Starting phenix.real_space_refine on Mon Mar 25 10:20:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyo_18760/03_2024/8qyo_18760.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyo_18760/03_2024/8qyo_18760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyo_18760/03_2024/8qyo_18760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyo_18760/03_2024/8qyo_18760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyo_18760/03_2024/8qyo_18760.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyo_18760/03_2024/8qyo_18760.pdb" } resolution = 2.84 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= 0.112 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 300 5.16 5 C 30294 2.51 5 N 8220 2.21 5 O 9126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 215": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "G GLU 145": "OE1" <-> "OE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G GLU 192": "OE1" <-> "OE2" Residue "G GLU 196": "OE1" <-> "OE2" Residue "G GLU 214": "OE1" <-> "OE2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "I GLU 151": "OE1" <-> "OE2" Residue "K TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 197": "OE1" <-> "OE2" Residue "M GLU 245": "OE1" <-> "OE2" Residue "N PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 49": "OE1" <-> "OE2" Residue "P GLU 219": "OE1" <-> "OE2" Residue "Q GLU 105": "OE1" <-> "OE2" Residue "R GLU 125": "OE1" <-> "OE2" Residue "S GLU 220": "OE1" <-> "OE2" Residue "U GLU 19": "OE1" <-> "OE2" Residue "U GLU 146": "OE1" <-> "OE2" Residue "U TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 107": "OE1" <-> "OE2" Residue "W GLU 75": "OE1" <-> "OE2" Residue "W GLU 97": "OE1" <-> "OE2" Residue "W GLU 144": "OE1" <-> "OE2" Residue "Y TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 212": "OE1" <-> "OE2" Residue "a GLU 120": "OE1" <-> "OE2" Residue "a GLU 245": "OE1" <-> "OE2" Residue "b PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 185": "OE1" <-> "OE2" Residue "b GLU 215": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47940 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1783 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1922 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 239} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1867 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1736 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1837 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain: "F" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1870 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1839 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 1 Chain: "H" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1650 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain: "I" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "J" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1561 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1553 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1613 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 201} Chain breaks: 1 Chain: "M" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1680 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 207} Chain: "N" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1468 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 6, 'TRANS': 189} Chain: "O" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1783 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "P" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1922 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 239} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1867 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1736 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain breaks: 1 Chain: "S" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1837 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain: "T" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1870 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1839 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 1 Chain: "V" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1650 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain: "W" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "X" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1561 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Y" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1553 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Z" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1613 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 201} Chain breaks: 1 Chain: "a" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1680 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 207} Chain: "b" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1468 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 6, 'TRANS': 189} Time building chain proxies: 23.09, per 1000 atoms: 0.48 Number of scatterers: 47940 At special positions: 0 Unit cell: (164.159, 192.503, 146.444, 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 300 16.00 O 9126 8.00 N 8220 7.00 C 30294 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: 17.19 Conformation dependent library (CDL) restraints added in 8.4 seconds 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11364 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 73 sheets defined 39.8% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.53 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 removed outlier: 3.570A pdb=" N GLU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 102 removed outlier: 3.563A pdb=" N VAL A 85 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 removed outlier: 3.546A pdb=" N GLN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 177 removed outlier: 3.615A pdb=" N GLY A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.574A pdb=" N GLU B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 102 removed outlier: 3.749A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.736A pdb=" N ILE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.679A pdb=" N ALA B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 229 through 246 removed outlier: 3.573A pdb=" N GLN B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 27 Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.671A pdb=" N THR C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG C 60 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 99 removed outlier: 3.538A pdb=" N ILE C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 89 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 117 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 164 through 176 removed outlier: 3.542A pdb=" N VAL C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 removed outlier: 3.611A pdb=" N ILE C 181 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU C 182 " --> pdb=" O GLU C 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 178 through 182' Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.549A pdb=" N GLU C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 204 removed outlier: 3.896A pdb=" N LYS C 204 " --> pdb=" O SER C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 204' Processing helix chain 'C' and resid 221 through 235 Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'D' and resid 21 through 32 removed outlier: 3.823A pdb=" N LYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 84 through 104 removed outlier: 4.224A pdb=" N LEU D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 