing helix chain 'N' and resid 266 through 281 removed outlier: 3.940A pdb=" N ILE N 272 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU N 273 " --> pdb=" O LEU N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 290 Processing helix chain 'N' and resid 292 through 307 Processing helix chain 'N' and resid 310 through 321 Processing helix chain 'N' and resid 325 through 341 removed outlier: 3.856A pdb=" N HIS N 329 " --> pdb=" O PHE N 325 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY N 337 " --> pdb=" O SER N 333 " (cutoff:3.500A) Processing helix chain 'N' and resid 346 through 352 removed outlier: 3.679A pdb=" N ALA N 351 " --> pdb=" O SER N 347 " (cutoff:3.500A) Processing helix chain 'N' and resid 353 through 359 removed outlier: 4.363A pdb=" N GLY N 357 " --> pdb=" O LEU N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 360 through 375 removed outlier: 3.916A pdb=" N LEU N 371 " --> pdb=" O ALA N 367 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY N 372 " --> pdb=" O THR N 368 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL N 373 " --> pdb=" O ALA N 369 " (cutoff:3.500A) Processing helix chain 'N' and resid 380 through 387 Processing helix chain 'N' and resid 388 through 390 No H-bonds generated for 'chain 'N' and resid 388 through 390' Processing helix chain 'N' and resid 397 through 413 removed outlier: 3.558A pdb=" N SER N 404 " --> pdb=" O ILE N 400 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU N 405 " --> pdb=" O LYS N 401 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR N 406 " --> pdb=" O GLY N 402 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY N 409 " --> pdb=" O LEU N 405 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU N 410 " --> pdb=" O TYR N 406 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE N 411 " --> pdb=" O GLY N 407 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR N 412 " --> pdb=" O LEU N 408 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 432 removed outlier: 4.228A pdb=" N GLY N 432 " --> pdb=" O VAL N 428 " (cutoff:3.500A) Processing helix chain 'N' and resid 436 through 455 removed outlier: 4.539A pdb=" N GLY N 451 " --> pdb=" O SER N 447 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 472 Processing helix chain 'N' and resid 476 through 490 removed outlier: 4.125A pdb=" N ALA N 480 " --> pdb=" O THR N 476 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY N 486 " --> pdb=" O ALA N 482 " (cutoff:3.500A) Processing helix chain 'N' and resid 494 through 508 Processing helix chain 'N' and resid 510 through 525 removed outlier: 3.532A pdb=" N THR N 514 " --> pdb=" O HIS N 510 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA N 518 " --> pdb=" O THR N 514 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL N 519 " --> pdb=" O ARG N 515 " (cutoff:3.500A) Processing helix chain 'N' and resid 532 through 542 Processing helix chain 'N' and resid 544 through 560 removed outlier: 3.803A pdb=" N ARG N 548 " --> pdb=" O GLU N 544 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE N 553 " --> pdb=" O TYR N 549 " (cutoff:3.500A) Processing helix chain 'N' and resid 564 through 578 Processing helix chain 'N' and resid 580 through 595 removed outlier: 4.027A pdb=" N GLY N 592 " --> pdb=" O VAL N 588 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE N 593 " --> pdb=" O ILE N 589 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL N 594 " --> pdb=" O ALA N 590 " (cutoff:3.500A) Processing helix chain 'N' and resid 601 through 611 removed outlier: 3.818A pdb=" N LEU N 608 " --> pdb=" O ARG N 604 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU N 609 " --> pdb=" O ILE N 605 " (cutoff:3.500A) Processing helix chain 'N' and resid 614 through 629 removed outlier: 3.684A pdb=" N ALA N 622 " --> pdb=" O ARG N 618 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE N 623 " --> pdb=" O CYS N 619 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA N 624 " --> pdb=" O GLY N 620 " (cutoff:3.500A) Processing helix chain 'N' and resid 634 through 646 removed outlier: 3.683A pdb=" N LEU N 641 " --> pdb=" O ALA N 637 " (cutoff:3.500A) Proline residue: N 643 - end of helix Processing helix chain 'N' and resid 649 through 665 removed outlier: 3.589A pdb=" N ILE N 665 " --> pdb=" O SER N 661 " (cutoff:3.500A) Processing helix chain 'N' and resid 674 through 688 Processing helix chain 'N' and resid 694 through 708 Processing helix chain 'N' and resid 709 through 711 No H-bonds generated for 'chain 'N' and resid 709 through 711' Processing helix chain 'N' and resid 726 through 738 removed outlier: 3.931A pdb=" N GLY N 732 " --> pdb=" O LYS N 728 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU N 733 " --> pdb=" O SER N 729 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL N 734 " --> pdb=" O VAL N 730 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN N 738 " --> pdb=" O VAL N 734 " (cutoff:3.500A) Processing helix chain 'N' and resid 745 through 751 Processing helix chain 'N' and resid 875 through 881 Processing helix chain 'N' and resid 919 through 925 Processing helix chain 'O' and resid 2 through 8 Processing helix chain 'O' and resid 9 through 14 Processing helix chain 'O' and resid 23 through 34 removed outlier: 3.963A pdb=" N GLN O 28 " --> pdb=" O PRO O 24 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU O 30 " --> pdb=" O PHE O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 63 Processing helix chain 'O' and resid 85 through 90 removed outlier: 3.777A pdb=" N LYS O 90 " --> pdb=" O LYS O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 100 Processing helix chain 'O' and resid 125 through 138 Processing helix chain 'O' and resid 142 through 160 removed outlier: 3.562A pdb=" N LEU O 149 " --> pdb=" O LYS O 145 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS O 159 " --> pdb=" O LYS O 155 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS O 160 " --> pdb=" O THR O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 181 removed outlier: 3.786A pdb=" N SER O 173 " --> pdb=" O ASN O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 200 removed outlier: 3.698A pdb=" N TYR O 190 " --> pdb=" O ASN O 186 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 223 removed outlier: 3.531A pdb=" N GLN O 212 " --> pdb=" O ALA O 208 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 243 Processing helix chain 'O' and resid 246 through 258 removed outlier: 3.722A pdb=" N TRP O 250 " --> pdb=" O SER O 246 " (cutoff:3.500A) Processing helix chain 'O' and resid 262 through 266 Processing helix chain 'O' and resid 271 through 276 Processing helix chain 'O' and resid 278 through 299 removed outlier: 4.062A pdb=" N GLN O 282 " --> pdb=" O PRO O 278 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR O 295 " --> pdb=" O ILE O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 316 Processing helix chain 'O' and resid 320 through 325 Processing helix chain 'O' and resid 361 through 381 removed outlier: 3.657A pdb=" N LYS O 365 " --> pdb=" O ASP O 361 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS O 367 " --> pdb=" O ILE O 363 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP O 368 " --> pdb=" O THR O 364 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG O 369 " --> pdb=" O LYS O 365 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN O 374 " --> pdb=" O LEU O 370 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU O 378 " --> pdb=" O ASN O 374 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS O 379 " --> pdb=" O ASP O 375 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU O 380 " --> pdb=" O GLN O 376 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 25 removed outlier: 3.606A pdb=" N ILE P 12 " --> pdb=" O ASP P 8 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE P 17 " --> pdb=" O LEU P 13 " (cutoff:3.500A) Proline residue: P 18 - end of helix Processing helix chain 'P' and resid 34 through 46 removed outlier: 3.662A pdb=" N VAL P 41 " --> pdb=" O ASP P 37 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU P 42 " --> pdb=" O GLN P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 70 Processing helix chain 'P' and resid 71 through 86 removed outlier: 3.533A pdb=" N HIS P 86 " --> pdb=" O LEU P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 106 removed outlier: 3.545A pdb=" N TYR P 95 " --> pdb=" O LEU P 91 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET P 96 " --> pdb=" O SER P 92 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU P 102 " --> pdb=" O GLN P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 122 removed outlier: 4.225A pdb=" N GLU P 120 " --> pdb=" O ILE P 116 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE P 122 " --> pdb=" O VAL P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 123 through 126 Processing helix chain 'P' and resid 132 through 151 removed outlier: 4.470A pdb=" N ARG P 138 " --> pdb=" O VAL P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 153 through 162 removed outlier: 3.542A pdb=" N GLU P 162 " --> pdb=" O ASP P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 191 removed outlier: 3.508A pdb=" N GLN P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 209 removed outlier: 4.042A pdb=" N ALA P 196 " --> pdb=" O ASP P 192 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU P 204 " --> pdb=" O SER P 200 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LYS P 205 " --> pdb=" O ARG P 201 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS P 206 " --> pdb=" O LYS P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 232 Processing helix chain 'P' and resid 233 through 251 Processing helix chain 'P' and resid 253 through 271 removed outlier: 3.591A pdb=" N TRP P 257 " --> pdb=" O ASP P 253 " (cutoff:3.500A) Proline residue: P 259 - end of helix removed outlier: 3.782A pdb=" N TYR P 266 " --> pdb=" O SER P 262 " (cutoff:3.500A) Processing helix chain 'P' and resid 274 through 281 Processing helix chain 'P' and resid 294 through 305 removed outlier: 4.394A pdb=" N THR P 304 " --> pdb=" O VAL P 300 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR P 305 " --> pdb=" O LYS P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 309 through 318 removed outlier: 4.278A pdb=" N ILE P 313 " --> pdb=" O MET P 309 " (cutoff:3.500A) Processing helix chain 'P' and resid 333 through 336 removed outlier: 3.720A pdb=" N HIS P 336 " --> pdb=" O ALA P 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 333 through 336' Processing helix chain 'P' and resid 337 through 357 Processing helix chain 'P' and resid 362 through 370 Processing helix chain 'P' and resid 372 through 386 Processing helix chain 'P' and resid 409 through 411 No H-bonds generated for 'chain 'P' and resid 409 through 411' Processing helix chain 'P' and resid 412 through 441 removed outlier: 3.620A pdb=" N GLU P 427 " --> pdb=" O LEU P 423 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU P 432 " --> pdb=" O THR P 428 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE P 433 " --> pdb=" O ILE P 429 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR P 434 " --> pdb=" O GLY P 430 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS P 435 " --> pdb=" O HIS P 431 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 18 Processing helix chain 'Q' and resid 19 through 33 removed outlier: 3.607A pdb=" N VAL Q 26 " --> pdb=" O GLU Q 22 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER Q 29 " --> pdb=" O GLN Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 69 Processing helix chain 'Q' and resid 70 through 87 removed outlier: 3.589A pdb=" N GLU Q 76 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) Proline residue: Q 79 - end of helix Processing helix chain 'Q' and resid 89 through 106 removed outlier: 3.702A pdb=" N LYS Q 98 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 110 through 127 Processing helix chain 'Q' and resid 133 through 148 Processing helix chain 'Q' and resid 150 through 166 Processing helix chain 'Q' and resid 170 through 188 Processing helix chain 'Q' and resid 190 through 208 Processing helix chain 'Q' and resid 211 through 229 removed outlier: 3.919A pdb=" N GLU Q 228 " --> pdb=" O ILE Q 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 231 through 250 Processing helix chain 'Q' and resid 256 through 273 Processing helix chain 'Q' and resid 274 through 284 removed outlier: 3.655A pdb=" N VAL Q 278 " --> pdb=" O LEU Q 274 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 309 Processing helix chain 'Q' and resid 310 through 322 Processing helix chain 'Q' and resid 328 through 352 removed outlier: 4.438A pdb=" N ASN Q 336 " --> pdb=" O ARG Q 332 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA Q 337 " --> pdb=" O SER Q 333 " (cutoff:3.500A) Processing helix chain 'Q' and resid 359 through 367 Processing helix chain 'Q' and resid 369 through 383 removed outlier: 4.263A pdb=" N LYS Q 376 " --> pdb=" O GLN Q 372 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE Q 381 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) Processing helix chain 'Q' and resid 408 through 431 removed outlier: 3.559A pdb=" N GLU Q 414 " --> pdb=" O ASP Q 410 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU Q 415 " --> pdb=" O SER Q 411 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASN Q 420 " --> pdb=" O VAL Q 416 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS Q 421 " --> pdb=" O GLY Q 417 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL Q 422 " --> pdb=" O GLN Q 418 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 35 Processing helix chain 'R' and resid 39 through 57 removed outlier: 3.972A pdb=" N ALA R 46 " --> pdb=" O GLN R 42 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE R 49 " --> pdb=" O GLU R 45 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS R 55 " --> pdb=" O LEU R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 70 removed outlier: 3.660A pdb=" N TYR R 70 " --> pdb=" O LEU R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 123 removed outlier: 3.609A pdb=" N TYR R 99 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 145 removed outlier: 3.640A pdb=" N ALA R 133 " --> pdb=" O GLU R 129 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR R 141 " --> pdb=" O LEU R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 159 Processing helix chain 'R' and resid 163 through 181 removed outlier: 3.699A pdb=" N TYR R 181 " --> pdb=" O LEU R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 198 removed outlier: 4.608A pdb=" N ILE R 198 " --> pdb=" O VAL R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 218 Processing helix chain 'R' and resid 225 through 234 removed outlier: 3.880A pdb=" N LYS R 229 " --> pdb=" O LYS R 225 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU R 230 " --> pdb=" O GLU R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 261 removed outlier: 3.912A pdb=" N ILE R 249 " --> pdb=" O SER R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 269 Processing helix chain 'R' and resid 273 through 280 Processing helix chain 'R' and resid 290 through 298 Processing helix chain 'R' and resid 303 through 316 removed outlier: 4.555A pdb=" N LEU R 309 " --> pdb=" O PHE R 305 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN R 314 " --> pdb=" O GLU R 310 " (cutoff:3.500A) Processing helix chain 'R' and resid 319 through 326 removed outlier: 3.758A pdb=" N ALA R 326 " --> pdb=" O LEU R 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 344 removed outlier: 4.128A pdb=" N VAL R 330 " --> pdb=" O ALA R 326 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG R 331 " --> pdb=" O ASP R 327 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU R 332 " --> pdb=" O PHE R 328 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET R 333 " --> pdb=" O PHE R 329 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG R 334 " --> pdb=" O VAL R 330 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR R 338 " --> pdb=" O ARG R 334 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA R 339 " --> pdb=" O ARG R 335 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN R 340 " --> pdb=" O LYS R 336 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 355 Processing helix chain 'R' and resid 360 through 370 Processing helix chain 'R' and resid 370 through 375 removed outlier: 3.533A pdb=" N ASN R 374 " --> pdb=" O LYS R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 398 through 421 removed outlier: 3.826A pdb=" N LEU R 403 " --> pdb=" O GLN R 399 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL R 404 " --> pdb=" O TYR R 400 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LYS R 405 " --> pdb=" O HIS R 401 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN R 406 " --> pdb=" O LEU R 402 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY R 407 " --> pdb=" O LEU R 403 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL R 421 " --> pdb=" O TYR R 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 21 Processing helix chain 'S' and resid 25 through 42 removed outlier: 4.099A pdb=" N ASN S 39 " --> pdb=" O LEU S 35 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU S 40 " --> pdb=" O LYS S 36 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE S 41 " --> pdb=" O VAL S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 50 through 55 Processing helix chain 'S' and resid 58 through 69 removed outlier: 3.879A pdb=" N GLU S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 130 through 143 Processing helix chain 'S' and resid 151 through 164 removed outlier: 4.146A pdb=" N LEU S 155 " --> pdb=" O GLU S 151 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU S 157 " --> pdb=" O GLU S 153 " (cutoff:3.500A) Processing helix chain 'S' and resid 180 through 192 removed outlier: 3.775A pdb=" N ILE S 187 " --> pdb=" O LEU S 183 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR S 188 " --> pdb=" O TRP S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 204 through 221 Processing helix chain 'S' and resid 231 through 244 Processing helix chain 'S' and resid 246 through 248 No H-bonds generated for 'chain 'S' and resid 246 through 248' Processing helix chain 'S' and resid 249 through 257 Processing helix chain 'S' and resid 265 through 284 removed outlier: 3.857A pdb=" N ILE S 282 " --> pdb=" O LYS S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 286 through 295 Processing helix chain 'S' and resid 308 through 324 removed outlier: 3.685A pdb=" N GLN S 321 " --> pdb=" O HIS S 317 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU S 322 " --> pdb=" O CYS S 318 " (cutoff:3.500A) Processing helix chain 'S' and resid 329 through 334 removed outlier: 4.124A pdb=" N PHE S 333 " --> pdb=" O GLU S 329 " (cutoff:3.500A) Processing helix chain 'S' and resid 343 through 355 removed outlier: 3.886A pdb=" N LEU S 354 " --> pdb=" O LYS S 350 " (cutoff:3.500A) Processing helix chain 'S' and resid 356 through 375 removed outlier: 5.987A pdb=" N GLN S 369 " --> pdb=" O THR S 365 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU S 370 " --> pdb=" O LYS S 366 " (cutoff:3.500A) Processing helix chain 'S' and resid 382 through 394 Processing helix chain 'S' and resid 404 through 413 Processing helix chain 'S' and resid 417 through 429 removed outlier: 3.861A pdb=" N TYR S 421 " --> pdb=" O GLN S 417 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP S 429 " --> pdb=" O ARG S 425 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 468 Processing helix chain 'S' and resid 469 through 487 removed outlier: 3.759A pdb=" N LEU S 476 " --> pdb=" O HIS S 472 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG S 480 " --> pdb=" O LEU S 476 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TYR S 481 " --> pdb=" O VAL S 477 " (cutoff:3.500A) Proline residue: S 482 - end of helix removed outlier: 3.794A pdb=" N THR S 487 " --> pdb=" O GLU S 483 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 17 Processing helix chain 'T' and resid 19 through 37 removed outlier: 4.204A pdb=" N LYS T 25 " --> pdb=" O ALA T 21 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU T 26 " --> pdb=" O ALA T 22 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU T 27 " --> pdb=" O CYS T 23 " (cutoff:3.500A) Proline residue: T 28 - end of helix Processing helix chain 'T' and resid 54 through 72 removed outlier: 3.968A pdb=" N THR T 58 " --> pdb=" O ASP T 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 90 Proline residue: T 87 - end of helix Processing helix chain 'T' and resid 100 through 116 removed outlier: 3.783A pdb=" N LYS T 104 " --> pdb=" O ASP T 100 " (cutoff:3.500A) Processing helix chain 'T' and resid 118 through 129 Processing helix chain 'T' and resid 132 through 137 Processing helix chain 'T' and resid 139 through 155 Proline residue: T 145 - end of helix removed outlier: 3.868A pdb=" N GLU T 154 " --> pdb=" O ARG T 150 " (cutoff:3.500A) Processing helix chain 'T' and resid 157 through 166 removed outlier: 3.527A pdb=" N GLN T 165 " --> pdb=" O TRP T 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 174 through 197 removed outlier: 3.893A pdb=" N THR T 178 " --> pdb=" O PHE T 174 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP T 179 " --> pdb=" O ASP T 175 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE T 180 " --> pdb=" O SER T 176 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU T 188 " --> pdb=" O ALA T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 210 Processing helix chain 'T' and resid 213 through 224 removed outlier: 3.690A pdb=" N THR T 217 " --> pdb=" O ASN T 213 " (cutoff:3.500A) Processing helix chain 'T' and resid 253 through 270 removed outlier: 3.572A pdb=" N THR T 257 " --> pdb=" O GLU T 253 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 25 Processing helix chain 'U' and resid 70 through 84 Processing helix chain 'U' and resid 85 through 87 No H-bonds generated for 'chain 'U' and resid 85 through 87' Processing helix chain 'U' and resid 101 through 114 removed outlier: 3.832A pdb=" N LYS U 105 " --> pdb=" O ALA U 101 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE U 110 " --> pdb=" O ILE U 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS U 112 " --> pdb=" O GLU U 108 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR U 113 " --> pdb=" O LEU U 109 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 173 removed outlier: 3.637A pdb=" N GLY U 170 " --> pdb=" O ALA U 166 " (cutoff:3.500A) Processing helix chain 'U' and resid 189 through 195 removed outlier: 3.553A pdb=" N GLN U 193 " --> pdb=" O ARG U 189 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS U 195 " --> pdb=" O THR U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 196 through 214 removed outlier: 4.691A pdb=" N LEU U 200 " --> pdb=" O SER U 196 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS U 205 " --> pdb=" O GLN U 201 " (cutoff:3.500A) Processing helix chain 'U' and resid 224 through 233 removed outlier: 4.512A pdb=" N VAL U 232 " --> pdb=" O LYS U 228 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE U 233 " --> pdb=" O LEU U 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 264 through 284 removed outlier: 3.906A pdb=" N LYS U 268 " --> pdb=" O ALA U 264 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR U 269 " --> pdb=" O LEU U 265 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL U 275 " --> pdb=" O ASP U 271 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASN U 280 " --> pdb=" O ILE U 276 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU U 281 " --> pdb=" O TYR U 277 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL U 282 " --> pdb=" O ILE U 278 " (cutoff:3.500A) Processing helix chain 'U' and resid 284 through 291 removed outlier: 3.689A pdb=" N LEU U 291 " --> pdb=" O ALA U 287 " (cutoff:3.500A) Processing helix chain 'U' and resid 292 through 295 removed outlier: 3.795A pdb=" N LYS U 295 " --> pdb=" O ILE U 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 292 through 295' Processing helix chain 'U' and resid 298 through 304 removed outlier: 3.531A pdb=" N GLN U 304 " --> pdb=" O LYS U 300 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 45 Processing helix chain 'V' and resid 84 through 99 removed outlier: 4.217A pdb=" N GLN V 88 " --> pdb=" O ASP V 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 131 removed outlier: 3.575A pdb=" N GLN V 131 " --> pdb=" O LYS V 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 142 through 147 Processing helix chain 'V' and resid 185 through 190 removed outlier: 3.539A pdb=" N ILE V 189 " --> pdb=" O ILE V 185 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 215 removed outlier: 3.605A pdb=" N THR V 210 " --> pdb=" O THR V 206 " (cutoff:3.500A) Processing helix chain 'V' and resid 231 through 236 Processing helix chain 'V' and resid 243 through 245 No H-bonds generated for 'chain 'V' and resid 243 through 245' Processing helix chain 'V' and resid 246 through 267 removed outlier: 3.600A pdb=" N GLU V 258 " --> pdb=" O ARG V 254 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS V 259 " --> pdb=" O ILE V 255 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU V 260 " --> pdb=" O GLU V 256 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU V 261 " --> pdb=" O GLU V 257 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR V 262 " --> pdb=" O GLU V 258 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS V 267 " --> pdb=" O GLU V 263 " (cutoff:3.500A) Processing helix chain 'V' and resid 278 through 285 removed outlier: 3.908A pdb=" N GLU V 282 " --> pdb=" O LYS V 278 " (cutoff:3.500A) Processing helix chain 'V' and resid 285 through 290 removed outlier: 3.991A pdb=" N GLU V 289 " --> pdb=" O ASP V 285 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN V 290 " --> pdb=" O GLU V 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 285 through 290' Processing helix chain 'V' and resid 292 through 297 Processing helix chain 'W' and resid 24 through 44 removed outlier: 3.726A pdb=" N ASP W 31 " --> pdb=" O GLU W 27 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER W 32 " --> pdb=" O ALA W 28 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 75 removed outlier: 4.076A pdb=" N ILE W 72 " --> pdb=" O GLU W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 100 Processing helix chain 'W' and resid 121 through 136 Processing helix chain 'W' and resid 152 through 162 Processing helix chain 'W' and resid 164 through 168 Processing helix chain 'W' and resid 180 through 188 removed outlier: 4.121A pdb=" N SER W 187 " --> pdb=" O GLU W 183 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER W 188 " --> pdb=" O ASN W 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 131 removed outlier: 4.289A pdb=" N ASN X 123 " --> pdb=" O LYS X 119 " (cutoff:3.500A) Processing helix chain 'Y' and resid 71 through 89 removed outlier: 3.505A pdb=" N ARG Y 83 " --> pdb=" O ALA Y 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 112 through 125 removed outlier: 4.148A pdb=" N SER Z 120 " --> pdb=" O ALA Z 116 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 140 Processing helix chain 'Z' and resid 151 through 170 removed outlier: 3.751A pdb=" N ARG Z 155 " --> pdb=" O HIS Z 151 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU Z 159 " --> pdb=" O ARG Z 155 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE Z 161 " --> pdb=" O LEU Z 157 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL Z 164 " --> pdb=" O GLU Z 160 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP Z 167 " --> pdb=" O GLU Z 163 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN Z 168 " --> pdb=" O VAL Z 164 " (cutoff:3.500A) Processing helix chain 'Z' and resid 171 through 174 Processing helix chain 'Z' and resid 197 through 213 Proline residue: Z 209 - end of helix Processing helix chain 'Z' and resid 216 through 228 removed outlier: 5.083A pdb=" N ASP Z 222 " --> pdb=" O GLU Z 218 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU Z 223 " --> pdb=" O ASP Z 219 " (cutoff:3.500A) Processing helix chain 'Z' and resid 231 through 237 Processing helix chain 'Z' and resid 242 through 256 removed outlier: 3.561A pdb=" N TYR Z 248 " --> pdb=" O ARG Z 244 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET Z 249 " --> pdb=" O VAL Z 245 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS Z 252 " --> pdb=" O TYR Z 248 " (cutoff:3.500A) Proline residue: Z 254 - end of helix Processing helix chain 'Z' and resid 262 through 268 removed outlier: 3.578A pdb=" N LYS Z 266 " --> pdb=" O VAL Z 262 " (cutoff:3.500A) Processing helix chain 'Z' and resid 268 through 276 Processing helix chain 'Z' and resid 278 through 286 removed outlier: 3.866A pdb=" N ALA Z 283 " --> pdb=" O THR Z 279 " (cutoff:3.500A) Processing helix chain 'Z' and resid 290 through 301 Processing helix chain 'Z' and resid 303 through 314 Processing helix chain 'Z' and resid 317 through 323 removed outlier: 3.520A pdb=" N PHE Z 321 " --> pdb=" O GLN Z 317 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR Z 323 " --> pdb=" O THR Z 319 " (cutoff:3.500A) Processing helix chain 'Z' and resid 342 through 348 Processing helix chain 'Z' and resid 352 through 365 removed outlier: 3.564A pdb=" N ASP Z 363 " --> pdb=" O LYS Z 359 " (cutoff:3.500A) Processing helix chain 'Z' and resid 376 through 391 removed outlier: 4.044A pdb=" N ALA Z 382 " --> pdb=" O GLN Z 378 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE Z 385 " --> pdb=" O LEU Z 381 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY Z 388 " --> pdb=" O SER Z 384 " (cutoff:3.500A) Processing helix chain 'Z' and resid 396 through 403 removed outlier: 3.945A pdb=" N ILE Z 400 " --> pdb=" O ASN Z 396 " (cutoff:3.500A) Processing helix chain 'Z' and resid 404 through 410 Processing helix chain 'Z' and resid 412 through 426 removed outlier: 3.799A pdb=" N THR Z 416 " --> pdb=" O GLY Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 432 through 440 removed outlier: 3.866A pdb=" N LEU Z 436 " --> pdb=" O GLY Z 432 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS Z 438 " --> pdb=" O GLN Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 444 through 459 removed outlier: 3.763A pdb=" N ALA Z 451 " --> pdb=" O VAL Z 447 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY Z 456 " --> pdb=" O LEU Z 452 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA Z 459 " --> pdb=" O ILE Z 455 " (cutoff:3.500A) Processing helix chain 'Z' and resid 469 through 479 removed outlier: 4.035A pdb=" N GLN Z 475 " --> pdb=" O LEU Z 471 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP Z 476 " --> pdb=" O LEU Z 472 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR Z 479 " --> pdb=" O GLN Z 475 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 501 removed outlier: 5.088A pdb=" N GLY Z 499 " --> pdb=" O ILE Z 495 " (cutoff:3.500A) Processing helix chain 'Z' and resid 502 through 516 removed outlier: 4.174A pdb=" N LEU Z 506 " --> pdb=" O ASN Z 502 " (cutoff:3.500A) Proline residue: Z 511 - end of helix Processing helix chain 'Z' and resid 522 through 532 Processing helix chain 'Z' and resid 539 through 548 Processing helix chain 'Z' and resid 559 through 574 removed outlier: 3.565A pdb=" N VAL Z 563 " --> pdb=" O LYS Z 559 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU Z 566 " --> pdb=" O TRP Z 562 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA Z 569 " --> pdb=" O PHE Z 565 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU Z 573 " --> pdb=" O ALA Z 569 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR Z 574 " --> pdb=" O LEU Z 570 " (cutoff:3.500A) Processing helix chain 'Z' and resid 577 through 588 removed outlier: 3.672A pdb=" N GLN Z 580 " --> pdb=" O GLN Z 577 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP Z 582 " --> pdb=" O GLU Z 579 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASP Z 583 " --> pdb=" O GLN Z 580 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU Z 585 " --> pdb=" O ASP Z 582 " (cutoff:3.500A) Processing helix chain 'Z' and resid 598 through 608 removed outlier: 3.526A pdb=" N LEU Z 602 " --> pdb=" O ALA Z 598 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLY Z 604 " --> pdb=" O GLU Z 600 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N CYS Z 606 " --> pdb=" O LEU Z 602 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA Z 607 " --> pdb=" O VAL Z 603 " (cutoff:3.500A) Processing helix chain 'Z' and resid 614 through 625 removed outlier: 3.587A pdb=" N GLN Z 618 " --> pdb=" O VAL Z 614 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU Z 620 " --> pdb=" O LEU Z 616 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS Z 622 " --> pdb=" O GLN Z 618 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG Z 623 " --> pdb=" O ASP Z 619 " (cutoff:3.500A) Processing helix chain 'Z' and resid 737 through 750 removed outlier: 4.032A pdb=" N ILE Z 743 " --> pdb=" O ALA Z 739 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA Z 744 " --> pdb=" O VAL Z 740 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU Z 745 " --> pdb=" O LEU Z 741 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE Z 746 " --> pdb=" O GLY Z 742 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU Z 748 " --> pdb=" O ALA Z 744 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY Z 749 " --> pdb=" O LEU Z 745 " (cutoff:3.500A) Processing helix chain 'Z' and resid 756 through 767 removed outlier: 3.673A pdb=" N HIS Z 760 " --> pdb=" O MET Z 756 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLY Z 762 " --> pdb=" O LEU Z 758 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS Z 763 " --> pdb=" O ARG Z 759 " (cutoff:3.500A) Processing helix chain 'Z' and resid 769 through 785 Proline residue: Z 777 - end of helix removed outlier: 3.631A pdb=" N GLY Z 781 " --> pdb=" O PRO Z 777 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE Z 782 " --> pdb=" O LEU Z 778 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL Z 783 " --> pdb=" O ALA Z 779 " (cutoff:3.500A) Processing helix chain 'Z' and resid 791 through 801 removed outlier: 3.751A pdb=" N THR Z 797 " --> pdb=" O PHE Z 793 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N HIS Z 801 " --> pdb=" O THR Z 797 " (cutoff:3.500A) Processing helix chain 'Z' and resid 804 through 819 removed outlier: 3.762A pdb=" N SER Z 808 " --> pdb=" O ASP Z 804 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET Z 815 " --> pdb=" O SER Z 811 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY Z 816 " --> pdb=" O ILE Z 812 " (cutoff:3.500A) Processing helix chain 'Z' and resid 824 through 826 No H-bonds generated for 'chain 'Z' and resid 824 through 826' Processing helix chain 'Z' and resid 827 through 837 removed outlier: 3.667A pdb=" N LEU Z 831 " --> pdb=" O LEU Z 827 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG Z 832 " --> pdb=" O ALA Z 828 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLN Z 833 " --> pdb=" O GLN Z 829 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU Z 834 " --> pdb=" O LEU Z 830 " (cutoff:3.500A) Processing helix chain 'Z' and resid 841 through 856 Processing helix chain 'Z' and resid 874 through 887 removed outlier: 3.577A pdb=" N LEU Z 878 " --> pdb=" O ASN Z 874 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU Z 882 " --> pdb=" O LEU Z 878 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR Z 883 " --> pdb=" O ALA Z 879 " (cutoff:3.500A) Processing helix chain 'Z' and resid 897 through 907 removed outlier: 3.644A pdb=" N LEU Z 900 " --> pdb=" O HIS Z 897 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR Z 902 " --> pdb=" O GLN Z 899 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET Z 903 " --> pdb=" O LEU Z 900 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU Z 904 " --> pdb=" O PHE Z 901 " (cutoff:3.500A) Processing helix chain 'Z' and resid 986 through 990 Processing helix chain 'a' and resid 11 through 16 removed outlier: 4.038A pdb=" N HIS a 15 " --> pdb=" O GLY a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 38 removed outlier: 3.979A pdb=" N ASN a 36 " --> pdb=" O PHE a 32 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR a 38 " --> pdb=" O ALA a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 69 Processing helix chain 'a' and resid 86 through 109 removed outlier: 3.510A pdb=" N ALA a 94 " --> pdb=" O ALA a 90 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU a 95 " --> pdb=" O ARG a 91 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU a 100 " --> pdb=" O ARG a 96 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA a 102 " --> pdb=" O LYS a 98 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 131 removed outlier: 3.701A pdb=" N SER a 125 " --> pdb=" O MET a 121 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN a 126 " --> pdb=" O ALA a 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 174 through 190 Processing helix chain 'a' and resid 198 through 215 Processing helix chain 'a' and resid 237 through 252 Processing helix chain 'b' and resid 18 through 31 removed outlier: 3.663A pdb=" N THR b 26 " --> pdb=" O ASP b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 58 through 61 Processing helix chain 'b' and resid 78 through 97 removed outlier: 4.215A