118 Processing helix chain 'D' and resid 173 through 185 removed outlier: 3.831A pdb=" N GLU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 239 Processing helix chain 'E' and resid 19 through 30 removed outlier: 3.577A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS E 30 " --> pdb=" O MET E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 99 Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.027A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 165 through 176 Processing helix chain 'E' and resid 177 through 182 removed outlier: 4.383A pdb=" N MET E 180 " --> pdb=" O SER E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 197 Processing helix chain 'E' and resid 225 through 228 Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'F' and resid 21 through 32 removed outlier: 3.795A pdb=" N GLU F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA F 30 " --> pdb=" O TYR F 26 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 104 removed outlier: 3.633A pdb=" N ASP F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 122 removed outlier: 3.569A pdb=" N ASP F 114 " --> pdb=" O LYS F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 179 through 180 No H-bonds generated for 'chain 'F' and resid 179 through 180' Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.975A pdb=" N GLU F 184 " --> pdb=" O GLN F 181 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET F 185 " --> pdb=" O MET F 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 181 through 185' Processing helix chain 'F' and resid 186 through 202 removed outlier: 3.561A pdb=" N ILE F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA F 195 " --> pdb=" O VAL F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 229 through 245 Processing helix chain 'G' and resid 22 through 31 removed outlier: 3.745A pdb=" N ALA G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE G 29 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 66 Processing helix chain 'G' and resid 83 through 106 removed outlier: 3.670A pdb=" N TYR G 96 " --> pdb=" O GLN G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 125 removed outlier: 3.942A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 184 Processing helix chain 'G' and resid 193 through 207 removed outlier: 4.058A pdb=" N THR G 197 " --> pdb=" O GLN G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 245 Processing helix chain 'H' and resid 91 through 114 Processing helix chain 'H' and resid 118 through 133 removed outlier: 3.545A pdb=" N ALA H 122 " --> pdb=" O ARG H 118 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR H 133 " --> pdb=" O MET H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 185 removed outlier: 3.787A pdb=" N ALA H 177 " --> pdb=" O GLY H 173 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 209 Processing helix chain 'I' and resid 56 through 79 Processing helix chain 'I' and resid 83 through 97 Processing helix chain 'I' and resid 142 through 154 removed outlier: 3.702A pdb=" N SER I 152 " --> pdb=" O GLY I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 176 Processing helix chain 'J' and resid 51 through 72 Processing helix chain 'J' and resid 76 through 93 removed outlier: 3.593A pdb=" N CYS J 91 " --> pdb=" O ASN J 87 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG J 93 " --> pdb=" O ALA J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 147 removed outlier: 4.319A pdb=" N LEU J 138 " --> pdb=" O TYR J 134 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER J 141 " --> pdb=" O PHE J 137 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE J 142 " --> pdb=" O LEU J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 171 Processing helix chain 'K' and resid 107 through 130 Processing helix chain 'K' and resid 134 through 147 removed outlier: 3.504A pdb=" N VAL K 146 " --> pdb=" O LEU K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 150 No H-bonds generated for 'chain 'K' and resid 148 through 150' Processing helix chain 'K' and resid 190 through 202 removed outlier: 3.628A pdb=" N ALA K 194 " --> pdb=" O GLY K 190 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY K 196 " --> pdb=" O VAL K 192 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL K 197 " --> pdb=" O TYR K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 226 removed outlier: 3.822A pdb=" N ARG K 225 " --> pdb=" O GLN K 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 removed outlier: 4.513A pdb=" N GLU K 256 " --> pdb=" O ALA K 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 108 Processing helix chain 'L' and resid 112 through 126 removed outlier: 3.689A pdb=" N THR L 122 " --> pdb=" O ALA L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 181 Proline residue: L 175 - end of helix Processing helix chain 'L' and resid 195 through 212 removed outlier: 3.871A pdb=" N GLU L 212 " --> pdb=" O ILE L 208 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 121 removed outlier: 3.521A pdb=" N GLN M 114 " --> pdb=" O GLN M 110 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET M 115 " --> pdb=" O VAL M 111 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU M 119 " --> pdb=" O MET M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 146 removed outlier: 3.669A pdb=" N ILE M 133 " --> pdb=" O SER M 129 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG M 144 " --> pdb=" O ALA M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 191 Processing helix chain 'M' and resid 191 through 202 removed outlier: 3.870A pdb=" N VAL M 198 " --> pdb=" O LEU M 194 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU M 200 " --> pdb=" O ARG M 196 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS M 201 " --> pdb=" O GLU M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 224 removed outlier: 3.703A pdb=" N MET M 218 " --> pdb=" O VAL M 214 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG M 219 " --> pdb=" O GLU M 215 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL M 220 " --> pdb=" O ARG M 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 259 Processing helix chain 'N' and resid 82 through 105 Processing helix chain 'N' and resid 109 through 124 removed outlier: 3.615A pdb=" N ALA N 113 " --> pdb=" O LEU N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 163 through 168 removed outlier: 3.666A pdb=" N SER N 166 " --> pdb=" O GLY N 163 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER N 167 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR N 168 " --> pdb=" O GLY N 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 163 through 168' Processing helix chain 'N' and resid 169 through 177 Processing helix chain 'N' and resid 182 through 201 removed outlier: 3.570A pdb=" N LEU N 187 " --> pdb=" O LYS N 183 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN N 188 " --> pdb=" O GLU N 184 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE N 189 " --> pdb=" O GLU N 185 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG N 200 " --> pdb=" O LEU N 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 30 removed outlier: 3.556A pdb=" N GLU O 23 " --> pdb=" O LEU O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 102 removed outlier: 3.565A pdb=" N VAL O 85 " --> pdb=" O PRO O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 121 removed outlier: 3.860A pdb=" N TYR O 121 " --> pdb=" O VAL O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 166 through 178 Processing helix chain 'O' and resid 183 through 197 Processing helix chain 'O' and resid 222 through 233 Processing helix chain 'P' and resid 18 through 29 removed outlier: 3.564A pdb=" N GLU P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 102 removed outlier: 3.912A pdb=" N VAL P 85 " --> pdb=" O SER P 81 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU P 92 " --> pdb=" O ASN P 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 124 removed outlier: 3.738A pdb=" N ILE P 117 " --> pdb=" O ALA P 113 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR P 121 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 179 removed outlier: 3.570A pdb=" N ALA P 171 " --> pdb=" O ASN P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 201 removed outlier: 3.548A pdb=" N ALA P 191 " --> pdb=" O LYS P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 209 No H-bonds generated for 'chain 'P' and resid 207 through 209' Processing helix chain 'P' and resid 229 through 246 removed outlier: 3.634A pdb=" N GLN P 235 " --> pdb=" O LYS P 231 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 27 Processing helix chain 'Q' and resid 56 through 60 removed outlier: 4.183A pdb=" N ARG Q 60 " --> pdb=" O ARG Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 99 removed outlier: 3.535A pdb=" N ILE Q 82 " --> pdb=" O ALA Q 78 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL Q 89 " --> pdb=" O ASN Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 117 Processing helix chain 'Q' and resid 164 through 176 removed outlier: 3.554A pdb=" N VAL Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS Q 174 " --> pdb=" O GLU Q 170 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 182 removed outlier: 3.629A pdb=" N ILE Q 181 " --> pdb=" O ASP Q 178 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU Q 182 " --> pdb=" O GLU Q 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 178 through 182' Processing helix chain 'Q' and resid 183 through 197 removed outlier: 3.551A pdb=" N GLU Q 197 " --> pdb=" O LYS Q 193 " (cutoff:3.500A) Processing helix chain 'Q' and resid 201 through 204 removed outlier: 3.882A pdb=" N LYS Q 204 " --> pdb=" O SER Q 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 201 through 204' Processing helix chain 'Q' and resid 221 through 235 Processing helix chain 'Q' and resid 236 through 238 No H-bonds generated for 'chain 'Q' and resid 236 through 238' Processing helix chain 'R' and resid 21 through 32 removed outlier: 3.824A pdb=" N LYS R 32 " --> pdb=" O ILE R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 64 Processing helix chain 'R' and resid 84 through 104 removed outlier: 4.183A pdb=" N LEU R 88 " --> pdb=" O ASP R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 118 Processing helix chain 'R' and resid 173 through 185 removed outlier: 3.773A pdb=" N GLU R 183 " --> pdb=" O SER R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 206 Processing helix chain 'R' and resid 230 through 239 Processing helix chain 'S' and resid 19 through 30 removed outlier: 3.553A pdb=" N GLU S 23 " --> pdb=" O ILE S 19 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL S 29 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS S 30 " --> pdb=" O MET S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 99 Processing helix chain 'S' and resid 104 through 118 removed outlier: 4.060A pdb=" N ILE S 118 " --> pdb=" O SER S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 121 No H-bonds generated for 'chain 'S' and resid 119 through 121' Processing helix chain 'S' and resid 165 through 176 Processing helix chain 'S' and resid 177 through 182 removed outlier: 4.343A pdb=" N MET S 180 " --> pdb=" O SER S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 183 through 197 Processing helix chain 'S' and resid 225 through 228 Processing helix chain 'S' and resid 229 through 234 Processing helix chain 'T' and resid 21 through 32 removed outlier: 3.804A pdb=" N GLU T 25 " --> pdb=" O VAL T 21 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA T 30 " --> pdb=" O TYR T 26 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL T 31 " --> pdb=" O ALA T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 104 removed outlier: 3.628A pdb=" N ASP T 90 " --> pdb=" O ARG T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 108 through 122 Processing helix chain 'T' and resid 169 through 178 Processing helix chain 'T' and resid 179 through 180 No H-bonds generated for 'chain 'T' and resid 179 through 180' Processing helix chain 'T' and resid 181 through 185 removed outlier: 4.094A pdb=" N GLU T 184 " --> pdb=" O GLN T 181 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET T 185 " --> pdb=" O MET T 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 181 through 185' Processing helix chain 'T' and resid 186 through 202 removed outlier: 3.572A pdb=" N ILE T 190 " --> pdb=" O THR T 186 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS T 192 " --> pdb=" O ARG T 188 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA T 195 " --> pdb=" O VAL T 191 " (cutoff:3.500A) Processing helix chain 'T' and resid 220 through 222 No H-bonds generated for 'chain 'T' and resid 220 through 222' Processing helix chain 'T' and resid 229 through 245 Processing helix chain 'U' and resid 22 through 34 removed outlier: 3.748A pdb=" N ALA U 28 " --> pdb=" O GLN U 24 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE U 29 " --> pdb=" O VAL U 25 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS U 30 " --> pdb=" O GLU U 26 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE U 32 " --> pdb=" O ALA U 28 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN U 33 " --> pdb=" O PHE U 29 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN U 34 " --> pdb=" O LYS U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 66 Processing helix chain 'U' and resid 83 through 106 removed outlier: 3.669A pdb=" N TYR U 96 " --> pdb=" O GLN U 92 " (cutoff:3.500A) Processing helix chain 'U' and resid 110 through 125 removed outlier: 3.935A pdb=" N VAL U 124 " --> pdb=" O ASP U 120 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR U 125 " --> pdb=" O ILE U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 171 through 184 Processing helix chain 'U' and resid 193 through 207 removed outlier: 4.130A pdb=" N THR U 197 " --> pdb=" O GLN U 193 " (cutoff:3.500A) Processing helix chain 'U' and resid 231 through 245 removed outlier: 3.510A pdb=" N HIS U 238 " --> pdb=" O GLU U 234 " (cutoff:3.500A) Processing helix chain 'V' and resid 91 through 114 Processing helix chain 'V' and resid 118 through 133 removed outlier: 3.546A pdb=" N ALA V 122 " --> pdb=" O ARG V 118 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR V 133 " --> pdb=" O MET V 129 " (cutoff:3.500A) Processing helix chain 'V' and resid 173 through 185 removed outlier: 3.722A pdb=" N ALA V 177 " --> pdb=" O GLY V 173 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL V 180 " --> pdb=" O ALA V 176 " (cutoff:3.500A) Processing helix chain 'V' and resid 190 through 209 Processing helix chain 'W' and resid 56 through 79 Processing helix chain 'W' and resid 83 through 97 Processing helix chain 'W' and resid 142 through 154 removed outlier: 3.708A pdb=" N SER W 152 " --> pdb=" O GLY W 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 176 Processing helix chain 'X' and resid 51 through 72 Processing helix chain 'X' and resid 76 through 93 removed outlier: 3.594A pdb=" N CYS X 91 " --> pdb=" O ASN X 87 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG X 93 " --> pdb=" O ALA X 89 " (cutoff:3.500A) Processing helix chain 'X' and resid 134 through 147 removed outlier: 4.319A pdb=" N LEU X 138 " --> pdb=" O TYR X 134 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER X 141 " --> pdb=" O PHE X 137 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE X 142 " --> pdb=" O LEU X 138 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 171 Processing helix chain 'Y' and resid 107 through 130 Processing helix chain 'Y' and resid 134 through 147 removed outlier: 3.557A pdb=" N VAL Y 146 " --> pdb=" O LEU Y 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 150 No H-bonds generated for 'chain 'Y' and resid 148 through 150' Processing helix chain 'Y' and resid 190 through 202 removed outlier: 3.634A pdb=" N ALA Y 194 " --> pdb=" O GLY Y 190 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY Y 196 " --> pdb=" O VAL Y 192 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL Y 197 " --> pdb=" O TYR Y 193 " (cutoff:3.500A) Processing helix chain 'Y' and resid 207 through 226 removed outlier: 3.829A pdb=" N ARG Y 225 " --> pdb=" O GLN Y 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 251 through 260 removed outlier: 4.661A pdb=" N GLU Y 256 " --> pdb=" O ALA Y 252 " (cutoff:3.500A) Processing helix chain 'Z' and resid 85 through 108 Processing helix chain 'Z' and resid 112 through 126 removed outlier: 3.661A pdb=" N THR Z 122 " --> pdb=" O ALA Z 118 " (cutoff:3.500A) Processing helix chain 'Z' and resid 169 through 181 Proline residue: Z 175 - end of helix Processing helix chain 'Z' and resid 195 through 212 removed outlier: 3.869A pdb=" N GLU Z 212 " --> pdb=" O ILE Z 208 " (cutoff:3.500A) Processing helix chain 'a' and resid 101 through 122 removed outlier: 3.545A pdb=" N PHE a 105 " --> pdb=" O ASP a 101 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU a 122 " --> pdb=" O ASP a 118 " (cutoff:3.500A) Processing helix chain 'a' and resid 129 through 146 Processing helix chain 'a' and resid 186 through 191 Processing helix chain 'a' and resid 191 through 202 removed outlier: 3.725A pdb=" N LYS a 201 " --> pdb=" O GLU a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 206 through 225 Processing helix chain 'a' and resid 255 through 259 Processing helix chain 'b' and resid 82 through 105 Processing helix chain 'b' and resid 109 through 124 removed outlier: 4.406A pdb=" N GLU b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET b 120 " --> pdb=" O LEU b 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR b 124 " --> pdb=" O MET b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 168 removed outlier: 3.809A pdb=" N TYR b 168 " --> pdb=" O GLY b 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 165 through 168' Processing helix chain 'b' and resid 169 through 177 Processing helix chain 'b' and resid 182 through 201 removed outlier: 3.618A pdb=" N GLN b 188 " --> pdb=" O GLU b 184 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE b 189 " --> pdb=" O GLU b 185 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA b 191 " --> pdb=" O LEU b 187 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG b 200 " --> pdb=" O LEU b 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.565A pdb=" N GLY A 138 " --> pdb=" O TYR A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.694A pdb=" N LEU B 134 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'C' and resid 62 through 64 Processing sheet with id=AA7, first strand: chain 'D' and resid 167 through 170 Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.538A pdb=" N ILE D 67 " --> pdb=" O MET D 78 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N MET D 78 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLU D 69 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS D 76 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU D 153 " --> pdb=" O CYS D 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 161 removed outlier: 5.244A pdb=" N GLY E 216 " --> pdb=" O GLU E 220 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLU E 220 " --> pdb=" O GLY E 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 63 through 67 removed outlier: 7.047A pdb=" N ILE E 63 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE E 74 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N HIS E 65 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE E 72 " --> pdb=" O HIS E 65 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE E 144 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 163 through 166 Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 71 removed outlier: 6.646A pdb=" N LEU F 67 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL F 78 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ASN F 69 " --> pdb=" O MET F 76 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N MET F 76 " --> pdb=" O ASN F 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.946A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 69 through 73 removed outlier: 6.541A pdb=" N LEU G 69 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N MET G 80 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LYS G 71 " --> pdb=" O CYS G 78 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N CYS G 78 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR G 73 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 167 through 171 removed outlier: 6.936A pdb=" N ILE H 216 " --> pdb=" O TYR H 232 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N LEU H 218 " --> pdb=" O ARG H 230 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ARG H 230 " --> pdb=" O LEU H 218 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL H 220 " --> pdb=" O PHE H 228 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE H 228 " --> pdb=" O VAL H 220 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N SER H 222 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU H 226 " --> pdb=" O SER H 222 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 63 through 65 removed outlier: 6.180A pdb=" N GLU H 65 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL H 69 " --> pdb=" O GLU H 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 77 through 81 removed outlier: 6.236A pdb=" N ILE H 84 " --> pdb=" O ILE H 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 254 through 261 removed outlier: 6.705A pdb=" N THR I 199 " --> pdb=" O LEU H 255 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU H 257 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR I 197 " --> pdb=" O GLU H 257 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ILE H 259 " --> pdb=" O ILE I 195 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE I 195 " --> pdb=" O ILE H 259 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL I 185 " --> pdb=" O LEU I 200 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA I 10 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 28 through 30 removed outlier: 6.073A pdb=" N ILE I 30 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N MET I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 42 through 44 Processing sheet with id=AC3, first strand: chain 'J' and resid 129 through 132 Processing sheet with id=AC4, first strand: chain 'J' and resid 129 through 132 Processing sheet with id=AC5, first strand: chain 'J' and resid 21 through 23 removed outlier: 6.236A pdb=" N SER J 23 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN J 27 " --> pdb=" O SER J 23 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 35 through 39 removed outlier: 6.298A pdb=" N ILE J 42 " --> pdb=" O MET J 