pdb=" N LEU b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL b 86 " --> pdb=" O TYR b 82 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP b 87 " --> pdb=" O ARG b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 97 through 102 Processing helix chain 'b' and resid 106 through 124 removed outlier: 3.620A pdb=" N VAL b 114 " --> pdb=" O LEU b 110 " (cutoff:3.500A) Processing helix chain 'b' and resid 167 through 179 Processing helix chain 'b' and resid 184 through 200 Processing helix chain 'b' and resid 205 through 207 No H-bonds generated for 'chain 'b' and resid 205 through 207' Processing helix chain 'b' and resid 218 through 222 Processing helix chain 'b' and resid 239 through 249 Processing helix chain 'c' and resid 2 through 7 Processing helix chain 'c' and resid 19 through 31 removed outlier: 3.991A pdb=" N HIS c 31 " --> pdb=" O GLU c 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 103 removed outlier: 3.789A pdb=" N GLU c 85 " --> pdb=" O THR c 81 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE c 86 " --> pdb=" O ALA c 82 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU c 87 " --> pdb=" O ASP c 83 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 125 removed outlier: 3.886A pdb=" N TYR c 122 " --> pdb=" O ILE c 118 " (cutoff:3.500A) Processing helix chain 'c' and resid 168 through 180 Processing helix chain 'c' and resid 185 through 201 Processing helix chain 'c' and resid 207 through 209 No H-bonds generated for 'chain 'c' and resid 207 through 209' Processing helix chain 'c' and resid 231 through 242 Processing helix chain 'd' and resid 17 through 30 removed outlier: 3.585A pdb=" N GLU d 25 " --> pdb=" O GLU d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 78 through 101 removed outlier: 3.504A pdb=" N ARG d 83 " --> pdb=" O ASN d 79 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE d 84 " --> pdb=" O ALA d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 123 removed outlier: 3.516A pdb=" N GLY d 115 " --> pdb=" O ARG d 111 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL d 116 " --> pdb=" O TYR d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 167 through 179 Processing helix chain 'd' and resid 187 through 204 removed outlier: 3.958A pdb=" N VAL d 202 " --> pdb=" O SER d 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 225 through 242 removed outlier: 3.510A pdb=" N GLU d 239 " --> pdb=" O GLN d 235 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 34 removed outlier: 3.638A pdb=" N LYS e 32 " --> pdb=" O LEU e 28 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU e 33 " --> pdb=" O GLU e 29 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY e 34 " --> pdb=" O ALA e 30 " (cutoff:3.500A) Processing helix chain 'e' and resid 60 through 64 Processing helix chain 'e' and resid 81 through 104 removed outlier: 4.418A pdb=" N ALA e 85 " --> pdb=" O LEU e 81 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG e 86 " --> pdb=" O THR e 82 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N SER e 87 " --> pdb=" O ALA e 83 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET e 88 " --> pdb=" O ASP e 84 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 Processing helix chain 'e' and resid 119 through 123 removed outlier: 4.167A pdb=" N PHE e 123 " --> pdb=" O ALA e 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 175 through 187 Processing helix chain 'e' and resid 192 through 208 Processing helix chain 'e' and resid 232 through 248 Processing helix chain 'f' and resid 3 through 7 Processing helix chain 'f' and resid 19 through 32 removed outlier: 3.875A pdb=" N LYS f 30 " --> pdb=" O LEU f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 77 through 99 removed outlier: 3.830A pdb=" N ALA f 81 " --> pdb=" O LEU f 77 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 122 removed outlier: 3.656A pdb=" N LEU f 112 " --> pdb=" O ALA f 108 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS f 113 " --> pdb=" O GLY f 109 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP f 114 " --> pdb=" O HIS f 110 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN f 119 " --> pdb=" O LYS f 115 " (cutoff:3.500A) Processing helix chain 'f' and resid 165 through 182 removed outlier: 5.713A pdb=" N ASP f 177 " --> pdb=" O GLU f 173 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR f 178 " --> pdb=" O ARG f 174 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE f 179 " --> pdb=" O THR f 175 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE f 180 " --> pdb=" O LEU f 176 " (cutoff:3.500A) Processing helix chain 'f' and resid 185 through 201 Processing helix chain 'f' and resid 227 through 232 removed outlier: 3.652A pdb=" N LYS f 232 " --> pdb=" O GLU f 228 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 34 Processing helix chain 'g' and resid 81 through 104 removed outlier: 3.902A pdb=" N ALA g 97 " --> pdb=" O ARG g 93 " (cutoff:3.500A) Processing helix chain 'g' and resid 108 through 126 removed outlier: 3.597A pdb=" N LEU g 116 " --> pdb=" O PHE g 112 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR g 126 " --> pdb=" O ALA g 122 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 183 removed outlier: 3.577A pdb=" N GLU g 175 " --> pdb=" O SER g 171 " (cutoff:3.500A) Processing helix chain 'g' and resid 188 through 207 removed outlier: 3.677A pdb=" N ASP g 206 " --> pdb=" O LEU g 202 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN g 207 " --> pdb=" O ALA g 203 " (cutoff:3.500A) Processing helix chain 'g' and resid 232 through 247 removed outlier: 3.589A pdb=" N LEU g 236 " --> pdb=" O LYS g 232 " (cutoff:3.500A) Processing helix chain 'h' and resid 67 through 90 Processing helix chain 'h' and resid 93 through 109 Processing helix chain 'h' and resid 149 through 161 removed outlier: 4.815A pdb=" N GLY h 155 " --> pdb=" O THR h 151 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYR h 156 " --> pdb=" O PHE h 152 " (cutoff:3.500A) Processing helix chain 'h' and resid 166 through 185 Processing helix chain 'h' and resid 208 through 213 Processing helix chain 'i' and resid 77 through 100 Processing helix chain 'i' and resid 104 through 119 removed outlier: 4.287A pdb=" N ALA i 108 " --> pdb=" O ARG i 104 " (cutoff:3.500A) Processing helix chain 'i' and resid 159 through 171 Processing helix chain 'i' and resid 176 through 195 Processing helix chain 'j' and resid 3 through 9 removed outlier: 3.724A pdb=" N ASN j 8 " --> pdb=" O PRO j 4 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY j 9 " --> pdb=" O SER j 5 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 79 removed outlier: 3.594A pdb=" N GLU j 65 " --> pdb=" O THR j 61 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 97 Processing helix chain 'j' and resid 142 through 154 removed outlier: 3.641A pdb=" N SER j 152 " --> pdb=" O GLY j 148 " (cutoff:3.500A) Processing helix chain 'j' and resid 159 through 177 Processing helix chain 'k' and resid 49 through 72 removed outlier: 3.526A pdb=" N ASN k 63 " --> pdb=" O TYR k 59 " (cutoff:3.500A) Processing helix chain 'k' and resid 76 through 94 removed outlier: 3.522A pdb=" N GLU k 87 " --> pdb=" O PHE k 83 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU k 88 " --> pdb=" O VAL k 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 134 through 148 removed outlier: 4.533A pdb=" N PHE k 138 " --> pdb=" O GLY k 134 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR k 139 " --> pdb=" O TYR k 135 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR k 140 " --> pdb=" O SER k 136 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER k 142 " --> pdb=" O PHE k 138 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU k 143 " --> pdb=" O TYR k 139 " (cutoff:3.500A) Processing helix chain 'k' and resid 153 through 172 removed outlier: 3.749A pdb=" N GLY k 157 " --> pdb=" O THR k 153 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU k 158 " --> pdb=" O THR k 154 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP k 159 " --> pdb=" O GLU k 155 " (cutoff:3.500A) Processing helix chain 'l' and resid 123 through 146 Processing helix chain 'l' and resid 150 through 166 removed outlier: 3.541A pdb=" N TYR l 165 " --> pdb=" O LEU l 161 " (cutoff:3.500A) Processing helix chain 'l' and resid 207 through 219 removed outlier: 3.533A pdb=" N ALA l 211 " --> pdb=" O GLY l 207 " (cutoff:3.500A) Processing helix chain 'l' and resid 224 through 243 removed outlier: 3.590A pdb=" N ALA l 239 " --> pdb=" O SER l 235 " (cutoff:3.500A) Processing helix chain 'l' and resid 268 through 280 Processing sheet with id= A, first strand: chain '1' and resid 155 through 159 removed outlier: 6.450A pdb=" N THR 1 30 " --> pdb=" O ASP 1 45 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY 1 44 " --> pdb=" O GLU 1 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 49 through 50 Processing sheet with id= C, first strand: chain '1' and resid 63 through 64 removed outlier: 3.509A pdb=" N THR 1 128 " --> pdb=" O PHE 1 144 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL 1 141 " --> pdb=" O GLU 1 153 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER 1 143 " --> pdb=" O GLU 1 151 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU 1 151 " --> pdb=" O SER 1 143 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 66 through 69 removed outlier: 4.634A pdb=" N LEU 2 67 " --> pdb=" O TYR 2 63 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR 2 63 " --> pdb=" O LEU 2 67 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '2' and resid 66 through 69 removed outlier: 4.634A pdb=" N LEU 2 67 " --> pdb=" O TYR 2 63 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR 2 63 " --> pdb=" O LEU 2 67 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '2' and resid 174 through 176 removed outlier: 4.561A pdb=" N PHE 2 228 " --> pdb=" O ASN 2 244 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 143 through 145 Processing sheet with id= H, first strand: chain '3' and resid 39 through 41 removed outlier: 6.498A pdb=" N THR 3 39 " --> pdb=" O ALA 3 46 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 53 through 55 removed outlier: 3.988A pdb=" N VAL 3 129 " --> pdb=" O LEU 3 141 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '4' and resid 153 through 157 removed outlier: 6.057A pdb=" N THR 4 31 " --> pdb=" O ASP 4 46 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL 4 202 " --> pdb=" O ASN 4 218 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA 4 213 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '4' and resid 49 through 51 removed outlier: 5.265A pdb=" N GLN 4 51 " --> pdb=" O VAL 4 55 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL 4 55 " --> pdb=" O GLN 4 51 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '4' and resid 63 through 67 removed outlier: 5.919A pdb=" N ILE 4 70 " --> pdb=" O ILE 4 66 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 241 through 247 removed outlier: 3.625A pdb=" N VAL 5 195 " --> pdb=" O VAL 4 247 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA 5 185 " --> pdb=" O LEU 5 200 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE 5 11 " --> pdb=" O ASP 5 26 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '5' and resid 30 through 31 Processing sheet with id= O, first strand: chain '5' and resid 43 through 46 Processing sheet with id= P, first strand: chain '6' and resid 130 through 132 removed outlier: 3.806A pdb=" N VAL 6 181 " --> pdb=" O VAL 6 192 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '6' and resid 22 through 23 Processing sheet with id= R, first strand: chain '6' and resid 36 through 39 removed outlier: 5.976A pdb=" N THR 6 42 " --> pdb=" O LEU 6 38 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '7' and resid 201 through 205 removed outlier: 3.691A pdb=" N VAL 7 91 " --> pdb=" O ASN 7 251 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN 7 251 " --> pdb=" O VAL 7 91 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL 7 250 " --> pdb=" O ASN 7 265 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN 7 265 " --> pdb=" O VAL 7 250 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU 7 252 " --> pdb=" O HIS 7 263 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '7' and resid 95 through 97 removed outlier: 6.070A pdb=" N ALA 7 95 " --> pdb=" O ALA 7 102 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '7' and resid 109 through 111 Processing sheet with id= V, first strand: chain '7' and resid 121 through 122 Processing sheet with id= W, first strand: chain '8' and resid 155 through 158 removed outlier: 3.597A pdb=" N GLY 8 44 " --> pdb=" O GLU 8 222 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '8' and resid 49 through 50 Processing sheet with id= Y, first strand: chain '8' and resid 63 through 64 removed outlier: 3.509A pdb=" N THR 8 128 " --> pdb=" O PHE 8 144 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL 8 141 " --> pdb=" O GLU 8 153 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER 8 143 " --> pdb=" O GLU 8 151 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU 8 151 " --> pdb=" O SER 8 143 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '9' and resid 66 through 69 removed outlier: 4.634A pdb=" N LEU 9 67 " --> pdb=" O TYR 9 63 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR 9 63 " --> pdb=" O LEU 9 67 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain '9' and resid 66 through 69 removed outlier: 4.634A pdb=" N LEU 9 67 " --> pdb=" O TYR 9 63 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR 9 63 " --> pdb=" O LEU 9 67 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain '9' and resid 174 through 176 removed outlier: 4.561A pdb=" N PHE 9 228 " --> pdb=" O ASN 9 244 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 168 through 171 Processing sheet with id= AD, first strand: chain 'A' and resid 64 through 65 removed outlier: 4.150A pdb=" N GLY G 159 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 72 through 73 removed outlier: 4.301A pdb=" N ILE A 154 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 156 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 165 " --> pdb=" O MET B 57 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= AG, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.158A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 162 through 165 removed outlier: 4.755A pdb=" N PHE C 213 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 66 through 68 removed outlier: 3.744A pdb=" N PHE C 135 " --> pdb=" O SER C 151 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'D' and resid 161 through 164 Processing sheet with id= AK, first strand: chain 'D' and resid 65 through 68 removed outlier: 5.075A pdb=" N LYS D 66 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU D 73 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 169 through 172 removed outlier: 4.331A pdb=" N LEU E 219 " --> pdb=" O TYR E 231 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 67 through 69 Processing sheet with id= AN, first strand: chain 'F' and resid 158 through 161 Processing sheet with id= AO, first strand: chain 'F' and resid 51 through 52 removed outlier: 3.615A pdb=" N ARG F 51 " --> pdb=" O GLN F 60 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'F' and resid 63 through 65 removed outlier: 3.913A pdb=" N LEU F 144 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 162 through 165 Processing sheet with id= AR, first strand: chain 'G' and resid 68 through 70 Processing sheet with id= AS, first strand: chain 'H' and resid 199 through 202 removed outlier: 6.517A pdb=" N CYS H 304 " --> pdb=" O LYS H 350 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N MET H 352 " --> pdb=" O CYS H 304 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE H 306 " --> pdb=" O MET H 352 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA H 354 " --> pdb=" O ILE H 306 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE H 308 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL H 375 " --> pdb=" O GLY H 245 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU H 247 " --> pdb=" O VAL H 375 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'I' and resid 118 through 121 removed outlier: 6.364A pdb=" N ILE I 119 " --> pdb=" O GLU I 110 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU I 148 " --> pdb=" O VAL I 157 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'I' and resid 172 through 175 removed outlier: 5.596A pdb=" N THR I 243 " --> pdb=" O ILE I 278 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE I 280 " --> pdb=" O THR I 243 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU I 245 " --> pdb=" O PHE I 280 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP I 282 " --> pdb=" O LEU I 245 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE I 247 " --> pdb=" O ASP I 282 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER I 277 " --> pdb=" O LYS I 323 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE I 325 " --> pdb=" O SER I 277 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL I 279 " --> pdb=" O ILE I 325 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA I 327 " --> pdb=" O VAL I 279 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE I 281 " --> pdb=" O ALA I 327 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY I 218 " --> pdb=" O ARG I 346 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE I 348 " --> pdb=" O GLY I 218 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE I 220 " --> pdb=" O ILE I 348 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 93 through 97 removed outlier: 5.478A pdb=" N LYS J 87 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL J 75 " --> pdb=" O LYS J 87 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG J 116 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU J 122 " --> pdb=" O ARG J 116 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'J' and resid 184 through 185 Processing sheet with id= AX, first strand: chain 'J' and resid 211 through 214 Processing sheet with id= AY, first strand: chain 'K' and resid 109 through 110 removed outlier: 6.984A pdb=" N SER K 136 " --> pdb=" O ILE K 149 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE K 149 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA K 138 " --> pdb=" O VAL K 147 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'K' and resid 109 through 110 Processing sheet with id= BA, first strand: chain 'K' and resid 314 through 318 removed outlier: 3.795A pdb=" N MET K 316 " --> pdb=" O VAL K 209 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU K 211 " --> pdb=" O