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 184 through 188 removed outlier: 3.789A pdb=" N SER K 247 " --> pdb=" O LEU K 235 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N HIS K 237 " --> pdb=" O ARG K 245 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ARG K 245 " --> pdb=" O HIS K 237 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG K 239 " --> pdb=" O TRP K 243 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TRP K 243 " --> pdb=" O ARG K 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 79 through 81 removed outlier: 6.908A pdb=" N ALA K 79 " --> pdb=" O ALA K 86 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR K 84 " --> pdb=" O ALA K 81 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 93 through 94 removed outlier: 4.828A pdb=" N MET K 159 " --> pdb=" O THR K 103 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 163 through 167 removed outlier: 5.713A pdb=" N THR L 39 " --> pdb=" O ASP L 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP L 54 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 57 through 59 removed outlier: 6.506A pdb=" N GLU L 59 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 71 through 75 removed outlier: 6.390A pdb=" N THR L 78 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN L 136 " --> pdb=" O PHE L 152 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL L 149 " --> pdb=" O ASP L 161 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 51 through 52 Processing sheet with id=AD5, first strand: chain 'M' and resid 181 through 183 removed outlier: 3.631A pdb=" N GLY M 64 " --> pdb=" O PHE M 61 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE M 232 " --> pdb=" O PRO M 247 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 87 through 91 removed outlier: 6.674A pdb=" N THR M 94 " --> pdb=" O VAL M 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 159 through 162 Processing sheet with id=AD8, first strand: chain 'N' and resid 54 through 56 removed outlier: 6.472A pdb=" N THR N 56 " --> pdb=" O ILE N 60 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE N 60 " --> pdb=" O THR N 56 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 68 through 70 removed outlier: 3.543A pdb=" N VAL N 155 " --> pdb=" O SER N 147 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 160 through 163 Processing sheet with id=AE2, first strand: chain 'O' and resid 66 through 69 removed outlier: 6.533A pdb=" N ILE O 72 " --> pdb=" O ILE O 68 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY O 138 " --> pdb=" O TYR O 145 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 161 through 164 Processing sheet with id=AE4, first strand: chain 'P' and resid 65 through 67 removed outlier: 3.672A pdb=" N LEU P 134 " --> pdb=" O SER P 150 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.672A pdb=" N HIS Q 15 " --> pdb=" O SER Q 11 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 158 through 161 Processing sheet with id=AE7, first strand: chain 'Q' and resid 62 through 64 Processing sheet with id=AE8, first strand: chain 'R' and resid 167 through 170 Processing sheet with id=AE9, first strand: chain 'R' and resid 67 through 71 removed outlier: 6.573A pdb=" N ILE R 67 " --> pdb=" O MET R 78 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N MET R 78 " --> pdb=" O ILE R 67 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU R 69 " --> pdb=" O CYS R 76 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N CYS R 76 " --> pdb=" O GLU R 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP R 147 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU R 153 " --> pdb=" O CYS R 165 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 158 through 161 removed outlier: 5.142A pdb=" N GLY S 216 " --> pdb=" O GLU S 220 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLU S 220 " --> pdb=" O GLY S 216 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 63 through 67 removed outlier: 7.049A pdb=" N ILE S 63 " --> pdb=" O ILE S 74 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE S 74 " --> pdb=" O ILE S 63 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N HIS S 65 " --> pdb=" O ILE S 72 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE S 72 " --> pdb=" O HIS S 65 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE S 144 " --> pdb=" O CYS S 156 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 163 through 166 Processing sheet with id=AF4, first strand: chain 'T' and resid 67 through 71 removed outlier: 3.594A pdb=" N VAL T 70 " --> pdb=" O VAL T 74 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL T 74 " --> pdb=" O VAL T 70 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 165 through 169 removed outlier: 6.637A pdb=" N THR U 38 " --> pdb=" O GLN U 53 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN U 53 " --> pdb=" O THR U 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 69 through 73 removed outlier: 6.537A pdb=" N LEU U 69 " --> pdb=" O MET U 80 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N MET U 80 " --> pdb=" O LEU U 69 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS U 71 " --> pdb=" O CYS U 78 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N CYS U 78 " --> pdb=" O LYS U 71 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR U 73 " --> pdb=" O ILE U 76 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 167 through 171 removed outlier: 6.642A pdb=" N THR V 45 " --> pdb=" O ASP V 60 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE V 216 " --> pdb=" O TYR V 232 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU V 218 " --> pdb=" O ARG V 230 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG V 230 " --> pdb=" O LEU V 218 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL V 220 " --> pdb=" O PHE V 228 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE V 228 " --> pdb=" O VAL V 220 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N SER V 222 " --> pdb=" O LEU V 226 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LEU V 226 " --> pdb=" O SER V 222 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 63 through 65 removed outlier: 6.130A pdb=" N GLU V 65 " --> pdb=" O VAL V 69 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL V 69 " --> pdb=" O GLU V 65 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 77 through 81 removed outlier: 6.236A pdb=" N ILE V 84 " --> pdb=" O ILE V 80 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 254 through 261 removed outlier: 6.705A pdb=" N THR W 199 " --> pdb=" O LEU V 255 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU V 257 " --> pdb=" O THR W 197 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR W 197 " --> pdb=" O GLU V 257 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE V 259 " --> pdb=" O ILE W 195 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE W 195 " --> pdb=" O ILE V 259 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL W 185 " --> pdb=" O LEU W 200 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA W 10 " --> pdb=" O ASP W 25 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 28 through 30 removed outlier: 6.153A pdb=" N ILE W 30 " --> pdb=" O MET W 34 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N MET W 34 " --> pdb=" O ILE W 30 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 42 through 44 Processing sheet with id=AG4, first strand: chain 'X' and resid 129 through 132 Processing sheet with id=AG5, first strand: chain 'X' and resid 129 through 132 Processing sheet with id=AG6, first