MET K 316 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY K 208 " --> pdb=" O ARG K 336 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ILE K 338 " --> pdb=" O GLY K 208 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU K 210 " --> pdb=" O ILE K 338 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'L' and resid 155 through 158 removed outlier: 5.827A pdb=" N THR L 147 " --> pdb=" O MET L 156 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ILE L 158 " --> pdb=" O ARG L 145 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ARG L 145 " --> pdb=" O ILE L 158 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N THR M 126 " --> pdb=" O ILE L 105 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'L' and resid 171 through 174 removed outlier: 5.726A pdb=" N CYS L 276 " --> pdb=" O LYS L 322 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE L 324 " --> pdb=" O CYS L 276 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE L 278 " --> pdb=" O ILE L 324 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA L 326 " --> pdb=" O ILE L 278 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N MET L 280 " --> pdb=" O ALA L 326 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL L 218 " --> pdb=" O MET L 325 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU L 219 " --> pdb=" O VAL L 347 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'M' and resid 145 through 149 removed outlier: 3.919A pdb=" N LEU M 145 " --> pdb=" O LEU M 159 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASN M 149 " --> pdb=" O ILE M 155 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE M 155 " --> pdb=" O ASN M 149 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'M' and resid 172 through 173 removed outlier: 5.634A pdb=" N THR M 242 " --> pdb=" O ILE M 277 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE M 279 " --> pdb=" O THR M 242 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU M 244 " --> pdb=" O PHE M 279 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP M 281 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU M 246 " --> pdb=" O ASP M 281 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR M 276 " --> pdb=" O LYS M 322 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU M 324 " --> pdb=" O THR M 276 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE M 278 " --> pdb=" O LEU M 324 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA M 326 " --> pdb=" O ILE M 278 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE M 280 " --> pdb=" O ALA M 326 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'M' and resid 217 through 221 removed outlier: 7.901A pdb=" N GLY M 217 " --> pdb=" O ARG M 345 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N ILE M 347 " --> pdb=" O GLY M 217 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU M 219 " --> pdb=" O ILE M 347 " (cutoff:3.500A) No H-bonds generated for sheet with id= BF Processing sheet with id= BG, first strand: chain 'N' and resid 713 through 715 Processing sheet with id= BH, first strand: chain 'O' and resid 341 through 342 Processing sheet with id= BI, first strand: chain 'P' and resid 359 through 361 Processing sheet with id= BJ, first strand: chain 'Q' and resid 357 through 358 removed outlier: 10.071A pdb=" N GLY Q 388 " --> pdb=" O TYR R 345 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N THR R 347 " --> pdb=" O GLY Q 388 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU Q 390 " --> pdb=" O THR R 347 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'R' and resid 380 through 381 Processing sheet with id= BL, first strand: chain 'S' and resid 402 through 403 Processing sheet with id= BM, first strand: chain 'T' and resid 199 through 201 Processing sheet with id= BN, first strand: chain 'U' and resid 9 through 10 Processing sheet with id= BO, first strand: chain 'U' and resid 47 through 53 removed outlier: 5.982A pdb=" N VAL U 48 " --> pdb=" O ASP U 40 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP U 40 " --> pdb=" O VAL U 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY U 91 " --> pdb=" O ILE U 37 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY U 39 " --> pdb=" O LEU U 89 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU U 89 " --> pdb=" O GLY U 39 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'U' and resid 56 through 58 Processing sheet with id= BQ, first strand: chain 'U' and resid 122 through 123 Processing sheet with id= BR, first strand: chain 'U' and resid 137 through 138 Processing sheet with id= BS, first strand: chain 'V' and resid 26 through 27 removed outlier: 6.615A pdb=" N THR V 26 " --> pdb=" O VAL V 63 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL V 65 " --> pdb=" O THR V 26 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU V 54 " --> pdb=" O VAL V 66 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'V' and resid 107 through 108 removed outlier: 6.925A pdb=" N TRP V 107 " --> pdb=" O VAL V 139 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL V 141 " --> pdb=" O TRP V 107 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'W' and resid 4 through 5 removed outlier: 6.583A pdb=" N VAL W 9 " --> pdb=" O PHE W 113 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU W 8 " --> pdb=" O ILE W 52 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'W' and resid 4 through 5 removed outlier: 6.371A pdb=" N GLN W 108 " --> pdb=" O ALA W 138 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ASP W 140 " --> pdb=" O GLN W 108 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE W 110 " --> pdb=" O ASP W 140 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE W 142 " --> pdb=" O ILE W 110 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ALA W 112 " --> pdb=" O ILE W 142 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N HIS W 170 " --> pdb=" O VAL W 137 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL W 139 " --> pdb=" O HIS W 170 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU W 172 " --> pdb=" O VAL W 139 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ILE W 141 " --> pdb=" O LEU W 172 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'X' and resid 32 through 36 Processing sheet with id= BX, first strand: chain 'X' and resid 74 through 75 removed outlier: 4.204A pdb=" N MET X 74 " --> pdb=" O VAL X 90 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL X 90 " --> pdb=" O MET X 74 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'Z' and resid 915 through 916 Processing sheet with id= BZ, first strand: chain 'a' and resid 168 through 171 Processing sheet with id= CA, first strand: chain 'a' and resid 72 through 73 removed outlier: 4.301A pdb=" N ILE a 154 " --> pdb=" O TYR a 166 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS a 156 " --> pdb=" O VAL a 164 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY a 165 " --> pdb=" O MET b 57 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'b' and resid 161 through 164 Processing sheet with id= CC, first strand: chain 'b' and resid 64 through 68 removed outlier: 6.159A pdb=" N ILE b 71 " --> pdb=" O LEU b 67 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'b' and resid 224 through 225 removed outlier: 6.062A pdb=" N THR b 225 " --> pdb=" O TYR i 215 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ARG i 217 " --> pdb=" O THR b 225 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL i 202 " --> pdb=" O ASN i 218 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N THR i 31 " --> pdb=" O ASP i 46 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'c' and resid 162 through 165 removed outlier: 4.755A pdb=" N PHE c 213 " --> pdb=" O PHE c 230 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'c' and resid 66 through 68 removed outlier: 3.743A pdb=" N PHE c 135 " --> pdb=" O SER c 151 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'd' and resid 161 through 164 Processing sheet with id= CH, first strand: chain 'd' and resid 65 through 68 removed outlier: 5.075A pdb=" N LYS d 66 " --> pdb=" O LEU d 73 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU d 73 " --> pdb=" O LYS d 66 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'e' and resid 169 through 172 removed outlier: 4.331A pdb=" N LEU e 219 " --> pdb=" O TYR e 231 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'e' and resid 67 through 69 Processing sheet with id= CK, first strand: chain 'f' and resid 158 through 161 Processing sheet with id= CL, first strand: chain 'f' and resid 51 through 52 removed outlier: 3.615A pdb=" N ARG f 51 " --> pdb=" O GLN f 60 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'f' and resid 63 through 65 removed outlier: 3.912A pdb=" N LEU f 144 " --> pdb=" O LEU f 156 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'g' and resid 162 through 165 Processing sheet with id= CO, first strand: chain 'g' and resid 68 through 70 Processing sheet with id= CP, first strand: chain 'h' and resid 143 through 145 Processing sheet with id= CQ, first strand: chain 'h' and resid 39 through 41 removed outlier: 6.497A pdb=" N THR h 39 " --> pdb=" O ALA h 46 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'h' and resid 53 through 55 removed outlier: 3.987A pdb=" N VAL h 129 " --> pdb=" O LEU h 141 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'i' and resid 49 through 51 removed outlier: 5.265A pdb=" N GLN i 51 " --> pdb=" O VAL i 55 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL i 55 " --> pdb=" O GLN i 51 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'i' and resid 63 through 67 removed outlier: 5.918A pdb=" N ILE i 70 " --> pdb=" O ILE i 66 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'i' and resid 241 through 247 removed outlier: 3.696A pdb=" N VAL j 195 " --> pdb=" O VAL i 247 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA j 185 " --> pdb=" O LEU j 200 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE j 11 " --> pdb=" O ASP j 26 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'j' and resid 30 through 31 Processing sheet with id= CW, first strand: chain 'j' and resid 43 through 46 Processing sheet with id= CX, first strand: chain 'k' and resid 130 through 132 removed outlier: 3.806A pdb=" N VAL k 181 " --> pdb=" O VAL k 192 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'k' and resid 22 through 23 Processing sheet with id= CZ, first strand: chain 'k' and resid 36 through 39 removed outlier: 5.977A pdb=" N THR k 42 " --> pdb=" O LEU k 38 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'l' and resid 201 through 205 removed outlier: 3.691A pdb=" N VAL l 91 " --> pdb=" O ASN l 251 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN l 251 " --> pdb=" O VAL l 91 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL l 250 " --> pdb=" O ASN l 265 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN l 265 " --> pdb=" O VAL l 250 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU l 252 " --> pdb=" O HIS l 263 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'l' and resid 95 through 97 removed outlier: 6.070A pdb=" N ALA l 95 " --> pdb=" O ALA l 102 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'l' and resid 109 through 111 Processing sheet with id= DD, first strand: chain 'l' and resid 121 through 122 5505 hydrogen bonds defined for protein. 15864 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: 59.11 Time building geometry restraints manager: 41.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.52: 88631 1.52 - 1.84: 17435 1.84 - 2.17: 0 2.17 - 2.49: 0 2.49 - 2.82: 1 Bond restraints: 106067 Sorted by residual: bond pdb=" C ASP M 38 " pdb=" N LYS M 70 " ideal model delta sigma weight residual 1.332 2.820 -1.488 1.40e-02 5.10e+03 1.13e+04 bond pdb=" CA MET N 217 " pdb=" C MET N 217 " ideal model delta sigma weight residual 1.532 1.489 0.043 6.50e-03 2.37e+04 4.36e+01 bond pdb=" C PHE J 316 " pdb=" N PRO J 317 " ideal model delta sigma weight residual 1.329 1.404 -0.075 1.18e-02 7.18e+03 4.02e+01 bond pdb=" C LEU K 362 " pdb=" N ALA K 363 " ideal model delta sigma weight residual 1.331 1.204 0.127 2.07e-02 2.33e+03 3.76e+01 bond pdb=" CA ASP P 287 " pdb=" C ASP P 287 " ideal model delta sigma weight residual 1.532 1.478 0.055 9.60e-03 1.09e+04 3.25e+01 ... (remaining 106062 not shown) Histogram of bond angle deviations from ideal: 92.05 - 101.90: 293 101.90 - 111.75: 52591 111.75 - 121.60: 67012 121.60 - 131.46: 23296 131.46 - 141.31: 133 Bond angle restraints: 143325 Sorted by residual: angle pdb=" C ALA V 70 " pdb=" N MET V 71 " pdb=" CA MET V 71 " ideal model delta sigma weight residual 120.68 102.71 17.97 1.52e+00 4.33e-01 1.40e+02 angle pdb=" N ASP P 287 " pdb=" CA ASP P 287 " pdb=" C ASP P 287 " ideal model delta sigma weight residual 110.91 97.62 13.29 1.17e+00 7.31e-01 1.29e+02 angle pdb=" O ASP M 38 " pdb=" C ASP M 38 " pdb=" N LYS M 70 " ideal model delta sigma weight residual 122.59 137.19 -14.60 1.33e+00 5.65e-01 1.21e+02 angle pdb=" CA ASP M 38 " pdb=" C ASP M 38 " pdb=" N LYS M 70 " ideal model delta sigma weight residual 116.84 99.26 17.58 1.71e+00 3.42e-01 1.06e+02 angle pdb=" N GLU O 240 " pdb=" CA GLU O 240 " pdb=" C GLU O 240 " ideal model delta sigma weight residual 112.88 126.04 -13.16 1.29e+00 6.01e-01 1.04e+02 ... (remaining 143320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.78: 63495 26.78 - 53.56: 819 53.56 - 80.34: 120 80.34 - 107.12: 24 107.12 - 133.91: 1 Dihedral angle restraints: 64459 sinusoidal: 25774 harmonic: 38685 Sorted by residual: dihedral pdb=" CA SER S 203 " pdb=" C SER S 203 " pdb=" N ASP S 204 " pdb=" CA ASP S 204 " ideal model delta harmonic sigma weight residual -180.00 -46.09 -133.91 0 5.00e+00 4.00e-02 7.17e+02 dihedral pdb=" C ASP U 289 " pdb=" N ASP U 289 " pdb=" CA ASP U 289 " pdb=" CB ASP U 289 " ideal model delta harmonic sigma weight residual -122.60 -159.51 36.91 0 2.50e+00 1.60e-01 2.18e+02 dihedral pdb=" N ASP U 289 " pdb=" C ASP U 289 " pdb=" CA ASP U 289 " pdb=" CB ASP U 289 " ideal model delta harmonic sigma weight residual 122.80 157.63 -34.83 0 2.50e+00 1.60e-01 1.94e+02 ... (remaining 64456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 16337 0.321 - 0.642: 11 0.642 - 0.963: 0 0.963 - 1.284: 0 1.284 - 1.605: 1 Chirality restraints: 16349 Sorted by residual: chirality pdb=" CA ASP U 289 " pdb=" N ASP U 289 " pdb=" C ASP U 289 " pdb=" CB ASP U 289 " both_signs ideal model delta sigma weight residual False 2.51 0.91 1.61 2.00e-01 2.50e+01 6.44e+01 chirality pdb=" CB ILE O 341 " pdb=" CA ILE O 341 " pdb=" CG1 ILE O 341 " pdb=" CG2 ILE O 341 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" CB ILE O 7 " pdb=" CA ILE O 7 " pdb=" CG1 ILE O 7 " pdb=" CG2 ILE O 7 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.86e+00 ... (remaining 16346 not shown) Planarity restraints: 18459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP M 38 " -0.026 2.00e-02 2.50e+03 5.44e-02 2.96e+01 pdb=" C ASP M 38 " 0.092 2.00e-02 2.50e+03 pdb=" O ASP M 38 " -0.048 2.00e-02 2.50e+03 pdb=" N LYS M 70 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET N 217 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.49e+01 pdb=" N PRO N 218 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO N 218 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO N 218 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 310 " 0.028 2.00e-02 2.50e+03 3.35e-02 1.96e+01 pdb=" CG PHE O 310 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 PHE O 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE O 310 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE O 310 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE O 310 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE O 310 " -0.013 2.00e-02 2.50e+03 ... (remaining 18456 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.99: 173 1.99 - 2.72: 14512 2.72 - 3.45: 199669 3.45 - 4.17: 321918 4.17 - 4.90: 515424 Nonbonded interactions: 1051696 Sorted by model distance: nonbonded pdb=" O GLY R 369 " pdb=" CG2 ILE S 395 " model vdw 1.268 3.460 nonbonded pdb=" N HIS H 95 " pdb=" O PRO H 189 " model vdw 1.355 2.520 nonbonded pdb=" O THR R 283 " pdb=" N ALA R 285 " model vdw 1.373 2.520 nonbonded pdb=" CD1 ILE R 372 " pdb=" CA ILE S 395 " model vdw 1.402 3.890 nonbonded pdb=" NH1 ARG Y 83 " pdb=" OE2 GLU Y 87 " model vdw 1.446 2.520 ... (remaining 1051691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain '8' } ncs_group { reference = chain '2' selection = chain '9' } ncs_group { reference = chain '3' selection = chain 'h' } ncs_group { reference = chain '4' selection = chain 'i' } ncs_group { reference = chain '5' selection = chain 'j' } ncs_group { reference = chain '6' selection = chain 'k' } ncs_group { reference = chain '7' selection = chain 'l' } ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 0.000 Extract box with map and model: 9.200 Check model and map are aligned: 1.440 Set scattering table: 0.760 Process input model: 245.560 Find NCS groups from input model: 6.680 Set up NCS constraints: 0.850 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 269.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.012 1.488 106067 Z= 0.797 Angle : 1.352 24.250 143325 Z= 0.760 Chirality : 0.061 1.605 16349 Planarity : 0.007 0.125 18459 Dihedral : 10.708 133.906 39567 Min Nonbonded Distance : 1.268 Molprobity Statistics. All-atom Clashscore : 95.78 Ramachandran Plot: Outliers : 1.53 % Allowed : 13.50 % Favored : 84.97 % Rotamer: Outliers : 0.41 % Allowed : 0.98 % Favored : 98.61 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.17 % Twisted Proline : 1.96 % Twisted General : 1.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.05), residues: 13191 helix: -4.54 (0.04), residues: 4707 sheet: -1.94 (0.10), residues: 1748 loop : -3.03 (0.06), residues: 6736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.006 TRP O 373 HIS 0.035 0.005 HIS P 337 PHE 0.077 0.005 PHE O 310 TYR 0.066 0.005 TYR A 128 ARG 0.019 0.002 ARG d 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26382 Ramachandran restraints generated. 13191 Oldfield, 0 Emsley, 13191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26382 Ramachandran restraints generated. 13191 Oldfield, 0 Emsley, 13191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 805 time to evaluate : 9.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 47 MET cc_start: 0.9273 (ptm) cc_final: 0.8606 (ppp) REVERT: 2 140 MET cc_start: 0.8690 (mmm) cc_final: 0.8472 (mmm) REVERT: 4 111 MET cc_start: 0.9456 (mtp) cc_final: 0.9099 (mmm) REVERT: 4 127 LEU cc_start: 0.9578 (mt) cc_final: 0.9295 (mt) REVERT: 5 202 MET cc_start: 0.9004 (ptm) cc_final: 0.8622 (ptm) REVERT: 6 121 TYR cc_start: 0.9229 (p90) cc_final: 0.8999 (p90) REVERT: 6 152 MET cc_start: 0.7708 (mtp) cc_final: 0.7166 (mtt) REVERT: 7 120 MET cc_start: 0.8861 (ttm) cc_final: 0.8399 (tmm) REVERT: 8 71 MET cc_start: 0.8883 (ttt) cc_final: 0.8633 (ttm) REVERT: 9 133 MET cc_start: 0.9480 (mmm) cc_final: 0.8424 (tpp) REVERT: 9 140 MET cc_start: 0.8979 (mmm) cc_final: 0.8683 (mmm) REVERT: A 121 MET cc_start: 0.9505 (mmm) cc_final: 0.8984 (mmm) REVERT: B 78 MET cc_start: 0.9355 (mtp) cc_final: 0.9122 (ttt) REVERT: E 103 TYR cc_start: 0.8615 (m-80) cc_final: 0.8138 (m-10) REVERT: E 134 MET cc_start: 0.7843 (ttp) cc_final: 0.7278 (ttp) REVERT: G 150 MET cc_start: 0.7940 (ttp) cc_final: 0.7423 (ptm) REVERT: H 197 MET cc_start: 0.6930 (ptp) cc_final: 0.6661 (pmm) REVERT: H 290 MET cc_start: 0.9351 (mtp) cc_final: 0.8693 (mtt) REVERT: H 361 LEU cc_start: 0.7778 (mt) cc_final: 0.7445 (pp) REVERT: H 396 MET cc_start: -0.0981 (mtp) cc_final: -0.1304 (mtm) REVERT: I 171 MET cc_start: 0.1700 (ttm) cc_final: 0.1413 (ttm) REVERT: J 91 GLU cc_start: 0.9321 (mt-10) cc_final: 0.8915 (mt-10) REVERT: J 123 HIS cc_start: 0.8152 (t70) cc_final: 0.7916 (t70) REVERT: J 137 MET cc_start: 0.6563 (ptm) cc_final: 0.6315 (tmm) REVERT: K 161 MET cc_start: -0.2550 (ptp) cc_final: -0.2841 (pmm) REVERT: K 328 LEU cc_start: 0.8640 (mt) cc_final: 0.8232 (tp) REVERT: K 353 PHE cc_start: 0.7609 (m-10) cc_final: 0.7127 (m-10) REVERT: L 116 LYS cc_start: 0.9017 (mttt) cc_final: 0.8549 (tppt) REVERT: M 368 MET cc_start: 0.2599 (mmm) cc_final: 0.1689 (mmt) REVERT: N 108 MET cc_start: 0.9728 (mtp) cc_final: 0.9509 (mtp) REVERT: N 657 MET cc_start: 0.9654 (mtt) cc_final: 0.9438 (mtt) REVERT: N 923 MET cc_start: 0.9060 (mtp) cc_final: 0.8842 (tmm) REVERT: O 2 PHE cc_start: 0.9195 (m-80) cc_final: 0.8911 (m-80) REVERT: O 190 TYR cc_start: 0.8706 (t80) cc_final: 0.8428 (t80) REVERT: P 108 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8116 (mtmm) REVERT: P 208 PHE cc_start: 0.8235 (t80) cc_final: 0.7955 (t80) REVERT: Q 221 MET cc_start: 0.9120 (mmm) cc_final: 0.8678 (mmm) REVERT: Q 265 MET cc_start: 0.8914 (ttt) cc_final: 0.8681 (ttp) REVERT: R 408 ASP cc_start: 0.9364 (t70) cc_final: 0.9123 (t0) REVERT: S 297 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7812 (tp) REVERT: U 76 MET cc_start: 0.9261 (ttm) cc_final: 0.8912 (ttm) REVERT: U 294 ASN cc_start: 0.7346 (t0) cc_final: 0.6558 (t0) REVERT: V 94 MET cc_start: 0.9516 (mtp) cc_final: 0.9034 (ttm) REVERT: V 251 TYR cc_start: 0.8680 (m-80) cc_final: 0.8402 (m-80) REVERT: W 1 MET cc_start: 0.4069 (mtp) cc_final: 0.3518 (ttp) REVERT: a 121 MET cc_start: 0.9633 (mmm) cc_final: 0.9089 (mmm) REVERT: c 174 THR cc_start: 0.9595 (m) cc_final: 0.9364 (m) REVERT: f 88 LEU cc_start: 0.9703 (tp) cc_final: 0.9287 (mt) REVERT: f 218 LYS cc_start: 0.9369 (ttmt) cc_final: 0.8871 (tptp) REVERT: g 176 LEU cc_start: 0.9578 (mp) cc_final: 0.9306 (tp) REVERT: h 23 MET cc_start: 0.8602 (ptm) cc_final: 0.8058 (ppp) REVERT: h 111 ASN cc_start: 0.9126 (m-40) cc_final: 0.8886 (t0) REVERT: i 111 MET cc_start: 0.9383 (mtp) cc_final: 0.9175 (mtp) REVERT: j 79 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8776 (mp0) REVERT: j 149 MET cc_start: 0.9576 (mmm) cc_final: 0.9192 (mmm) REVERT: k 1 MET cc_start: 0.8453 (tpp) cc_final: 0.7294 (ttp) REVERT: l 99 ASN cc_start: 0.9118 (m-40) cc_final: 0.8867 (m-40) outliers start: 47 outliers final: 22 residues processed: 844 average time/residue: 1.1075 time to fit residues: 1522.9819 Evaluate side-chains 465 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 441 time to evaluate : 9.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1315 random chunks: chunk 1110 optimal weight: 5.9990 chunk 996 optimal weight: 10.0000 chunk 553 optimal weight: 30.0000 chunk 340 optimal weight: 5.9990 chunk 672 optimal weight: 0.8980 chunk 532 optimal weight: 7.9990 chunk 1030 optimal weight: 2.9990 chunk 398 optimal weight: 10.0000 chunk 626 optimal weight: 0.9980 chunk 767 optimal weight: 6.9990 chunk 1194 optimal weight: 8.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 51 ASN 2 70 ASN 2 246 GLN 3 164 ASN ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 86 GLN 4 115 HIS 4 122 HIS ** 4 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 89 GLN 6 78 GLN ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 141 HIS 7 251 ASN ** 9 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 51 ASN 9 70 ASN ** 9 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS C 21 GLN C 31 HIS ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 ASN D 16 HIS ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN E 91 HIS E 114 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 ASN H 51 GLN ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 GLN J 49 ASN J 52 ASN J 111 GLN J 331 HIS J 393 ASN ** K 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 GLN ** K 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 ASN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 359 GLN ** M 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 405 ASN ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 216 ASN N 226 ASN N 267 GLN ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 870 ASN ** N 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN O 107 GLN O 169 ASN O 212 GLN ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 244 ASN ** O 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 326 HIS O 354 GLN ** O 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 349 ASN P 440 HIS ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 186 HIS Q 226 HIS Q 283 ASN ** Q 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN R 74 ASN ** R 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 314 ASN R 366 ASN R 374 ASN ** R 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN ** S 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 243 ASN ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 158 GLN ** T 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 GLN U 192 ASN ** U 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 223 HIS ** U 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 ASN V 126 GLN ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 190 HIS V 193 ASN ** V 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 250 GLN ** V 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 149 GLN ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 156 HIS ** Z 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 760 HIS Z 789 GLN ** Z 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 833 GLN Z 856 HIS ** Z 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 898 HIS ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 139 HIS ** b 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 GLN c 31 HIS c 96 GLN d 19 GLN ** d 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 91 HIS e 114 GLN ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 233 ASN ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 119 ASN g 23 GLN g 90 ASN g 182 HIS ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 164 ASN h 180 GLN i 115 HIS i 122 HIS ** i 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 170 HIS ** i 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 89 GLN k 55 GLN k 78 GLN ** k 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 141 HIS l 251 ASN Total number of N/Q/H flips: 100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 106067 Z= 0.368 Angle : 1.013 16.086 143325 Z= 0.540 Chirality : 0.053 0.380 16349 Planarity : 0.007 0.120 18459 Dihedral : 8.716 75.024 14405 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 46.49 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.06 % Favored : 89.51 % Rotamer: Outliers : 0.32 % Allowed : 2.59 % Favored : 97.09 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.18 % Twisted Proline : 0.98 % Twisted General : 0.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.06), residues: 13193 helix: -2.88 (0.05), residues: 5853 sheet: -2.12 (0.11), residues: 1741 loop : -2.44 (0.07), residues: 5599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP V 107 HIS 0.022 0.003 HIS P 348 PHE 0.050 0.003 PHE O 310 TYR 0.044 0.003 TYR 9 219 ARG 0.019 0.001 ARG O 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 673 time to evaluate : 12.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 47 MET cc_start: 0.9267 (ptm) cc_final: 0.8545 (ppp) REVERT: 2 141 ASN cc_start: 0.9036 (p0) cc_final: 0.8558 (p0) REVERT: 2 250 MET cc_start: 0.7789 (mpp) cc_final: 0.7570 (mpp) REVERT: 3 23 MET cc_start: 0.8459 (ptm) cc_final: 0.8210 (ppp) REVERT: 4 111 MET cc_start: 0.9597 (mtp) cc_final: 0.9392 (mtp) REVERT: 4 127 LEU cc_start: 0.9227 (mt) cc_final: 0.8925 (mt) REVERT: 4 207 MET cc_start: 0.8629 (mtt) cc_final: 0.8409 (mtt) REVERT: 5 126 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9024 (pp) REVERT: 6 121 TYR cc_start: 0.8809 (p90) cc_final: 0.8580 (p90) REVERT: 6 152 MET cc_start: 0.8322 (mtp) cc_final: 0.7013 (mtt) REVERT: 6 172 MET cc_start: 0.9537 (tpt) cc_final: 0.9232 (tpp) REVERT: 7 120 MET cc_start: 0.8847 (ttm) cc_final: 0.8282 (tmm) REVERT: 8 71 MET cc_start: 0.8596 (ttt) cc_final: 0.8177 (ttt) REVERT: 8 83 LEU cc_start: 0.9057 (tp) cc_final: 0.8850 (tt) REVERT: 8 166 MET cc_start: 0.7687 (tpp) cc_final: 0.7016 (tpp) REVERT: 9 127 GLU cc_start: 0.9207 (tp30) cc_final: 0.8856 (tp30) REVERT: A 121 MET cc_start: 0.9574 (mmm) cc_final: 0.9309 (mmp) REVERT: A 210 MET cc_start: 0.8923 (ttm) cc_final: 0.8433 (ttt) REVERT: B 1 MET cc_start: 0.7093 (mmp) cc_final: 0.6534 (mmp) REVERT: B 57 MET cc_start: 0.8314 (mtm) cc_final: 0.8004 (mtm) REVERT: B 78 MET cc_start: 0.9234 (mtp) cc_final: 0.8953 (ttm) REVERT: E 134 MET cc_start: 0.8287 (ttp) cc_final: 0.8078 (ttt) REVERT: G 150 MET cc_start: 0.7264 (ttp) cc_final: 0.6898 (ttp) REVERT: H 361 LEU cc_start: 0.7741 (mt) cc_final: 0.7453 (pp) REVERT: J 62 LEU cc_start: 0.8895 (tp) cc_final: 0.8245 (mp) REVERT: J 91 GLU cc_start: 0.8799 (mt-10) cc_final: 0.7054 (mt-10) REVERT: J 236 MET cc_start: 0.4940 (ttt) cc_final: 0.4381 (ttt) REVERT: M 201 MET cc_start: 0.8673 (ttm) cc_final: 0.8318 (ttp) REVERT: N 32 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.7897 (t) REVERT: N 108 MET cc_start: 0.9755 (mtp) cc_final: 0.9403 (mtp) REVERT: N 489 MET cc_start: 0.9605 (mtp) cc_final: 0.9328 (mmt) REVERT: N 735 MET cc_start: 0.9594 (mmp) cc_final: 0.9324 (mmm) REVERT: P 96 MET cc_start: 0.9021 (mpp) cc_final: 0.8749 (mpp) REVERT: P 184 MET cc_start: 0.8934 (mtm) cc_final: 0.8724 (mtp) REVERT: P 208 PHE cc_start: 0.7806 (t80) cc_final: 0.7536 (t80) REVERT: P 282 HIS cc_start: 0.7356 (t70) cc_final: 0.7032 (t-90) REVERT: Q 221 MET cc_start: 0.9094 (mmm) cc_final: 0.8322 (mtp) REVERT: Q 271 MET cc_start: 0.7751 (mtm) cc_final: 0.7389 (mtm) REVERT: Q 306 TYR cc_start: 0.7057 (t80) cc_final: 0.6831 (t80) REVERT: R 171 MET cc_start: 0.9061 (mtm) cc_final: 0.8611 (mtt) REVERT: S 1 MET cc_start: 0.6958 (ppp) cc_final: 0.6527 (ppp) REVERT: S 324 MET cc_start: 0.8892 (mpp) cc_final: 0.8614 (mpp) REVERT: V 37 MET cc_start: 0.7763 (mmp) cc_final: 0.7416 (mmt) REVERT: V 71 MET cc_start: 0.6881 (tpt) cc_final: 0.5976 (tpt) REVERT: V 92 MET cc_start: 0.9211 (tpt) cc_final: 0.8862 (tpt) REVERT: V 251 TYR cc_start: 0.8637 (m-80) cc_final: 0.8266 (m-80) REVERT: W 87 MET cc_start: 0.6938 (mmp) cc_final: 0.5907 (mmp) REVERT: Z 102 ILE cc_start: 0.8042 (tt) cc_final: 0.7837 (pt) REVERT: a 121 MET cc_start: 0.9415 (mmm) cc_final: 0.8629 (mmm) REVERT: b 120 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8770 (mm-30) REVERT: b 173 THR cc_start: 0.9226 (m) cc_final: 0.8899 (m) REVERT: c 39 MET cc_start: 0.9219 (ttp) cc_final: 0.8925 (ttp) REVERT: f 112 LEU cc_start: 0.9297 (mt) cc_final: 0.9061 (mp) REVERT: g 15 PHE cc_start: 0.7412 (m-80) cc_final: 0.7205 (m-10) REVERT: h 23 MET cc_start: 0.8288 (ptm) cc_final: 0.8047 (ppp) REVERT: i 111 MET cc_start: 0.9471 (mtp) cc_final: 0.9229 (mtp) REVERT: i 207 MET cc_start: 0.9169 (mtp) cc_final: 0.8880 (mtm) REVERT: j 149 MET cc_start: 0.9410 (mmm) cc_final: 0.8564 (mmm) REVERT: k 72 ASP cc_start: 0.8014 (m-30) cc_final: 0.7765 (p0) REVERT: l 99 ASN cc_start: 0.9100 (m-40) cc_final: 0.8762 (t0) outliers start: 36 outliers final: 12 residues processed: 709 average time/residue: 1.0831 time to fit residues: 1270.6308 Evaluate side-chains 452 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 438 time to evaluate : 9.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1315 random chunks: chunk 663 optimal weight: 6.9990 chunk 370 optimal weight: 0.7980 chunk 993 optimal weight: 5.9990 chunk 813 optimal weight: 9.9990 chunk 329 optimal weight: 0.7980 chunk 1196 optimal weight: 20.0000 chunk 1292 optimal weight: 7.9990 chunk 1065 optimal weight: 9.9990 chunk 1186 optimal weight: 9.9990 chunk 407 optimal weight: 20.0000 chunk 959 optimal weight: 5.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 173 GLN ** 4 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS C 96 GLN C 221 ASN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN J 391 ASN ** J 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 182 GLN ** K 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 414 GLN L 169 ASN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 182 ASN N 267 GLN ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 305 ASN ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 703 GLN N 870 ASN ** N 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 345 ASN ** O 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 296 GLN ** P 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 379 GLN ** Q 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 374 ASN ** R 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 401 HIS S 20 HIS ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 HIS T 204 ASN ** T 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 97 GLN V 102 GLN ** V 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 279 HIS ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 132 HIS ** Z 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 317 GLN ** Z 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 396 ASN Z 435 GLN ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 801 HIS ** Z 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 130 GLN ** a 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 251 GLN ** b 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 118 GLN ** g 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 173 GLN i 194 ASN ** j 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 55 GLN ** k 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 160 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 106067 Z= 0.322 Angle : 0.862 15.397 143325 Z= 0.461 Chirality : 0.048 0.612 16349 Planarity : 0.006 0.093 18459 Dihedral : 8.019 72.788 14405 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 42.49 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.59 % Favored : 90.00 % Rotamer: Outliers : 0.09 % Allowed : 2.64 % Favored : 97.27 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.18 % Twisted Proline : 0.73 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.06), residues: 13193 helix: -2.04 (0.06), residues: 5932 sheet: -2.13 (0.11), residues: 1784 loop : -2.19 (0.08), residues: 5477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP 7 273 HIS 0.019 0.002 HIS P 348 PHE 0.052 0.002 PHE O 310 TYR 0.037 0.002 TYR P 168 ARG 0.018 0.001 ARG 5 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 541 time to evaluate : 10.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 216 GLN cc_start: 0.9488 (mt0) cc_final: 0.9233 (mt0) REVERT: 2 47 MET cc_start: 0.9205 (ptm) cc_final: 0.8575 (ppp) REVERT: 2 129 LEU cc_start: 0.9829 (mt) cc_final: 0.9572 (mt) REVERT: 2 140 MET cc_start: 0.8235 (mmp) cc_final: 0.7581 (mmp) REVERT: 2 141 ASN cc_start: 0.9122 (p0) cc_final: 0.8790 (p0) REVERT: 2 250 MET cc_start: 0.8275 (mpp) cc_final: 0.8021 (mpp) REVERT: 3 23 MET cc_start: 0.8690 (ptm) cc_final: 0.8090 (ppp) REVERT: 4 127 LEU cc_start: 0.9261 (mt) cc_final: 0.9011 (mt) REVERT: 4 207 MET cc_start: 0.7832 (mtm) cc_final: 0.7465 (mtt) REVERT: 5 202 MET cc_start: 0.9007 (ptm) cc_final: 0.8382 (ppp) REVERT: 6 172 MET cc_start: 0.9594 (tpt) cc_final: 0.9333 (tpp) REVERT: 7 120 MET cc_start: 0.8900 (ttm) cc_final: 0.8444 (tmm) REVERT: 8 71 MET cc_start: 0.8644 (ttt) cc_final: 0.8441 (ttm) REVERT: 8 166 MET cc_start: 0.7667 (tpp) cc_final: 0.7051 (tpp) REVERT: 9 127 GLU cc_start: 0.9379 (tp30) cc_final: 0.8780 (tp30) REVERT: 9 129 LEU cc_start: 0.9593 (mt) cc_final: 0.9345 (mt) REVERT: 9 133 MET cc_start: 0.9220 (tpp) cc_final: 0.8542 (tpp) REVERT: A 121 MET cc_start: 0.9704 (mmm) cc_final: 0.8838 (mmm) REVERT: A 210 MET cc_start: 0.8863 (ttm) cc_final: 0.8326 (ttt) REVERT: B 1 MET cc_start: 0.7209 (mmp) cc_final: 0.6372 (mmp) REVERT: B 57 MET cc_start: 0.8273 (mtm) cc_final: 0.8001 (mtm) REVERT: B 78 MET cc_start: 0.9288 (mtp) cc_final: 0.8908 (ttm) REVERT: C 39 MET cc_start: 0.9389 (tmm) cc_final: 0.9189 (tmm) REVERT: E 134 MET cc_start: 0.8543 (ttp) cc_final: 0.7721 (ttt) REVERT: G 150 MET cc_start: 0.7390 (ttp) cc_final: 0.7060 (ttp) REVERT: H 361 LEU cc_start: 0.7714 (mt) cc_final: 0.7379 (pp) REVERT: I 171 MET cc_start: 0.3559 (ttm) cc_final: 0.2425 (tpp) REVERT: J 91 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8211 (mp0) REVERT: K 253 MET cc_start: 0.7831 (tpt) cc_final: 0.4766 (tpt) REVERT: L 170 MET cc_start: 0.6971 (ttm) cc_final: 0.6756 (ttm) REVERT: M 368 MET cc_start: 0.1362 (mmt) cc_final: 0.1096 (mmt) REVERT: N 108 MET cc_start: 0.9692 (mtp) cc_final: 0.9349 (mtp) REVERT: N 489 MET cc_start: 0.9601 (mtp) cc_final: 0.9371 (mmt) REVERT: N 599 TYR cc_start: 0.9577 (p90) cc_final: 0.9356 (p90) REVERT: N 735 MET cc_start: 0.9425 (mmp) cc_final: 0.9004 (mmp) REVERT: N 787 MET cc_start: 0.6543 (mmp) cc_final: 0.5732 (mmp) REVERT: O 294 MET cc_start: 0.9181 (tmm) cc_final: 0.8952 (tmm) REVERT: P 96 MET cc_start: 0.8492 (mpp) cc_final: 0.8102 (mpp) REVERT: P 101 MET cc_start: 0.7644 (mmp) cc_final: 0.6601 (mmm) REVERT: P 184 MET cc_start: 0.8922 (mtm) cc_final: 0.8673 (mtp) REVERT: P 208 PHE cc_start: 0.7739 (t80) cc_final: 0.7502 (t80) REVERT: P 282 HIS cc_start: 0.7052 (t70) cc_final: 0.6794 (t-90) REVERT: Q 1 MET cc_start: 0.6204 (ptm) cc_final: 0.5752 (tpt) REVERT: Q 68 MET cc_start: 0.8032 (mtt) cc_final: 0.7748 (mtt) REVERT: Q 221 MET cc_start: 0.9161 (mmm) cc_final: 0.8521 (mtp) REVERT: Q 271 MET cc_start: 0.7607 (mtm) cc_final: 0.7377 (mtm) REVERT: Q 311 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7956 (tp) REVERT: Q 413 LEU cc_start: 0.9010 (pp) cc_final: 0.8478 (tp) REVERT: R 171 MET cc_start: 0.9095 (mtm) cc_final: 0.8716 (mtt) REVERT: R 353 MET cc_start: 0.8910 (tmm) cc_final: 0.8113 (tmm) REVERT: S 215 MET cc_start: 0.8193 (ttt) cc_final: 0.7941 (tpp) REVERT: S 232 MET cc_start: 0.9401 (tmm) cc_final: 0.9196 (tmm) REVERT: T 257 THR cc_start: 0.8779 (m) cc_final: 0.8333 (p) REVERT: U 274 MET cc_start: 0.8959 (mtm) cc_final: 0.8513 (mtm) REVERT: V 92 MET cc_start: 0.9280 (tpt) cc_final: 0.8824 (tpt) REVERT: V 251 TYR cc_start: 0.8598 (m-80) cc_final: 0.8240 (m-80) REVERT: W 1 MET cc_start: 0.3254 (mtp) cc_final: 0.2777 (ttp) REVERT: W 87 MET cc_start: 0.6989 (mmp) cc_final: 0.5974 (mmp) REVERT: a 121 MET cc_start: 0.9431 (mmm) cc_final: 0.8399 (mmm) REVERT: b 118 MET cc_start: 0.9171 (tpp) cc_final: 0.8356 (tpp) REVERT: c 39 MET cc_start: 0.9155 (ttp) cc_final: 0.8910 (ttp) REVERT: f 88 LEU cc_start: 0.9626 (mt) cc_final: 0.9394 (mt) REVERT: f 147 PHE cc_start: 0.8432 (t80) cc_final: 0.8094 (t80) REVERT: h 23 MET cc_start: 0.8593 (ptm) cc_final: 0.8280 (ppp) REVERT: h 194 MET cc_start: 0.9145 (tpp) cc_final: 0.8396 (tpp) REVERT: i 207 MET cc_start: 0.9178 (mtp) cc_final: 0.8277 (mtp) REVERT: j 15 MET cc_start: 0.7788 (ttm) cc_final: 0.6785 (mmt) REVERT: j 149 MET cc_start: 0.9446 (mmm) cc_final: 0.8841 (mmm) REVERT: k 72 ASP cc_start: 0.8018 (m-30) cc_final: 0.7630 (p0) outliers start: 10 outliers final: 4 residues processed: 550 average time/residue: 1.0544 time to fit residues: 977.4682 Evaluate side-chains 409 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 404 time to evaluate : 9.