strand: chain 'X' and resid 21 through 23 removed outlier: 6.202A pdb=" N SER X 23 " --> pdb=" O GLN X 27 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLN X 27 " --> pdb=" O SER X 23 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 35 through 39 removed outlier: 6.287A pdb=" N ILE X 42 " --> pdb=" O MET X 38 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 184 through 188 removed outlier: 3.800A pdb=" N SER Y 247 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N HIS Y 237 " --> pdb=" O ARG Y 245 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ARG Y 245 " --> pdb=" O HIS Y 237 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG Y 239 " --> pdb=" O TRP Y 243 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP Y 243 " --> pdb=" O ARG Y 239 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 79 through 81 removed outlier: 6.905A pdb=" N ALA Y 79 " --> pdb=" O ALA Y 86 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR Y 84 " --> pdb=" O ALA Y 81 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 93 through 94 removed outlier: 4.869A pdb=" N MET Y 159 " --> pdb=" O THR Y 103 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 163 through 167 removed outlier: 5.719A pdb=" N THR Z 39 " --> pdb=" O ASP Z 54 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP Z 54 " --> pdb=" O THR Z 39 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 57 through 59 removed outlier: 6.505A pdb=" N GLU Z 59 " --> pdb=" O ILE Z 63 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE Z 63 " --> pdb=" O GLU Z 59 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Z' and resid 71 through 75 removed outlier: 6.392A pdb=" N THR Z 78 " --> pdb=" O LEU Z 74 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN Z 136 " --> pdb=" O PHE Z 152 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL Z 149 " --> pdb=" O ASP Z 161 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'a' and resid 51 through 52 Processing sheet with id=AH6, first strand: chain 'a' and resid 181 through 183 removed outlier: 3.658A pdb=" N GLY a 64 " --> pdb=" O PHE a 61 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE a 232 " --> pdb=" O PRO a 247 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'a' and resid 87 through 91 removed outlier: 6.626A pdb=" N THR a 94 " --> pdb=" O VAL a 90 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'b' and resid 159 through 163 Processing sheet with id=AH9, first strand: chain 'b' and resid 54 through 56 removed outlier: 6.906A pdb=" N THR b 54 " --> pdb=" O ALA b 61 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR b 59 " --> pdb=" O THR b 56 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'b' and resid 68 through 72 removed outlier: 6.977A pdb=" N LEU b 68 " --> pdb=" O ARG b 79 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ARG b 79 " --> pdb=" O LEU b 68 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N CYS b 77 " --> pdb=" O PRO b 70 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL b 155 " --> pdb=" O SER b 147 " (cutoff:3.500A) 2667 hydrogen bonds defined for protein. 7638 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: 19.92 Time building geometry restraints manager: 18.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13696 1.33 - 1.45: 7564 1.45 - 1.57: 27034 1.57 - 1.69: 0 1.69 - 1.81: 490 Bond restraints: 48784 Sorted by residual: bond pdb=" N ASP N 138 " pdb=" CA ASP N 138 " ideal model delta sigma weight residual 1.453 1.484 -0.031 1.18e-02 7.18e+03 7.00e+00 bond pdb=" N THR R 230 " pdb=" CA THR R 230 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.09e-02 8.42e+03 6.97e+00 bond pdb=" N ASN X 24 " pdb=" CA ASN X 24 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.76e+00 bond pdb=" N ASP b 138 " pdb=" CA ASP b 138 " ideal model delta sigma weight residual 1.453 1.483 -0.031 1.18e-02 7.18e+03 6.72e+00 bond pdb=" N SER X 23 " pdb=" CA SER X 23 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.19e-02 7.06e+03 5.19e+00 ... (remaining 48779 not shown) Histogram of bond angle deviations from ideal: 97.34 - 104.69: 671 104.69 - 112.04: 23553 112.04 - 119.38: 16875 119.38 - 126.73: 24369 126.73 - 134.08: 416 Bond angle restraints: 65884 Sorted by residual: angle pdb=" C MET M 50 " pdb=" CA MET M 50 " pdb=" CB MET M 50 " ideal model delta sigma weight residual 117.23 109.21 8.02 1.36e+00 5.41e-01 3.48e+01 angle pdb=" N GLY V 144 " pdb=" CA GLY V 144 " pdb=" C GLY V 144 " ideal model delta sigma weight residual 110.87 116.42 -5.55 1.54e+00 4.22e-01 1.30e+01 angle pdb=" N GLU a 215 " pdb=" CA GLU a 215 " pdb=" CB GLU a 215 " ideal model delta sigma weight residual 110.16 115.42 -5.26 1.48e+00 4.57e-01 1.26e+01 angle pdb=" N GLY H 144 " pdb=" CA GLY H 144 " pdb=" C GLY H 144 " ideal model delta sigma weight residual 110.87 116.25 -5.38 1.54e+00 4.22e-01 1.22e+01 angle pdb=" N SER b 52 " pdb=" CA SER b 52 " pdb=" C SER b 52 " ideal model delta sigma weight residual 110.61 114.54 -3.93 1.25e+00 6.40e-01 9.89e+00 ... (remaining 65879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 27134 17.97 - 35.95: 1892 35.95 - 53.92: 277 53.92 - 71.89: 92 71.89 - 89.87: 33 Dihedral angle restraints: 29428 sinusoidal: 11630 harmonic: 17798 Sorted by residual: dihedral pdb=" CA THR L 217 " pdb=" C THR L 217 " pdb=" N GLY L 218 " pdb=" CA GLY L 218 " ideal model delta harmonic sigma weight residual 180.00 154.55 25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA GLY I 101 " pdb=" C GLY I 101 " pdb=" N PRO I 102 " pdb=" CA PRO I 102 " ideal model delta harmonic sigma weight residual -180.00 -155.54 -24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA GLY W 101 " pdb=" C GLY W 101 " pdb=" N PRO W 102 " pdb=" CA PRO W 102 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 29425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 4466 0.037 - 0.073: 2079 0.073 - 0.110: 597 0.110 - 0.147: 247 0.147 - 0.183: 15 Chirality restraints: 7404 Sorted by residual: chirality pdb=" CA ASP C 148 " pdb=" N ASP C 148 " pdb=" C ASP C 148 " pdb=" CB ASP C 148 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA ASP Q 148 " pdb=" N ASP Q 148 " pdb=" C ASP Q 148 " pdb=" CB ASP Q 148 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA ILE b 133 " pdb=" N ILE b 133 " pdb=" C ILE b 133 " pdb=" CB ILE b 133 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 7401 not shown) Planarity restraints: 8484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 216 " 0.033 2.00e-02 2.50e+03 3.35e-02 2.81e+01 pdb=" CG TRP F 216 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP F 216 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP F 216 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 216 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 216 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP F 216 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 216 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 216 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP F 216 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP T 216 " 0.033 2.00e-02 2.50e+03 3.35e-02 2.80e+01 pdb=" CG TRP T 216 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP T 216 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP T 216 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP T 216 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP T 216 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP T 216 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP T 216 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP T 216 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP T 216 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE X 171 " -0.018 2.00e-02 2.50e+03 1.86e-02 6.05e+00 pdb=" CG PHE X 171 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE X 171 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE X 171 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE X 171 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE X 171 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE X 171 " -0.001 2.00e-02 2.50e+03 ... (remaining 8481 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5152 2.75 - 3.28: 42540 3.28 - 3.82: 72751 3.82 - 4.36: 89389 4.36 - 4.90: 166112 Nonbonded interactions: 375944 Sorted by model distance: nonbonded pdb=" OD1 ASP a 171 " pdb=" N MET a 172 " model vdw 2.208 2.520 nonbonded pdb=" OD1 ASN M 83 " pdb=" NH2 ARG M 231 " model vdw 2.218 2.520 nonbonded pdb=" OG1 THR D 230 " pdb=" OE1 GLU D 233 " model vdw 2.250 2.440 nonbonded pdb=" OD2 ASP B 6 " pdb=" OH TYR C 3 " model vdw 2.265 2.440 nonbonded pdb=" OD2 ASP P 6 " pdb=" OH TYR Q 3 " model vdw 2.280 2.440 ... (remaining 375939 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } 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 individual isotropic 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: 1.300 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: 0.040 Extract box with map and model: 7.640 Check model and map are aligned: 0.790 Set scattering table: 0.470 Process input model: 117.620 Find NCS groups from input model: 4.890 Set up NCS constraints: 0.450 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: 0.010 Load rotamer database and sin/cos tables:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.006 0.050 48784 Z= 0.359 Angle : 0.659 8.584 65884 Z= 0.365 Chirality : 0.047 0.183 7404 Planarity : 0.005 0.061 8484 Dihedral : 13.086 89.866 18064 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.02 % Allowed : 0.12 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.10), residues: 6102 helix: 1.71 (0.11), residues: 2160 sheet: 0.62 (0.13), residues: 1482 loop : -0.81 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.003 TRP T 216 HIS 0.008 0.001 HIS a 134 PHE 0.043 0.002 PHE X 171 TYR 0.024 0.002 TYR K 195 ARG 0.005 0.001 ARG O 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 826 time to evaluate : 5.456 Fit side-chains revert: symmetry clash REVERT: A 203 MET cc_start: 0.8362 (ptm) cc_final: 0.7802 (ptp) REVERT: B 178 ASP cc_start: 0.6933 (m-30) cc_final: 0.6658 (m-30) REVERT: D 186 HIS cc_start: 0.7567 (p90) cc_final: 0.7352 (p90) REVERT: D 235 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7102 (mp0) REVERT: E 61 LYS cc_start: 0.7389 (mtpt) cc_final: 0.7070 (mttt) REVERT: E 100 ASP cc_start: 0.7501 (t70) cc_final: 0.7216 (t0) REVERT: F 182 MET cc_start: 0.7975 (pmm) cc_final: 0.7467 (pmm) REVERT: I 155 GLU cc_start: 0.7960 (pt0) cc_final: 0.7727 (pt0) REVERT: I 204 MET cc_start: 0.8353 (mmm) cc_final: 0.8055 (mmm) REVERT: K 156 MET cc_start: 0.8157 (ptm) cc_final: 0.7748 (ptm) REVERT: K 174 ASP cc_start: 0.8503 (p0) cc_final: 0.8254 (p0) REVERT: K 178 ASN cc_start: 0.8734 (m-40) cc_final: 0.8271 (m110) REVERT: N 105 ASN cc_start: 0.8586 (t0) cc_final: 0.8292 (t0) REVERT: O 203 MET cc_start: 0.8237 (ptm) cc_final: 0.7849 (ptp) REVERT: P 178 ASP cc_start: 0.6950 (m-30) cc_final: 0.6678 (m-30) REVERT: S 61 LYS cc_start: 0.7412 (mtpt) cc_final: 0.7088 (mttt) REVERT: T 33 ASN cc_start: 0.7509 (m110) cc_final: 0.7206 (m110) REVERT: V 178 MET cc_start: 0.8210 (tpt) cc_final: 0.8002 (tpp) REVERT: W 155 GLU cc_start: 0.7948 (pt0) cc_final: 0.7707 (pt0) REVERT: Y 174 ASP cc_start: 0.8479 (p0) cc_final: 0.8235 (p0) REVERT: Y 178 ASN cc_start: 0.8688 (m-40) cc_final: 0.8219 (m110) REVERT: Z 146 LYS cc_start: 0.8106 (mttm) cc_final: 0.7872 (mttm) REVERT: b 105 ASN cc_start: 0.8598 (t0) cc_final: 0.8286 (t0) REVERT: b 178 ARG cc_start: 0.8246 (ptt-90) cc_final: 0.7899 (ptt-90) outliers start: 1 outliers final: 0 residues processed: 826 average time/residue: 1.8513 time to fit residues: 1840.3881 Evaluate side-chains 635 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 635 time to evaluate : 5.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 506 optimal weight: 1.9990 chunk 454 optimal weight: 6.9990 chunk 252 optimal weight: 0.0050 chunk 155 optimal weight: 8.9990 chunk 306 optimal weight: 2.9990 chunk 242 optimal weight: 10.0000 chunk 470 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 285 optimal weight: 6.9990 chunk 350 optimal weight: 0.4980 chunk 544 optimal weight: 2.9990 overall best weight: 1.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS B 123 GLN D 104 ASN D 225 ASN I 81 GLN I 157 ASN J 8 GLN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 ASN P 123 GLN P 235 GLN R 104 ASN R 225 ASN W 81 GLN X 8 GLN X 27 GLN Y 144 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 48784 Z= 0.203 Angle : 0.532 13.732 65884 Z= 0.288 Chirality : 0.043 0.165 7404 Planarity : 0.004 0.069 8484 Dihedral : 4.465 24.310 6778 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.68 % Allowed : 8.77 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.11), residues: 6102 helix: 2.17 (0.11), residues: 2202 sheet: 0.78 (0.13), residues: 1476 loop : -0.79 (0.11), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 216 HIS 0.006 0.001 HIS X 132 PHE 0.025 0.002 PHE J 171 TYR 0.014 0.001 TYR X 117 ARG 0.004 0.000 ARG O 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 675 time to evaluate : 5.473 Fit side-chains REVERT: A 102 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7118 (mp10) REVERT: A 203 MET cc_start: 0.8316 (ptm) cc_final: 0.7757 (ptp) REVERT: B 178 ASP cc_start: 0.6950 (m-30) cc_final: 0.6675 (m-30) REVERT: C 99 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7550 (mm-30) REVERT: D 235 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7107 (mp0) REVERT: E 61 LYS cc_start: 0.7417 (mtpt) cc_final: 0.7072 (mttt) REVERT: E 100 ASP cc_start: 0.7323 (t70) cc_final: 0.7033 (t0) REVERT: E 122 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7359 (mtp85) REVERT: F 182 MET cc_start: 0.7940 (pmm) cc_final: 0.7511 (pmm) REVERT: F 184 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6363 (pm20) REVERT: H 65 GLU cc_start: 0.7230 (tt0) cc_final: 0.6986 (tt0) REVERT: I 4 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7257 (mmm) REVERT: I 155 GLU cc_start: 0.7887 (pt0) cc_final: 0.7653 (pt0) REVERT: I 204 MET cc_start: 0.8351 (mmm) cc_final: 0.8115 (mmm) REVERT: K 152 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.6541 (mpt) REVERT: K 156 MET cc_start: 0.7971 (ptm) cc_final: 0.7695 (ptm) REVERT: K 174 ASP cc_start: 0.8490 (p0) cc_final: 0.8263 (p0) REVERT: K 178 ASN cc_start: 0.8664 (m-40) cc_final: 0.8240 (m110) REVERT: M 50 MET cc_start: 0.7316 (mmt) cc_final: 0.6992 (mmm) REVERT: M 200 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: N 105 ASN cc_start: 0.8419 (t0) cc_final: 0.8212 (t0) REVERT: N 126 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: O 102 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7105 (mp10) REVERT: O 203 MET cc_start: 0.8253 (ptm) cc_final: 0.7784 (ptp) REVERT: P 178 ASP cc_start: 0.6919 (m-30) cc_final: 0.6649 (m-30) REVERT: Q 99 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: R 235 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: S 61 LYS cc_start: 0.7444 (mtpt) cc_final: 0.7115 (mttt) REVERT: S 100 ASP cc_start: 0.7345 (t0) cc_final: 0.7029 (t0) REVERT: S 122 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7365 (mtp85) REVERT: S 166 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7721 (mm-40) REVERT: T 33 ASN cc_start: 0.7453 (m110) cc_final: 0.7190 (m110) REVERT: W 155 GLU cc_start: 0.7911 (pt0) cc_final: 0.7667 (pt0) REVERT: X 1 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7600 (ttt) REVERT: Y 174 ASP cc_start: 0.8497 (p0) cc_final: 0.8290 (p0) REVERT: Y 178 ASN cc_start: 0.8665 (m-40) cc_final: 0.8235 (m110) REVERT: a 245 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6588 (tp30) REVERT: b 126 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: b 178 ARG cc_start: 0.8213 (ptt-90) cc_final: 0.7827 (ptt-90) outliers start: 86 outliers final: 34 residues processed: 717 average time/residue: 1.8626 time to fit residues: 1609.1505 Evaluate side-chains 691 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 642 time to evaluate : 5.