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1315 random chunks: chunk 1181 optimal weight: 10.0000 chunk 899 optimal weight: 20.0000 chunk 620 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 570 optimal weight: 8.9990 chunk 803 optimal weight: 20.0000 chunk 1200 optimal weight: 10.0000 chunk 1271 optimal weight: 20.0000 chunk 627 optimal weight: 0.8980 chunk 1137 optimal weight: 3.9990 chunk 342 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 57 HIS ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 146 HIS 6 147 HIS ** 6 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 160 ASN 7 164 GLN ** 9 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 ASN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 ASN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN J 269 GLN J 391 ASN J 393 ASN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN ** M 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 267 GLN ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 870 ASN ** N 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 345 ASN ** O 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 308 ASN ** Q 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN ** R 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 374 ASN ** R 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 401 HIS ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 459 GLN S 472 HIS ** U 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 260 ASN ** V 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 237 ASN ** V 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 387 ASN Z 434 GLN ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 251 GLN ** b 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 201 ASN ** j 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 55 GLN k 112 ASN ** k 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 160 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 106067 Z= 0.300 Angle : 0.816 15.192 143325 Z= 0.434 Chirality : 0.047 0.468 16349 Planarity : 0.006 0.093 18459 Dihedral : 7.590 72.191 14405 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 40.32 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.41 % Favored : 90.23 % Rotamer: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.17 % Twisted Proline : 0.24 % Twisted General : 0.33 % 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: -2.83 (0.07), residues: 13193 helix: -1.51 (0.06), residues: 6066 sheet: -2.03 (0.11), residues: 1814 loop : -2.07 (0.08), residues: 5313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 36 HIS 0.013 0.002 HIS P 348 PHE 0.051 0.002 PHE O 310 TYR 0.047 0.002 TYR F 137 ARG 0.017 0.001 ARG j 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 510 time to evaluate : 9.499 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: 1 216 GLN cc_start: 0.9474 (mt0) cc_final: 0.9232 (mt0) REVERT: 2 93 MET cc_start: 0.8707 (mtt) cc_final: 0.8490 (mtt) REVERT: 2 133 MET cc_start: 0.9455 (tpp) cc_final: 0.9246 (tpp) REVERT: 2 140 MET cc_start: 0.8213 (mmp) cc_final: 0.7609 (mmp) REVERT: 2 141 ASN cc_start: 0.9109 (p0) cc_final: 0.8793 (p0) REVERT: 2 250 MET cc_start: 0.8246 (mpp) cc_final: 0.8020 (mpp) REVERT: 3 23 MET cc_start: 0.8653 (ptm) cc_final: 0.8232 (ptt) REVERT: 5 202 MET cc_start: 0.9096 (ptm) cc_final: 0.8353 (ppp) REVERT: 6 152 MET cc_start: 0.8898 (mtp) cc_final: 0.7878 (mtp) REVERT: 6 172 MET cc_start: 0.9638 (tpt) cc_final: 0.9345 (tpp) REVERT: 7 120 MET cc_start: 0.8826 (ttm) cc_final: 0.8401 (tmm) REVERT: 8 166 MET cc_start: 0.8801 (tpp) cc_final: 0.8472 (tpp) REVERT: 9 127 GLU cc_start: 0.9399 (tp30) cc_final: 0.8775 (tp30) REVERT: A 121 MET cc_start: 0.9814 (mmm) cc_final: 0.8870 (mmm) REVERT: A 210 MET cc_start: 0.8898 (ttm) cc_final: 0.8440 (ttt) REVERT: B 1 MET cc_start: 0.7230 (mmp) cc_final: 0.6494 (mmp) REVERT: B 57 MET cc_start: 0.8299 (mtm) cc_final: 0.8071 (mtm) REVERT: B 78 MET cc_start: 0.9298 (mtp) cc_final: 0.8949 (ttm) REVERT: C 39 MET cc_start: 0.9194 (tmm) cc_final: 0.8990 (tmm) REVERT: G 150 MET cc_start: 0.7478 (ttp) cc_final: 0.7203 (ttp) REVERT: H 290 MET cc_start: 0.8876 (mtt) cc_final: 0.8611 (mtt) REVERT: H 352 MET cc_start: 0.8424 (ptm) cc_final: 0.7662 (ttp) REVERT: H 361 LEU cc_start: 0.7612 (mt) cc_final: 0.7300 (pp) REVERT: I 171 MET cc_start: 0.2408 (ttm) cc_final: 0.1880 (tpp) REVERT: J 91 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8029 (mp0) REVERT: J 138 MET cc_start: 0.6055 (mpp) cc_final: 0.5403 (mpp) REVERT: K 303 MET cc_start: 0.5839 (tpt) cc_final: 0.5528 (tpt) REVERT: K 316 MET cc_start: 0.6520 (mpp) cc_final: 0.6260 (mpp) REVERT: K 353 PHE cc_start: 0.6315 (m-10) cc_final: 0.5990 (m-80) REVERT: L 170 MET cc_start: 0.7128 (ttm) cc_final: 0.6847 (ttm) REVERT: N 108 MET cc_start: 0.9660 (mtp) cc_final: 0.9326 (mtp) REVERT: N 455 MET cc_start: 0.9314 (ppp) cc_final: 0.9024 (ptt) REVERT: N 489 MET cc_start: 0.9624 (mtp) cc_final: 0.9415 (mmt) REVERT: N 735 MET cc_start: 0.9372 (mmp) cc_final: 0.8962 (mmp) REVERT: N 773 MET cc_start: 0.5242 (mmp) cc_final: 0.4873 (mmp) REVERT: N 787 MET cc_start: 0.5770 (mmp) cc_final: 0.5473 (mmp) REVERT: O 366 MET cc_start: 0.9128 (ptp) cc_final: 0.8890 (ptt) REVERT: P 96 MET cc_start: 0.8970 (mpp) cc_final: 0.8664 (mpp) REVERT: P 282 HIS cc_start: 0.7078 (t70) cc_final: 0.6840 (t-90) REVERT: P 353 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9027 (mp) REVERT: Q 1 MET cc_start: 0.6647 (ptm) cc_final: 0.6369 (mmt) REVERT: Q 68 MET cc_start: 0.7774 (mtt) cc_final: 0.6619 (mtt) REVERT: Q 86 MET cc_start: 0.6892 (mmp) cc_final: 0.6413 (mmm) REVERT: Q 221 MET cc_start: 0.9144 (mmm) cc_final: 0.8812 (mtp) REVERT: Q 265 MET cc_start: 0.8794 (mmt) cc_final: 0.8275 (mmm) REVERT: Q 413 LEU cc_start: 0.9125 (pp) cc_final: 0.8874 (tp) REVERT: R 171 MET cc_start: 0.9070 (mtm) cc_final: 0.8646 (mtt) REVERT: S 232 MET cc_start: 0.9351 (tmm) cc_final: 0.8983 (tmm) REVERT: U 274 MET cc_start: 0.8904 (mtm) cc_final: 0.8494 (mtm) REVERT: V 92 MET cc_start: 0.9307 (tpt) cc_final: 0.8788 (tpt) REVERT: V 251 TYR cc_start: 0.8622 (m-80) cc_final: 0.8012 (m-80) REVERT: W 87 MET cc_start: 0.6931 (mmp) cc_final: 0.5860 (mmp) REVERT: Z 756 MET cc_start: 0.3658 (pmm) cc_final: 0.2980 (ptp) REVERT: a 121 MET cc_start: 0.9424 (mmm) cc_final: 0.8399 (mmm) REVERT: b 118 MET cc_start: 0.9313 (tpp) cc_final: 0.8844 (tpp) REVERT: b 173 THR cc_start: 0.9393 (m) cc_final: 0.9130 (m) REVERT: c 184 MET cc_start: 0.5634 (mtp) cc_final: 0.5419 (ttp) REVERT: f 88 LEU cc_start: 0.9709 (mt) cc_final: 0.9501 (mt) REVERT: f 147 PHE cc_start: 0.8381 (t80) cc_final: 0.8098 (t80) REVERT: h 194 MET cc_start: 0.8972 (tpp) cc_final: 0.8618 (tpp) REVERT: i 207 MET cc_start: 0.9155 (mtp) cc_final: 0.8212 (mtp) REVERT: j 15 MET cc_start: 0.7755 (ttm) cc_final: 0.7323 (tpp) REVERT: j 79 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8410 (mp0) REVERT: j 149 MET cc_start: 0.9382 (mmm) cc_final: 0.8898 (mmm) REVERT: k 1 MET cc_start: 0.8599 (tmm) cc_final: 0.7751 (ttp) REVERT: k 3 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7940 (mt) REVERT: k 172 MET cc_start: 0.8512 (tmm) cc_final: 0.7615 (tmm) REVERT: l 175 MET cc_start: 0.9340 (mmp) cc_final: 0.9114 (mmm) outliers start: 10 outliers final: 3 residues processed: 520 average time/residue: 1.0190 time to fit residues: 901.8794 Evaluate side-chains 400 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 395 time to evaluate : 9.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1315 random chunks: chunk 1058 optimal weight: 0.5980 chunk 721 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 946 optimal weight: 10.0000 chunk 524 optimal weight: 5.9990 chunk 1084 optimal weight: 9.9990 chunk 878 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 649 optimal weight: 20.0000 chunk 1140 optimal weight: 8.9990 chunk 320 optimal weight: 9.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 55 GLN ** 6 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 160 ASN ** 9 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 ASN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN J 391 ASN ** K 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 ASN ** M 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 267 GLN ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 716 GLN ** N 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 343 GLN ** O 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 GLN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 208 ASN ** R 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 401 HIS ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 ASN ** W 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 225 ASN ** j 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 106067 Z= 0.309 Angle : 0.801 14.388 143325 Z= 0.425 Chirality : 0.046 0.328 16349 Planarity : 0.005 0.094 18459 Dihedral : 7.390 73.525 14405 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 40.22 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.12 % Favored : 90.49 % Rotamer: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.17 % Twisted Proline : 0.24 % Twisted General : 0.30 % 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: -2.57 (0.07), residues: 13193 helix: -1.25 (0.06), residues: 6109 sheet: -1.94 (0.11), residues: 1822 loop : -2.00 (0.08), residues: 5262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 36 HIS 0.013 0.002 HIS K 74 PHE 0.057 0.002 PHE O 310 TYR 0.071 0.002 TYR S 475 ARG 0.007 0.001 ARG S 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 479 time to evaluate : 9.947 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: 1 216 GLN cc_start: 0.9507 (mt0) cc_final: 0.9274 (mt0) REVERT: 2 93 MET cc_start: 0.8750 (mtt) cc_final: 0.8524 (mtt) REVERT: 2 133 MET cc_start: 0.9465 (tpp) cc_final: 0.9224 (tpp) REVERT: 2 140 MET cc_start: 0.8291 (mmp) cc_final: 0.7932 (mmp) REVERT: 2 141 ASN cc_start: 0.9129 (p0) cc_final: 0.8825 (p0) REVERT: 3 23 MET cc_start: 0.8522 (ptm) cc_final: 0.8173 (ptt) REVERT: 4 127 LEU cc_start: 0.9260 (mt) cc_final: 0.8981 (mt) REVERT: 4 207 MET cc_start: 0.8093 (mtt) cc_final: 0.7631 (mtt) REVERT: 5 202 MET cc_start: 0.9154 (ptm) cc_final: 0.8604 (ptm) REVERT: 6 152 MET cc_start: 0.8778 (mtp) cc_final: 0.8166 (mtp) REVERT: 6 172 MET cc_start: 0.9672 (tpt) cc_final: 0.9337 (tpp) REVERT: 7 120 MET cc_start: 0.8853 (ttm) cc_final: 0.8392 (tmm) REVERT: 7 175 MET cc_start: 0.7867 (mtt) cc_final: 0.7361 (mmm) REVERT: 8 166 MET cc_start: 0.8734 (tpp) cc_final: 0.8495 (tpp) REVERT: 9 127 GLU cc_start: 0.9412 (tp30) cc_final: 0.8747 (tp30) REVERT: 9 129 LEU cc_start: 0.9612 (mt) cc_final: 0.9398 (mt) REVERT: 9 250 MET cc_start: 0.8104 (mtm) cc_final: 0.7523 (mtm) REVERT: A 121 MET cc_start: 0.9839 (mmm) cc_final: 0.9212 (mmm) REVERT: A 210 MET cc_start: 0.8910 (ttm) cc_final: 0.8438 (ttt) REVERT: B 1 MET cc_start: 0.7294 (mmp) cc_final: 0.6750 (mmp) REVERT: B 57 MET cc_start: 0.8320 (mtm) cc_final: 0.8120 (mtm) REVERT: B 78 MET cc_start: 0.9292 (mtp) cc_final: 0.8987 (ttm) REVERT: E 78 MET cc_start: 0.8027 (pmm) cc_final: 0.7726 (pmm) REVERT: H 290 MET cc_start: 0.8872 (mtt) cc_final: 0.8571 (mtt) REVERT: H 352 MET cc_start: 0.7568 (ptm) cc_final: 0.7160 (ttp) REVERT: H 361 LEU cc_start: 0.7647 (mt) cc_final: 0.7276 (pp) REVERT: H 396 MET cc_start: -0.0597 (mtp) cc_final: -0.0944 (mtp) REVERT: I 171 MET cc_start: 0.2297 (ttm) cc_final: 0.1771 (tpp) REVERT: J 91 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8143 (mp0) REVERT: J 138 MET cc_start: 0.6519 (mpp) cc_final: 0.6048 (mpp) REVERT: K 135 MET cc_start: 0.7773 (mpp) cc_final: 0.7479 (mpp) REVERT: K 303 MET cc_start: 0.6025 (tpt) cc_final: 0.5738 (tpp) REVERT: L 109 MET cc_start: 0.8146 (mpp) cc_final: 0.7913 (mpp) REVERT: L 133 ASN cc_start: 0.7550 (t0) cc_final: 0.7331 (t0) REVERT: L 170 MET cc_start: 0.7134 (ttm) cc_final: 0.6877 (ttm) REVERT: L 382 MET cc_start: 0.5331 (ptt) cc_final: 0.4681 (ptt) REVERT: N 108 MET cc_start: 0.9651 (mtp) cc_final: 0.9322 (mtp) REVERT: N 245 LEU cc_start: 0.5374 (OUTLIER) cc_final: 0.5073 (tt) REVERT: N 386 MET cc_start: 0.9654 (mmt) cc_final: 0.9134 (mmt) REVERT: N 455 MET cc_start: 0.9296 (ppp) cc_final: 0.9027 (ptt) REVERT: N 489 MET cc_start: 0.9704 (mtp) cc_final: 0.9410 (mmt) REVERT: N 599 TYR cc_start: 0.9671 (p90) cc_final: 0.9390 (p90) REVERT: N 735 MET cc_start: 0.9296 (mmp) cc_final: 0.8835 (mmp) REVERT: N 773 MET cc_start: 0.5319 (mmp) cc_final: 0.5040 (mmp) REVERT: N 787 MET cc_start: 0.5959 (mmp) cc_final: 0.5634 (mmp) REVERT: O 366 MET cc_start: 0.8863 (ptp) cc_final: 0.8629 (ptp) REVERT: P 74 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.7959 (t0) REVERT: P 96 MET cc_start: 0.9241 (mpp) cc_final: 0.8954 (mpp) REVERT: P 173 MET cc_start: 0.9613 (pmm) cc_final: 0.9212 (ppp) REVERT: P 282 HIS cc_start: 0.7159 (t70) cc_final: 0.6858 (t-90) REVERT: Q 1 MET cc_start: 0.6915 (ptm) cc_final: 0.6426 (mmt) REVERT: Q 68 MET cc_start: 0.7728 (mtt) cc_final: 0.6477 (mtt) REVERT: Q 221 MET cc_start: 0.9150 (mmm) cc_final: 0.8790 (mtp) REVERT: Q 271 MET cc_start: 0.8732 (mtm) cc_final: 0.7870 (mtm) REVERT: Q 377 LEU cc_start: 0.9315 (tp) cc_final: 0.9095 (tp) REVERT: Q 380 MET cc_start: 0.8961 (ttp) cc_final: 0.7137 (ppp) REVERT: R 171 MET cc_start: 0.9068 (mtm) cc_final: 0.8648 (mtt) REVERT: S 1 MET cc_start: 0.6894 (ppp) cc_final: 0.6620 (ppp) REVERT: S 232 MET cc_start: 0.9354 (tmm) cc_final: 0.9023 (tmm) REVERT: V 37 MET cc_start: 0.8332 (tpt) cc_final: 0.8095 (tpt) REVERT: V 47 MET cc_start: 0.7490 (ppp) cc_final: 0.7260 (ppp) REVERT: V 92 MET cc_start: 0.9254 (tpt) cc_final: 0.8715 (tpt) REVERT: V 251 TYR cc_start: 0.8542 (m-80) cc_final: 0.8307 (m-10) REVERT: W 87 MET cc_start: 0.7056 (mmp) cc_final: 0.5893 (mmp) REVERT: Z 575 MET cc_start: 0.2321 (mtm) cc_final: 0.1688 (ptp) REVERT: Z 756 MET cc_start: 0.4363 (pmm) cc_final: 0.3812 (ptp) REVERT: a 121 MET cc_start: 0.9406 (mmm) cc_final: 0.8343 (mmm) REVERT: c 184 MET cc_start: 0.5636 (mtp) cc_final: 0.5375 (ttp) REVERT: f 88 LEU cc_start: 0.9722 (mt) cc_final: 0.9514 (mt) REVERT: f 147 PHE cc_start: 0.8494 (t80) cc_final: 0.8136 (t80) REVERT: h 23 MET cc_start: 0.8763 (ptp) cc_final: 0.8520 (ptt) REVERT: h 194 MET cc_start: 0.8974 (tpp) cc_final: 0.8510 (tpp) REVERT: i 207 MET cc_start: 0.9179 (mtp) cc_final: 0.8425 (mtp) REVERT: j 15 MET cc_start: 0.7655 (ttm) cc_final: 0.7336 (tpp) REVERT: j 79 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8372 (mp0) REVERT: j 149 MET cc_start: 0.9379 (mmm) cc_final: 0.8883 (mmm) REVERT: k 1 MET cc_start: 0.8691 (tmm) cc_final: 0.7489 (ttt) REVERT: k 172 MET cc_start: 0.8536 (tmm) cc_final: 0.8091 (tmm) REVERT: l 120 MET cc_start: 0.8785 (mmp) cc_final: 0.8468 (mmm) REVERT: l 200 ASP cc_start: 0.8588 (p0) cc_final: 0.8368 (p0) outliers start: 7 outliers final: 1 residues processed: 486 average time/residue: 1.0176 time to fit residues: 843.4886 Evaluate side-chains 395 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 392 time to evaluate : 9.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1315 random chunks: chunk 427 optimal weight: 0.2980 chunk 1144 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 746 optimal weight: 5.9990 chunk 313 optimal weight: 20.0000 chunk 1272 optimal weight: 30.0000 chunk 1056 optimal weight: 9.9990 chunk 589 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 420 optimal weight: 30.0000 chunk 667 optimal weight: 6.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 157 ASN ** 6 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 283 ASN ** 9 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 ASN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN J 391 ASN K 144 ASN ** L 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 267 GLN ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 195 GLN ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 425 HIS ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 314 ASN ** R 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 401 HIS ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 206 GLN ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN ** T 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 143 ASN ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 60 GLN ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 45 HIS k 63 ASN k 146 HIS ** k 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 106067 Z= 0.305 Angle : 0.785 13.875 143325 Z= 0.417 Chirality : 0.046 0.311 16349 Planarity : 0.005 0.090 18459 Dihedral : 7.254 74.036 14405 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 40.62 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.23 % Favored : 90.37 % Rotamer: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.18 % Twisted Proline : 0.24 % Twisted General : 0.29 % 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: -2.39 (0.07), residues: 13193 helix: -1.04 (0.06), residues: 6095 sheet: -1.88 (0.11), residues: 1810 loop : -1.97 (0.08), residues: 5288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 36 HIS 0.013 0.002 HIS K 74 PHE 0.057 0.002 PHE O 310 TYR 0.058 0.002 TYR S 475 ARG 0.009 0.001 ARG V 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 472 time to evaluate : 12.038 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: 1 71 MET cc_start: 0.8837 (ptp) cc_final: 0.8569 (ptp) REVERT: 1 216 GLN cc_start: 0.9481 (mt0) cc_final: 0.9260 (mt0) REVERT: 2 133 MET cc_start: 0.9495 (tpp) cc_final: 0.9237 (tpp) REVERT: 2 140 MET cc_start: 0.8389 (mmp) cc_final: 0.7976 (mmp) REVERT: 2 141 ASN cc_start: 0.9143 (p0) cc_final: 0.8744 (p0) REVERT: 2 250 MET cc_start: 0.8094 (mpp) cc_final: 0.7683 (mpp) REVERT: 3 23 MET cc_start: 0.8522 (ptm) cc_final: 0.8161 (ptt) REVERT: 4 127 LEU cc_start: 0.9211 (mt) cc_final: 0.8929 (mt) REVERT: 5 149 MET cc_start: 0.8647 (mmm) cc_final: 0.8235 (mmp) REVERT: 5 202 MET cc_start: 0.9197 (ptm) cc_final: 0.8668 (ptm) REVERT: 6 1 MET cc_start: 0.7823 (tmm) cc_final: 0.7579 (ppp) REVERT: 6 152 MET cc_start: 0.8689 (mtp) cc_final: 0.8331 (mtp) REVERT: 6 172 MET cc_start: 0.9687 (tpt) cc_final: 0.9258 (tpp) REVERT: 7 120 MET cc_start: 0.8834 (ttm) cc_final: 0.8387 (tmm) REVERT: 8 166 MET cc_start: 0.8708 (tpp) cc_final: 0.8506 (tpp) REVERT: 9 127 GLU cc_start: 0.9401 (tp30) cc_final: 0.8970 (tp30) REVERT: 9 129 LEU cc_start: 0.9563 (mt) cc_final: 0.9355 (mt) REVERT: A 210 MET cc_start: 0.8931 (ttm) cc_final: 0.8500 (ttt) REVERT: B 78 MET cc_start: 0.9283 (mtp) cc_final: 0.9046 (ttm) REVERT: H 290 MET cc_start: 0.8945 (mtt) cc_final: 0.8562 (mtt) REVERT: H 352 MET cc_start: 0.7615 (ptm) cc_final: 0.7020 (tmm) REVERT: H 361 LEU cc_start: 0.7593 (mt) cc_final: 0.7163 (pp) REVERT: H 396 MET cc_start: -0.0603 (mtp) cc_final: -0.0922 (mtp) REVERT: I 171 MET cc_start: 0.2308 (ttm) cc_final: 0.1679 (tpp) REVERT: J 138 MET cc_start: 0.5951 (mpp) cc_final: 0.5266 (mpp) REVERT: K 316 MET cc_start: 0.6587 (mpp) cc_final: 0.6243 (mpp) REVERT: L 85 GLU cc_start: 0.9650 (tt0) cc_final: 0.9397 (tm-30) REVERT: L 109 MET cc_start: 0.8437 (mpp) cc_final: 0.7987 (mpp) REVERT: L 133 ASN cc_start: 0.7718 (t0) cc_final: 0.7280 (t0) REVERT: L 170 MET cc_start: 0.7216 (ttm) cc_final: 0.6854 (ttm) REVERT: L 382 MET cc_start: 0.4539 (ptt) cc_final: 0.3602 (ptt) REVERT: M 305 MET cc_start: 0.8640 (ttp) cc_final: 0.8203 (ptm) REVERT: M 368 MET cc_start: -0.0093 (tpp) cc_final: -0.0416 (ttm) REVERT: N 108 MET cc_start: 0.9654 (mtp) cc_final: 0.9339 (mtp) REVERT: N 386 MET cc_start: 0.9656 (mmt) cc_final: 0.9124 (mmt) REVERT: N 455 MET cc_start: 0.9320 (ppp) cc_final: 0.9089 (ptp) REVERT: N 489 MET cc_start: 0.9712 (mtp) cc_final: 0.9410 (mmt) REVERT: N 599 TYR cc_start: 0.9640 (p90) cc_final: 0.9296 (p90) REVERT: N 773 MET cc_start: 0.5435 (mmp) cc_final: 0.5141 (mmp) REVERT: N 787 MET cc_start: 0.6199 (mmp) cc_final: 0.5841 (mmp) REVERT: O 366 MET cc_start: 0.8891 (ptp) cc_final: 0.8653 (ptp) REVERT: P 96 MET cc_start: 0.9276 (mpp) cc_final: 0.8987 (mpp) REVERT: P 101 MET cc_start: 0.8214 (mmp) cc_final: 0.7880 (mmm) REVERT: P 173 MET cc_start: 0.9533 (pmm) cc_final: 0.9176 (ppp) REVERT: Q 1 MET cc_start: 0.6853 (ptm) cc_final: 0.6403 (mmt) REVERT: Q 68 MET cc_start: 0.7508 (mtt) cc_final: 0.6311 (mtt) REVERT: Q 86 MET cc_start: 0.5874 (mmp) cc_final: 0.5647 (mmm) REVERT: Q 221 MET cc_start: 0.9161 (mmm) cc_final: 0.8746 (mtp) REVERT: Q 271 MET cc_start: 0.8655 (mtm) cc_final: 0.7838 (mtm) REVERT: Q 377 LEU cc_start: 0.9355 (tp) cc_final: 0.9146 (tp) REVERT: Q 380 MET cc_start: 0.9149 (ttp) cc_final: 0.7408 (ppp) REVERT: R 171 MET cc_start: 0.9057 (mtm) cc_final: 0.8472 (mtm) REVERT: S 1 MET cc_start: 0.6800 (ppp) cc_final: 0.6469 (ppp) REVERT: S 232 MET cc_start: 0.9362 (tmm) cc_final: 0.9061 (tmm) REVERT: U 274 MET cc_start: 0.8847 (mtm) cc_final: 0.8279 (mtm) REVERT: U 277 TYR cc_start: 0.7307 (m-80) cc_final: 0.7040 (m-80) REVERT: V 92 MET cc_start: 0.9285 (tpt) cc_final: 0.8603 (tpt) REVERT: V 251 TYR cc_start: 0.8758 (m-80) cc_final: 0.8094 (m-10) REVERT: W 87 MET cc_start: 0.6859 (mmp) cc_final: 0.5811 (mmp) REVERT: Z 547 MET cc_start: 0.7298 (ppp) cc_final: 0.6817 (mmm) REVERT: Z 756 MET cc_start: 0.4613 (pmm) cc_final: 0.4115 (ptp) REVERT: a 37 GLN cc_start: 0.9006 (tt0) cc_final: 0.8357 (tm-30) REVERT: a 121 MET cc_start: 0.9471 (mmm) cc_final: 0.8370 (mmm) REVERT: b 118 MET cc_start: 0.9029 (tpp) cc_final: 0.8757 (tpp) REVERT: d 120 TYR cc_start: 0.8174 (m-80) cc_final: 0.7255 (m-80) REVERT: f 88 LEU cc_start: 0.9702 (mt) cc_final: 0.9485 (mt) REVERT: f 147 PHE cc_start: 0.8513 (t80) cc_final: 0.8135 (t80) REVERT: h 194 MET cc_start: 0.8943 (tpp) cc_final: 0.8498 (tpp) REVERT: i 207 MET cc_start: 0.9194 (mtp) cc_final: 0.8300 (mtp) REVERT: j 15 MET cc_start: 0.7703 (ttm) cc_final: 0.7452 (tpp) REVERT: j 79 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8413 (mp0) REVERT: j 149 MET cc_start: 0.9385 (mmm) cc_final: 0.8883 (mmm) REVERT: k 1 MET cc_start: 0.8384 (tmm) cc_final: 0.7347 (ttt) REVERT: k 172 MET cc_start: 0.8165 (tmm) cc_final: 0.7708 (tmm) REVERT: l 120 MET cc_start: 0.8798 (mmp) cc_final: 0.8478 (mmm) REVERT: l 175 MET cc_start: 0.9334 (mmp) cc_final: 0.9129 (mmm) REVERT: l 200 ASP cc_start: 0.8599 (p0) cc_final: 0.8381 (p0) outliers start: 4 outliers final: 0 residues processed: 476 average time/residue: 1.0096 time to fit residues: 827.0379 Evaluate side-chains 380 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 9.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1315 random chunks: chunk 1226 optimal weight: 30.0000 chunk 143 optimal weight: 20.0000 chunk 724 optimal weight: 4.9990 chunk 929 optimal weight: 10.0000 chunk 719 optimal weight: 1.9990 chunk 1071 optimal weight: 6.9990 chunk 710 optimal weight: 9.9990 chunk 1267 optimal weight: 5.9990 chunk 793 optimal weight: 6.9990 chunk 772 optimal weight: 2.9990 chunk 585 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 10 GLN ** 6 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 283 ASN ** 9 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 ASN H 148 ASN ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 295 ASN J 52 ASN ** L 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 226 ASN ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 GLN ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 401 HIS ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 177 ASN ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 250 GLN ** W 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 135 ASN ** Z 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 60 GLN ** f 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 63 ASN ** k 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 106067 Z= 0.284 Angle : 0.765 13.006 143325 Z= 0.406 Chirality : 0.045 0.292 16349 Planarity : 0.005 0.084 18459 Dihedral : 7.098 74.798 14405 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 38.60 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.97 % Favored : 90.66 % Rotamer: Outliers : 0.02 % Allowed : 1.31 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.18 % Twisted Proline : 0.24 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.07), residues: 13193 helix: -0.83 (0.06), residues: 6139 sheet: -1.87 (0.11), residues: 1804 loop : -1.89 (0.09), residues: 5250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 218 HIS 0.017 0.002 HIS P 337 PHE 0.051 0.002 PHE O 310 TYR 0.055 0.002 TYR S 475 ARG 0.008 0.001 ARG H 266 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 474 time to evaluate : 9.930 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: 2 133 MET cc_start: 0.9438 (tpp) cc_final: 0.9136 (tpp) REVERT: 2 140 MET cc_start: 0.8419 (mmp) cc_final: 0.7997 (mmp) REVERT: 2 141 ASN cc_start: 0.9125 (p0) cc_final: 0.8705 (p0) REVERT: 2 183 MET cc_start: 0.8902 (mmp) cc_final: 0.8503 (mmm) REVERT: 2 250 MET cc_start: 0.8199 (mpp) cc_final: 0.7729 (mpp) REVERT: 3 23 MET cc_start: 0.8497 (ptm) cc_final: 0.8170 (ptt) REVERT: 3 194 MET cc_start: 0.9156 (mtt) cc_final: 0.8699 (mtt) REVERT: 4 127 LEU cc_start: 0.9155 (mt) cc_final: 0.8874 (mt) REVERT: 4 207 MET cc_start: 0.9236 (mpp) cc_final: 0.8935 (mpp) REVERT: 5 149 MET cc_start: 0.8876 (mmm) cc_final: 0.8296 (mmp) REVERT: 5 202 MET cc_start: 0.9210 (ptm) cc_final: 0.8699 (ptm) REVERT: 6 1 MET cc_start: 0.7804 (tmm) cc_final: 0.7582 (ppp) REVERT: 6 152 MET cc_start: 0.8588 (mtp) cc_final: 0.8201 (mtp) REVERT: 6 172 MET cc_start: 0.9684 (tpt) cc_final: 0.9221 (tpp) REVERT: 7 120 MET cc_start: 0.8788 (ttm) cc_final: 0.8279 (tmm) REVERT: 9 127 GLU cc_start: 0.9394 (tp30) cc_final: 0.8981 (tp30) REVERT: 9 129 LEU cc_start: 0.9584 (mt) cc_final: 0.9379 (mt) REVERT: A 121 MET cc_start: 0.9735 (mmt) cc_final: 0.9170 (mmm) REVERT: A 210 MET cc_start: 0.8903 (ttm) cc_final: 0.8485 (ttt) REVERT: B 2 THR cc_start: 0.9172 (p) cc_final: 0.7149 (p) REVERT: C 39 MET cc_start: 0.9218 (tmm) cc_final: 0.8742 (tmm) REVERT: F 70 MET cc_start: 0.7595 (mmt) cc_final: 0.7045 (mmt) REVERT: G 88 LEU cc_start: 0.8961 (mt) cc_final: 0.8481 (mt) REVERT: G 127 ASN cc_start: 0.6757 (OUTLIER) cc_final: 0.6330 (p0) REVERT: H 290 MET cc_start: 0.8623 (mtt) cc_final: 0.8415 (mtt) REVERT: H 352 MET cc_start: 0.7793 (ptm) cc_final: 0.7157 (tmm) REVERT: H 361 LEU cc_start: 0.7623 (mt) cc_final: 0.7166 (pp) REVERT: H 396 MET cc_start: -0.0747 (mtp) cc_final: -0.1069 (mtp) REVERT: I 171 MET cc_start: 0.1746 (ttm) cc_final: 0.1201 (tpp) REVERT: J 138 MET cc_start: 0.6839 (mpp) cc_final: 0.6054 (mpp) REVERT: K 135 MET cc_start: 0.7601 (mpp) cc_final: 0.7308 (mpp) REVERT: K 161 MET cc_start: -0.1792 (pmm) cc_final: -0.2553 (ptt) REVERT: K 316 MET cc_start: 0.6576 (mpp) cc_final: 0.6228 (mpp) REVERT: L 85 GLU cc_start: 0.9552 (tt0) cc_final: 0.9243 (tm-30) REVERT: L 109 MET cc_start: 0.8262 (mpp) cc_final: 0.7956 (mpp) REVERT: L 133 ASN cc_start: 0.7597 (t0) cc_final: 0.7197 (t0) REVERT: L 170 MET cc_start: 0.6998 (ttm) cc_final: 0.6583 (ttm) REVERT: L 306 MET cc_start: 0.8208 (mtp) cc_final: 0.7842 (mtp) REVERT: L 382 MET cc_start: 0.3640 (ptt) cc_final: 0.2929 (ptt) REVERT: M 305 MET cc_start: 0.8646 (ttp) cc_final: 0.8184 (ptm) REVERT: M 368 MET cc_start: -0.0634 (tpp) cc_final: -0.0907 (ttm) REVERT: N 108 MET cc_start: 0.9631 (mtp) cc_final: 0.9317 (mtp) REVERT: N 386 MET cc_start: 0.9674 (mmt) cc_final: 0.9117 (mmt) REVERT: N 455 MET cc_start: 0.9236 (ppp) cc_final: 0.9021 (ptp) REVERT: N 489 MET cc_start: 0.9720 (mtp) cc_final: 0.9408 (mmt) REVERT: N 773 MET cc_start: 0.5387 (mmp) cc_final: 0.5113 (mmp) REVERT: N 787 MET cc_start: 0.6251 (mmp) cc_final: 0.5920 (mmp) REVERT: P 96 MET cc_start: 0.9312 (mpp) cc_final: 0.8938 (mpp) REVERT: P 101 MET cc_start: 0.8259 (mmp) cc_final: 0.7911 (mmm) REVERT: P 173 MET cc_start: 0.9325 (pmm) cc_final: 0.9096 (tmm) REVERT: Q 1 MET cc_start: 0.6785 (ptm) cc_final: 0.6409 (mmt) REVERT: Q 68 MET cc_start: 0.7443 (mtt) cc_final: 0.6185 (mtt) REVERT: Q 86 MET cc_start: 0.4833 (mmp) cc_final: 0.4631 (mmm) REVERT: Q 221 MET cc_start: 0.9148 (mmm) cc_final: 0.8862 (mmm) REVERT: Q 271 MET cc_start: 0.8619 (mtm) cc_final: 0.7796 (mtm) REVERT: Q 377 LEU cc_start: 0.9388 (tp) cc_final: 0.9129 (tp) REVERT: Q 380 MET cc_start: 0.8892 (ttp) cc_final: 0.7311 (ppp) REVERT: R 171 MET cc_start: 0.9042 (mtm) cc_final: 0.8402 (mtm) REVERT: S 1 MET cc_start: 0.6408 (ppp) cc_final: 0.6182 (ppp) REVERT: S 232 MET cc_start: 0.9340 (tmm) cc_final: 0.9092 (tmm) REVERT: U 274 MET cc_start: 0.8297 (mtm) cc_final: 0.7477 (mtm) REVERT: U 277 TYR cc_start: 0.7327 (m-80) cc_final: 0.7112 (m-80) REVERT: V 92 MET cc_start: 0.9365 (tpt) cc_final: 0.8696 (tpt) REVERT: V 251 TYR cc_start: 0.8425 (m-80) cc_final: 0.8221 (m-10) REVERT: W 87 MET cc_start: 0.6536 (mmp) cc_final: 0.5601 (mmp) REVERT: Z 756 MET cc_start: 0.4832 (pmm) cc_final: 0.4387 (ptp) REVERT: a 121 MET cc_start: 0.9433 (mmm) cc_final: 0.8387 (mmm) REVERT: b 173 THR cc_start: 0.9546 (m) cc_final: 0.9198 (m) REVERT: c 39 MET cc_start: 0.9058 (mmm) cc_final: 0.8672 (mmm) REVERT: f 88 LEU cc_start: 0.9696 (mt) cc_final: 0.9473 (mt) REVERT: f 147 PHE cc_start: 0.8476 (t80) cc_final: 0.8086 (t80) REVERT: h 23 MET cc_start: 0.9053 (ptp) cc_final: 0.8127 (pmm) REVERT: h 194 MET cc_start: 0.8863 (tpp) cc_final: 0.8536 (tpp) REVERT: i 207 MET cc_start: 0.9024 (mtp) cc_final: 0.7719 (ttm) REVERT: j 15 MET cc_start: 0.7573 (ttm) cc_final: 0.7354 (tpp) REVERT: j 79 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8470 (mp0) REVERT: j 149 MET cc_start: 0.9373 (mmm) cc_final: 0.8856 (mmm) REVERT: k 172 MET cc_start: 0.8327 (tmm) cc_final: 0.7705 (tmm) REVERT: l 120 MET cc_start: 0.8771 (mmt) cc_final: 0.8485 (mmm) REVERT: l 200 ASP cc_start: 0.8604 (p0) cc_final: 0.8386 (p0) outliers start: 2 outliers final: 0 residues processed: 476 average time/residue: 1.0144 time to fit residues: 824.9770 Evaluate side-chains 386 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 385 time to evaluate : 9.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1315 random chunks: chunk 784 optimal weight: 20.0000 chunk 506 optimal weight: 6.9990 chunk 756 optimal weight: 6.9990 chunk 381 optimal weight: 7.9990 chunk 249 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 chunk 805 optimal weight: 0.9990 chunk 863 optimal weight: 0.0970 chunk 626 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 996 optimal weight: 10.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 201 ASN ** 6 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 283 ASN ** 9 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 330 GLN ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 295 ASN J 52 ASN ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 226 ASN ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 169 ASN O 229 ASN ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 256 ASN ** O 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 401 HIS ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 172 ASN S 177 ASN ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 ASN ** V 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 ASN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 HIS ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 63 ASN ** k 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 283 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 106067 Z= 0.249 Angle : 0.743 14.691 143325 Z= 0.392 Chirality : 0.045 0.485 16349 Planarity : 0.005 0.117 18459 Dihedral : 6.934 75.525 14405 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 35.63 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.50 % Favored : 91.15 % Rotamer: Outliers : 0.01 % Allowed : 0.91 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.18 % Twisted Proline : 0.49 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.07), residues: 13193 helix: -0.57 (0.06), residues: 6130 sheet: -1.76 (0.11), residues: 1869 loop : -1.85 (0.09), residues: 5194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 218 HIS 0.032 0.002 HIS P 348 PHE 0.048 0.002 PHE N 211 TYR 0.057 0.002 TYR R 70 ARG 0.015 0.001 ARG N 880 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 470 time to evaluate : 10.278 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 93 MET cc_start: 0.8474 (mtt) cc_final: 0.8131 (mtt) REVERT: 2 133 MET cc_start: 0.9446 (tpp) cc_final: 0.9142 (tpp) REVERT: 2 140 MET cc_start: 0.8391 (mmp) cc_final: 0.8013 (mmp) REVERT: 2 141 ASN cc_start: 0.9021 (p0) cc_final: 0.8605 (p0) REVERT: 2 183 MET cc_start: 0.9000 (mmp) cc_final: 0.8648 (mmm) REVERT: 3 23 MET cc_start: 0.8502 (ptm) cc_final: 0.8163 (ptt) REVERT: 3 134 LEU cc_start: 0.8800 (mp) cc_final: 0.8441 (mp) REVERT: 3 165 MET cc_start: 0.8784 (mtp) cc_final: 0.8191 (ttm) REVERT: 4 127 LEU cc_start: 0.9132 (mt) cc_final: 0.8828 (mt) REVERT: 4 207 MET cc_start: 0.9279 (mpp) cc_final: 0.8844 (mpp) REVERT: 5 149 MET cc_start: 0.8848 (mmm) cc_final: 0.8282 (mmp) REVERT: 5 202 MET cc_start: 0.9199 (ptm) cc_final: 0.8714 (ptm) REVERT: 6 152 MET cc_start: 0.8602 (mtp) cc_final: 0.8283 (mtp) REVERT: 6 172 MET cc_start: 0.9674 (tpt) cc_final: 0.9193 (tpp) REVERT: 7 120 MET cc_start: 0.8661 (ttm) cc_final: 0.8253 (tmm) REVERT: 8 71 MET cc_start: 0.9022 (ppp) cc_final: 0.8424 (ppp) REVERT: 9 127 GLU cc_start: 0.9538 (tp30) cc_final: 0.8948 (tp30) REVERT: A 121 MET cc_start: 0.9742 (mmt) cc_final: 0.9149 (mmm) REVERT: A 210 MET cc_start: 0.8875 (ttm) cc_final: 0.8572 (ttt) REVERT: C 39 MET cc_start: 0.9198 (tmm) cc_final: 0.8700 (tmm) REVERT: E 78 MET cc_start: 0.7931 (pmm) cc_final: 0.7716 (pmm) REVERT: F 70 MET cc_start: 0.7572 (mmt) cc_final: 0.7038 (mmt) REVERT: G 88 LEU cc_start: 0.9234 (mt) cc_final: 0.8864 (mt) REVERT: H 290 MET cc_start: 0.8597 (mtt) cc_final: 0.8354 (mtt) REVERT: H 352 MET cc_start: 0.7699 (ptm) cc_final: 0.7105 (tmm) REVERT: H 361 LEU cc_start: 0.7610 (mt) cc_final: 0.7167 (pp) REVERT: H 396 MET cc_start: -0.0965 (mtp) cc_final: -0.1197 (mtp) REVERT: I 171 MET cc_start: 0.1818 (ttm) cc_final: 0.1207 (tpp) REVERT: J 138 MET cc_start: 0.6667 (mpp) cc_final: 0.5871 (mpp) REVERT: K 135 MET cc_start: 0.7596 (mpp) cc_final: 0.7239 (mpp) REVERT: K 161 MET cc_start: -0.2079 (pmm) cc_final: -0.3006 (ptt) REVERT: L 109 MET cc_start: 0.8198 (mpp) cc_final: 0.7906 (mpp) REVERT: L 133 ASN cc_start: 0.7566 (t0) cc_final: 0.7133 (t0) REVERT: L 170 MET cc_start: 0.6887 (ttm) cc_final: 0.6659 (ttm) REVERT: L 306 MET cc_start: 0.8030 (mtp) cc_final: 0.7335 (ptp) REVERT: L 382 MET cc_start: 0.3511 (ptt) cc_final: 0.2493 (ptt) REVERT: M 305 MET cc_start: 0.8669 (ttp) cc_final: 0.8178 (ptm) REVERT: M 372 ASP cc_start: 0.6454 (t70) cc_final: 0.6171 (t0) REVERT: N 108 MET cc_start: 0.9618 (mtp) cc_final: 0.9300 (mtp) REVERT: N 386 MET cc_start: 0.9658 (mmt) cc_final: 0.9096 (mmt) REVERT: N 485 MET cc_start: 0.9118 (mtt) cc_final: 0.8730 (mmm) REVERT: N 489 MET cc_start: 0.9714 (mtp) cc_final: 0.9399 (mmt) REVERT: N 662 MET cc_start: 0.9687 (ptp) cc_final: 0.9052 (mpp) REVERT: N 773 MET cc_start: 0.5367 (mmp) cc_final: 0.5046 (mmp) REVERT: N 787 MET cc_start: 0.6426 (mmp) cc_final: 0.5987 (mmp) REVERT: P 96 MET cc_start: 0.9299 (mpp) cc_final: 0.8814 (mpp) REVERT: P 101 MET cc_start: 0.8256 (mmp) cc_final: 0.7915 (mmm) REVERT: P 380 ILE cc_start: 0.9176 (mt) cc_final: 0.8959 (tp) REVERT: Q 1 MET cc_start: 0.6822 (ptm) cc_final: 0.6420 (tpt) REVERT: Q 68 MET cc_start: 0.7402 (mtt) cc_final: 0.6110 (mtt) REVERT: Q 86 MET cc_start: 0.4467 (mmp) cc_final: 0.4219 (mmm) REVERT: Q 221 MET cc_start: 0.9161 (mmm) cc_final: 0.8864 (mmm) REVERT: Q 286 TYR cc_start: 0.7344 (t80) cc_final: 0.7051 (t80) REVERT: Q 377 LEU cc_start: 0.9386 (tp) cc_final: 0.9151 (tp) REVERT: Q 380 MET cc_start: 0.8894 (ttp) cc_final: 0.7375 (ppp) REVERT: R 171 MET cc_start: 0.9019 (mtm) cc_final: 0.8426 (mtm) REVERT: S 8 MET cc_start: 0.8539 (ppp) cc_final: 0.8287 (ppp) REVERT: S 177 ASN cc_start: 0.7624 (OUTLIER) cc_final: 0.7275 (t0) REVERT: S 232 MET cc_start: 0.9610 (tmm) cc_final: 0.9304 (tmm) REVERT: U 277 TYR cc_start: 0.7578 (m-80) cc_final: 0.7340 (m-80) REVERT: V 92 MET cc_start: 0.9444 (tpt) cc_final: 0.8782 (tpt) REVERT: V 251 TYR cc_start: 0.8686 (m-80) cc_final: 0.8014 (m-10) REVERT: W 87 MET cc_start: 0.6459 (mmp) cc_final: 0.5570 (mmp) REVERT: Z 756 MET cc_start: 0.4979 (pmm) cc_final: 0.4606 (ptp) REVERT: a 121 MET cc_start: 0.9414 (mmm) cc_final: 0.8383 (mmm) REVERT: b 118 MET cc_start: 0.9037 (tpp) cc_final: 0.8693 (tpp) REVERT: f 88 LEU cc_start: 0.9675 (mt) cc_final: 0.9449 (mt) REVERT: f 147 PHE cc_start: 0.8401 (t80) cc_final: 0.8002 (t80) REVERT: h 23 MET cc_start: 0.9128 (ptp) cc_final: 0.7680 (pmm) REVERT: h 194 MET cc_start: 0.8817 (tpp) cc_final: 0.8450 (tpp) REVERT: i 207 MET cc_start: 0.8795 (mtp) cc_final: 0.7176 (ttm) REVERT: j 79 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8466 (mp0) REVERT: j 149 MET cc_start: 0.9344 (mmm) cc_final: 0.8842 (mmm) REVERT: k 122 LEU cc_start: 0.9645 (mt) cc_final: 0.9241 (mp) REVERT: k 172 MET cc_start: 0.8648 (tmm) cc_final: 0.8077 (tmm) REVERT: l 120 MET cc_start: 0.9027 (mmt) cc_final: 0.8668 (mmm) REVERT: l 200 ASP cc_start: 0.8628 (p0) cc_final: 0.8397 (p0) outliers start: 1 outliers final: 0 residues processed: 471 average time/residue: 1.0896 time to fit residues: 885.2025 Evaluate side-chains 377 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 376 time to evaluate : 9.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1315 random chunks: chunk 1152 optimal weight: 10.0000 chunk 1214 optimal weight: 0.9990 chunk 1107 optimal weight: 9.9990 chunk 1181 optimal weight: 20.0000 chunk 1213 optimal weight: 8.9990 chunk 710 optimal weight: 10.0000 chunk 514 optimal weight: 7.9990 chunk 927 optimal weight: 6.9990 chunk 362 optimal weight: 5.9990 chunk 1067 optimal weight: 8.9990 chunk 1117 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 111 ASN ** 2 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 283 ASN ** 9 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 246 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 295 ASN ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 226 ASN ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 899 ASN ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 16 ASN ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 401 HIS ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 ASN ** U 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 102 GLN X 105 ASN ** Z 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 763 HIS ** Z 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 833 GLN ** Z 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 16 HIS ** d 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 60 GLN ** f 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 63 ASN ** k 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 283 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 106067 Z= 0.307 Angle : 0.774 14.866 143325 Z= 0.411 Chirality : 0.046 0.443 16349 Planarity : 0.005 0.099 18459 Dihedral : 6.959 76.945 14405 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 39.94 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.13 % Favored : 90.50 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.18 % Twisted Proline : 0.24 % Twisted General : 0.24 % 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: -1.96 (0.07), residues: 13193 helix: -0.55 (0.06), residues: 6119 sheet: -1.79 (0.11), residues: 1883 loop : -1.89 (0.09), residues: 5191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP Q 396 HIS 0.031 0.002 HIS P 348 PHE 0.048 0.002 PHE O 310 TYR 0.051 0.002 TYR R 307 ARG 0.015 0.001 ARG 2 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 9.619 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: 2 133 MET cc_start: 0.9449 (tpp) cc_final: 0.9178 (tpp) REVERT: 2 140 MET cc_start: 0.8497 (mmp) cc_final: 0.8088 (mmp) REVERT: 2 141 ASN cc_start: 0.9068 (p0) cc_final: 0.8679 (p0) REVERT: 2 183 MET cc_start: 0.8971 (mmp) cc_final: 0.8617 (mmm) REVERT: 2 250 MET cc_start: 0.8987 (mmp) cc_final: 0.7883 (mpp) REVERT: 3 23 MET cc_start: 0.8517 (ptm) cc_final: 0.8193 (ptt) REVERT: 4 127 LEU cc_start: 0.9128 (mt) cc_final: 0.8866 (mt) REVERT: 4 207 MET cc_start: 0.9300 (mpp) cc_final: 0.8813 (mpp) REVERT: 5 202 MET cc_start: 0.9294 (ptm) cc_final: 0.8796 (ptm) REVERT: 6 1 MET cc_start: 0.8103 (ppp) cc_final: 0.7358 (ppp) REVERT: 6 152 MET cc_start: 0.8642 (mtp) cc_final: 0.8371 (mtp) REVERT: 6 172 MET cc_start: 0.9666 (tpt) cc_final: 0.8882 (tpp) REVERT: 7 120 MET cc_start: 0.8681 (ttm) cc_final: 0.8283 (tmm) REVERT: 8 71 MET cc_start: 0.9115 (ppp) cc_final: 0.8488 (ppp) REVERT: 9 127 GLU cc_start: 0.9577 (tp30) cc_final: 0.8998 (tp30) REVERT: A 121 MET cc_start: 0.9551 (mmt) cc_final: 0.9113 (mmm) REVERT: A 210 MET cc_start: 0.8892 (ttm) cc_final: 0.8583 (ttt) REVERT: B 2 THR cc_start: 0.8923 (p) cc_final: 0.6596 (p) REVERT: C 39 MET cc_start: 0.9231 (tmm) cc_final: 0.8747 (tmm) REVERT: E 78 MET cc_start: 0.8039 (pmm) cc_final: 0.7817 (pmm) REVERT: F 70 MET cc_start: 0.7614 (mmt) cc_final: 0.7116 (mmt) REVERT: G 88 LEU cc_start: 0.8984 (mt) cc_final: 0.8499 (mt) REVERT: G 150 MET cc_start: 0.7784 (ttp) cc_final: 0.7349 (ttp) REVERT: H 290 MET cc_start: 0.8574 (mtt) cc_final: 0.8335 (mtt) REVERT: H 352 MET cc_start: 0.7386 (ptm) cc_final: 0.6904 (tmm) REVERT: H 361 LEU cc_start: 0.7677 (mt) cc_final: 0.7202 (pp) REVERT: H 396 MET cc_start: -0.0902 (mtp) cc_final: -0.1133 (mtp) REVERT: I 171 MET cc_start: 0.1880 (ttm) cc_final: 0.1239 (tpp) REVERT: J 138 MET cc_start: 0.6122 (mpp) cc_final: 0.5418 (mpp) REVERT: K 161 MET cc_start: -0.2171 (pmm) cc_final: -0.2520 (pmm) REVERT: K 316 MET cc_start: 0.4690 (mpp) cc_final: 0.3778 (mpp) REVERT: L 109 MET cc_start: 0.8240 (mpp) cc_final: 0.7819 (mpp) REVERT: L 133 ASN cc_start: 0.7736 (t0) cc_final: 0.7325 (t0) REVERT: L 306 MET cc_start: 0.8143 (mtp) cc_final: 0.7394 (ptp) REVERT: L 382 MET cc_start: 0.3305 (ptt) cc_final: 0.2785 (ptt) REVERT: M 372 ASP cc_start: 0.6393 (t70) cc_final: 0.6173 (t0) REVERT: N 108 MET cc_start: 0.9617 (mtp) cc_final: 0.9320 (mtp) REVERT: N 489 MET cc_start: 0.9711 (mtp) cc_final: 0.9403 (mmt) REVERT: N 662 MET cc_start: 0.9591 (ptp) cc_final: 0.9090 (mpp) REVERT: N 773 MET cc_start: 0.5509 (mmp) cc_final: 0.5208 (mmp) REVERT: N 787 MET cc_start: 0.6776 (mmp) cc_final: 0.6369 (mmp) REVERT: P 96 MET cc_start: 0.9343 (mpp) cc_final: 0.8876 (mpp) REVERT: P 101 MET cc_start: 0.8015 (mmp) cc_final: 0.7743 (mmm) REVERT: Q 1 MET cc_start: 0.6775 (ptm) cc_final: 0.6349 (tpt) REVERT: Q 68 MET cc_start: 0.7490 (mtt) cc_final: 0.6147 (mtt) REVERT: Q 133 LEU cc_start: 0.8234 (mt) cc_final: 0.7981 (mt) REVERT: Q 221 MET cc_start: 0.9172 (mmm) cc_final: 0.8858 (mmm) REVERT: Q 271 MET cc_start: 0.8705 (mtm) cc_final: 0.7593 (mtm) REVERT: Q 286 TYR cc_start: 0.7543 (t80) cc_final: 0.7152 (t80) REVERT: Q 380 MET cc_start: 0.8871 (ttp) cc_final: 0.7406 (ppp) REVERT: R 171 MET cc_start: 0.9021 (mtm) cc_final: 0.8425 (mtm) REVERT: S 8 MET cc_start: 0.8622 (ppp) cc_final: 0.8396 (ppp) REVERT: S 232 MET cc_start: 0.9632 (tmm) cc_final: 0.9334 (tmm) REVERT: U 274 MET cc_start: 0.8942 (mtm) cc_final: 0.8653 (mtt) REVERT: U 277 TYR cc_start: 0.7729 (m-80) cc_final: 0.7395 (m-80) REVERT: V 92 MET cc_start: 0.8678 (tpt) cc_final: 0.8453 (tpt) REVERT: V 251 TYR cc_start: 0.8613 (m-80) cc_final: 0.8343 (m-10) REVERT: W 87 MET cc_start: 0.6701 (mmp) cc_final: 0.5691 (mmp) REVERT: Z 775 MET cc_start: 0.2098 (ptm) cc_final: 0.1644 (ptt) REVERT: a 112 MET cc_start: 0.9469 (tmm) cc_final: 0.8668 (tmm) REVERT: a 121 MET cc_start: 0.9458 (mmm) cc_final: 0.8487 (mmm) REVERT: c 39 MET cc_start: 0.9048 (mmm) cc_final: 0.8508 (mmm) REVERT: f 88 LEU cc_start: 0.9654 (mt) cc_final: 0.9376 (mt) REVERT: f 147 PHE cc_start: 0.8473 (t80) cc_final: 0.8080 (t80) REVERT: h 23 MET cc_start: 0.9130 (ptp) cc_final: 0.7688 (pmm) REVERT: h 194 MET cc_start: 0.8768 (tpp) cc_final: 0.8123 (tpp) REVERT: i 207 MET cc_start: 0.8938 (mtp) cc_final: 0.7293 (ttm) REVERT: j 15 MET cc_start: 0.7716 (tpp) cc_final: 0.7361 (tpp) REVERT: j 79 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8515 (mp0) REVERT: j 149 MET cc_start: 0.9390 (mmm) cc_final: 0.8672 (mmm) REVERT: k 1 MET cc_start: 0.8269 (tmm) cc_final: 0.7351 (tpp) REVERT: k 172 MET cc_start: 0.8680 (tmm) cc_final: 0.8155 (tmm) REVERT: l 120 MET cc_start: 0.8829 (mmt) cc_final: 0.8534 (mmm) REVERT: l 175 MET cc_start: 0.9201 (mmp) cc_final: 0.8992 (mmm) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.9930 time to fit residues: 780.4970 Evaluate side-chains 368 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 9.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1315 random chunks: chunk 1176 optimal weight: 10.0000 chunk 775 optimal weight: 6.9990 chunk 1248 optimal weight: 10.0000 chunk 762 optimal weight: 7.9990 chunk 592 optimal weight: 9.9990 chunk 868 optimal weight: 10.0000 chunk 1310 optimal weight: 30.0000 chunk 1205 optimal weight: 9.9990 chunk 1043 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 chunk 805 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 111 ASN ** 2 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 227 ASN ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 283 ASN ** 9 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 227 ASN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 391 ASN ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 226 ASN ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 342 GLN ** P 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 HIS ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 401 HIS ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 417 GLN ** S 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 102 GLN ** V 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 ASN Z 243 GLN ** Z 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 123 ASN ** a 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 60 GLN ** f 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 45 HIS ** k 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 283 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 106067 Z= 0.313 Angle : 0.781 16.668 143325 Z= 0.413 Chirality : 0.046 0.409 16349 Planarity : 0.005 0.088 18459 Dihedral : 6.983 78.168 14405 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 40.58 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.14 % Favored : 90.49 % Rotamer: Outliers : 0.01 % Allowed : 0.31 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.18 % Twisted Proline : 0.49 % Twisted General : 0.24 % 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: -1.96 (0.07), residues: 13193 helix: -0.55 (0.06), residues: 6134 sheet: -1.75 (0.11), residues: 1837 loop : -1.91 (0.08), residues: 5222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP O 352 HIS 0.029 0.002 HIS P 348 PHE 0.066 0.002 PHE O 310 TYR 0.054 0.002 TYR R 307 ARG 0.016 0.001 ARG 2 226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26386 Ramachandran restraints generated. 13193 Oldfield, 0 Emsley, 13193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 437 time to evaluate : 9.757 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: 2 133 MET cc_start: 0.9468 (tpp) cc_final: 0.9193 (tpp) REVERT: 2 140 MET cc_start: 0.8524 (mmp) cc_final: 0.7982 (mmp) REVERT: 2 141 ASN cc_start: 0.9103 (p0) cc_final: 0.8676 (p0) REVERT: 2 183 MET cc_start: 0.8990 (mmp) cc_final: 0.8644 (mmm) REVERT: 3 23 MET cc_start: 0.8511 (ptm) cc_final: 0.8194 (ptt) REVERT: 3 194 MET cc_start: 0.8984 (mtt) cc_final: 0.8526 (mtt) REVERT: 4 127 LEU cc_start: 0.9010 (mt) cc_final: 0.8768 (mt) REVERT: 4 207 MET cc_start: 0.9335 (mpp) cc_final: 0.8211 (mtt) REVERT: 5 149 MET cc_start: 0.8907 (mmm) cc_final: 0.8227 (mmp) REVERT: 5 202 MET cc_start: 0.9328 (ptm) cc_final: 0.8828 (ptm) REVERT: 6 1 MET cc_start: 0.7954 (ppp) cc_final: 0.6743 (ppp) REVERT: 6 152 MET cc_start: 0.8659 (mtp) cc_final: 0.8355 (mtp) REVERT: 7 120 MET cc_start: 0.8693 (ttm) cc_final: 0.8288 (tmm) REVERT: 8 71 MET cc_start: 0.9150 (ppp) cc_final: 0.8529 (ppp) REVERT: 9 93 MET cc_start: 0.9440 (tpt) cc_final: 0.9014 (tpp) REVERT: A 121 MET cc_start: 0.9591 (mmt) cc_final: 0.9152 (mmm) REVERT: A 210 MET cc_start: 0.8896 (ttm) cc_final: 0.8580 (ttt) REVERT: C 39 MET cc_start: 0.9238 (tmm) cc_final: 0.8759 (tmm) REVERT: E 78 MET cc_start: 0.8067 (pmm) cc_final: 0.7836 (pmm) REVERT: F 70 MET cc_start: 0.8023 (mmt) cc_final: 0.7774 (mmt) REVERT: G 150 MET cc_start: 0.7806 (ttp) cc_final: 0.7432 (ttp) REVERT: H 352 MET cc_start: 0.7717 (ptm) cc_final: 0.7128 (tmm) REVERT: H 361 LEU cc_start: 0.7760 (mt) cc_final: 0.7260 (pp) REVERT: I 171 MET cc_start: 0.1949 (ttm) cc_final: 0.1305 (tpp) REVERT: J 138 MET cc_start: 0.6209 (mpp) cc_final: 0.5435 (mpp) REVERT: J 335 MET cc_start: 0.1560 (tpt) cc_final: 0.1277 (tpt) REVERT: K 161 MET cc_start: -0.2114 (pmm) cc_final: -0.2967 (ptt) REVERT: L 109 MET cc_start: 0.7778 (mpp) cc_final: 0.7466 (mpp) REVERT: L 306 MET cc_start: 0.8182 (mtp) cc_final: 0.7451 (mtp) REVERT: L 382 MET cc_start: 0.3279 (ptt) cc_final: 0.2476 (ptt) REVERT: M 305 MET cc_start: 0.8675 (ttp) cc_final: 0.8191 (ptm) REVERT: N 108 MET cc_start: 0.9615 (mtp) cc_final: 0.9317 (mtp) REVERT: N 489 MET cc_start: 0.9748 (mtp) cc_final: 0.9523 (mmt) REVERT: N 662 MET cc_start: 0.9579 (ptp) cc_final: 0.9080 (mpp) REVERT: N 773 MET cc_start: 0.5371 (mmp) cc_final: 0.4997 (mmp) REVERT: N 787 MET cc_start: 0.6831 (mmp) cc_final: 0.6306 (mmp) REVERT: P 96 MET cc_start: 0.9365 (mpp) cc_final: 0.8897 (mpp) REVERT: P 101 MET cc_start: 0.7961 (mmp) cc_final: 0.7638 (mmm) REVERT: P 235 LEU cc_start: 0.8719 (mt) cc_final: 0.8378 (mp) REVERT: Q 68 MET cc_start: 0.7528 (mtt) cc_final: 0.6158 (mtt) REVERT: Q 86 MET cc_start: 0.5372 (mmp) cc_final: 0.4854 (mmt) REVERT: Q 133 LEU cc_start: 0.8180 (mt) cc_final: 0.7944 (mt) REVERT: Q 221 MET cc_start: 0.9177 (mmm) cc_final: 0.8873 (mmm) REVERT: Q 271 MET cc_start: 0.8670 (mtm) cc_final: 0.7602 (mtm) REVERT: Q 380 MET cc_start: 0.9123 (ttp) cc_final: 0.7751 (ppp) REVERT: R 171 MET cc_start: 0.9032 (mtm) cc_final: 0.8387 (mtm) REVERT: R 214 TYR cc_start: 0.8660 (t80) cc_final: 0.8158 (t80) REVERT: S 8 MET cc_start: 0.8663 (ppp) cc_final: 0.8443 (ppp) REVERT: S 232 MET cc_start: 0.9655 (tmm) cc_final: 0.9351 (tmm) REVERT: U 274 MET cc_start: 0.8977 (mtm) cc_final: 0.8515 (mtt) REVERT: U 277 TYR cc_start: 0.7665 (m-80) cc_final: 0.7447 (m-80) REVERT: V 91 MET cc_start: 0.8571 (mtm) cc_final: 0.8069 (mtp) REVERT: V 251 TYR cc_start: 0.8688 (m-80) cc_final: 0.7885 (m-10) REVERT: V 254 ARG cc_start: 0.8555 (mtt90) cc_final: 0.8073 (mtt90) REVERT: W 87 MET cc_start: 0.6554 (mmp) cc_final: 0.5512 (mmp) REVERT: a 112 MET cc_start: 0.9468 (tmm) cc_final: 0.8638 (tmm) REVERT: a 121 MET cc_start: 0.9485 (mmm) cc_final: 0.8494 (mmm) REVERT: e 134 MET cc_start: 0.8564 (ptt) cc_final: 0.8122 (ptt) REVERT: f 88 LEU cc_start: 0.9645 (mt) cc_final: 0.9381 (mt) REVERT: f 147 PHE cc_start: 0.8499 (t80) cc_final: 0.8106 (t80) REVERT: h 23 MET cc_start: 0.9120 (ptp) cc_final: 0.7750 (pmm) REVERT: h 194 MET cc_start: 0.8770 (tpp) cc_final: 0.8143 (tpp) REVERT: i 207 MET cc_start: 0.8939 (mtp) cc_final: 0.7315 (ttm) REVERT: j 79 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8478 (mp0) REVERT: j 149 MET cc_start: 0.9393 (mmm) cc_final: 0.8696 (mmm) REVERT: k 1 MET cc_start: 0.8233 (tmm) cc_final: 0.6871 (tmm) REVERT: k 172 MET cc_start: 0.8561 (tmm) cc_final: 0.8085 (tmm) REVERT: l 120 MET cc_start: 0.8797 (mmt) cc_final: 0.8514 (mmm) REVERT: l 175 MET cc_start: 0.9210 (mmp) cc_final: 0.8993 (mmm) outliers start: 1 outliers final: 0 residues processed: 438 average time/residue: 1.0244 time to fit residues: 779.0093 Evaluate side-chains 355 residues out of total 11464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 9.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1315 random chunks: chunk 639 optimal weight: 9.9990 chunk 828 optimal weight: 1.9990 chunk 1111 optimal weight: 6.9990 chunk 319 optimal weight: 0.9980 chunk 961 optimal weight: 50.0000 chunk 154 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 1044 optimal weight: 3.9990 chunk 437 optimal weight: 20.0000 chunk 1072 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 111 ASN ** 2 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 249 ASN 3 81 HIS ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 147 HIS ** 6 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 283 ASN ** 9 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 295 ASN ** I 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN J 111 GLN ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 176 GLN ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 226 ASN ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 472 ASN ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN ** O 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 425 HIS ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 193 GLN ** U 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 106 GLN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 ASN ** Z 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 143 HIS ** j 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 283 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.037260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.028024 restraints weight = 1544871.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.028705 restraints weight = 1091343.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.029204 restraints weight = 814815.315| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 106067 Z= 0.245 Angle : 0.734 14.006 143325 Z= 0.386 Chirality : 0.045 0.358 16349 Planarity : 0.005 0.086 18459 Dihedral : 6.797 79.217 14405 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 35.00 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.19 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.18 % Twisted Proline : 0.24 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.07), residues: 13193 helix: -0.31 (0.06), residues: 6139 sheet: -1.66 (0.11), residues: 1861 loop : -1.84 (0.09), residues: 5193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP O 352 HIS 0.026 0.002 HIS P 348 PHE 0.052 0.002 PHE O 310 TYR 0.050 0.002 TYR R 307 ARG 0.009 0.001 ARG V 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17645.47 seconds wall clock time: 322 minutes 54.19 seconds (19374.19 seconds total)