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain D residue 239 LYS Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 119 ASP Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 185 LYS Chi-restraints excluded: chain K residue 152 MET Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 218 MET Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain O residue 102 GLN Chi-restraints excluded: chain O residue 222 THR Chi-restraints excluded: chain Q residue 99 GLU Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 239 LYS Chi-restraints excluded: chain S residue 122 ARG Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 185 LYS Chi-restraints excluded: chain Y residue 88 GLN Chi-restraints excluded: chain Y residue 161 CYS Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain a residue 245 GLU Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 144 GLN Chi-restraints excluded: chain b residue 199 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 302 optimal weight: 7.9990 chunk 169 optimal weight: 0.8980 chunk 453 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 545 optimal weight: 7.9990 chunk 589 optimal weight: 6.9990 chunk 486 optimal weight: 4.9990 chunk 541 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 437 optimal weight: 6.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 HIS C 85 ASN D 104 ASN D 225 ASN F 181 GLN H 134 GLN I 81 GLN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 GLN P 100 GLN R 104 ASN R 186 HIS R 225 ASN V 134 GLN W 81 GLN b 105 ASN ** b 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 48784 Z= 0.422 Angle : 0.642 13.971 65884 Z= 0.342 Chirality : 0.047 0.191 7404 Planarity : 0.005 0.070 8484 Dihedral : 4.715 26.006 6778 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.78 % Allowed : 10.65 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.10), residues: 6102 helix: 1.94 (0.11), residues: 2198 sheet: 0.63 (0.13), residues: 1490 loop : -0.97 (0.11), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP T 216 HIS 0.010 0.001 HIS a 134 PHE 0.031 0.002 PHE X 171 TYR 0.022 0.002 TYR P 136 ARG 0.005 0.001 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 666 time to evaluate : 5.671 Fit side-chains REVERT: A 102 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7282 (mp10) REVERT: A 203 MET cc_start: 0.8384 (ptm) cc_final: 0.7876 (ptp) REVERT: B 218 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7906 (tpt-90) REVERT: B 238 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7298 (mppt) REVERT: D 186 HIS cc_start: 0.7836 (p-80) cc_final: 0.7489 (p90) REVERT: E 61 LYS cc_start: 0.7558 (mtpt) cc_final: 0.7078 (mttt) REVERT: E 100 ASP cc_start: 0.7617 (t70) cc_final: 0.7269 (t0) REVERT: E 122 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7331 (mtp85) REVERT: H 100 GLN cc_start: 0.8385 (mt0) cc_final: 0.7999 (mt0) REVERT: H 258 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6466 (ptpt) REVERT: I 40 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8859 (tt0) REVERT: I 155 GLU cc_start: 0.7934 (pt0) cc_final: 0.7684 (pt0) REVERT: J 28 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7976 (mtp) REVERT: J 40 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: K 152 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.6158 (mpt) REVERT: K 156 MET cc_start: 0.7829 (ptm) cc_final: 0.7596 (ptm) REVERT: K 159 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.7596 (mpp) REVERT: K 174 ASP cc_start: 0.8485 (p0) cc_final: 0.8257 (p0) REVERT: K 178 ASN cc_start: 0.8710 (m-40) cc_final: 0.8303 (m110) REVERT: M 200 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: N 105 ASN cc_start: 0.8462 (t0) cc_final: 0.8217 (t0) REVERT: N 126 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: O 96 GLN cc_start: 0.8237 (mt0) cc_final: 0.7960 (mt0) REVERT: O 102 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7045 (mp10) REVERT: O 203 MET cc_start: 0.8334 (ptm) cc_final: 0.7906 (ptp) REVERT: P 178 ASP cc_start: 0.6961 (m-30) cc_final: 0.6755 (m-30) REVERT: P 218 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7878 (tpt-90) REVERT: R 235 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: S 61 LYS cc_start: 0.7565 (mtpt) cc_final: 0.7086 (mttt) REVERT: S 100 ASP cc_start: 0.7504 (t0) cc_final: 0.7043 (t0) REVERT: S 122 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7328 (mtp85) REVERT: T 33 ASN cc_start: 0.7561 (m110) cc_final: 0.7306 (m110) REVERT: W 155 GLU cc_start: 0.7945 (pt0) cc_final: 0.7691 (pt0) REVERT: Y 159 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.7574 (mpp) REVERT: Y 174 ASP cc_start: 0.8468 (p0) cc_final: 0.8249 (p0) REVERT: Y 178 ASN cc_start: 0.8713 (m-40) cc_final: 0.8313 (m110) REVERT: a 71 MET cc_start: 0.9130 (mtp) cc_final: 0.8906 (mtp) REVERT: a 200 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: a 243 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: b 105 ASN cc_start: 0.8476 (t0) cc_final: 0.8219 (t0) REVERT: b 126 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: b 178 ARG cc_start: 0.8234 (ptt-90) cc_final: 0.7795 (ptt-90) outliers start: 142 outliers final: 67 residues processed: 735 average time/residue: 1.8762 time to fit residues: 1659.2699 Evaluate side-chains 723 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 636 time to evaluate : 5.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain H residue 258 LYS Chi-restraints excluded: chain I residue 40 GLN Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 40 GLU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 185 LYS Chi-restraints excluded: chain K residue 152 MET Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 226 VAL Chi-restraints excluded: chain M residue 88 MET Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 218 MET Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain N residue 144 GLN Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain O residue 102 GLN Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 222 THR Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 218 ARG Chi-restraints excluded: chain Q residue 163 ARG Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain Q residue 219 ILE Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain S residue 122 ARG Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 176 MET Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 91 ILE Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 217 ASP Chi-restraints excluded: chain V residue 230 ARG Chi-restraints excluded: chain W residue 106 GLU Chi-restraints excluded: chain W residue 152 SER Chi-restraints excluded: chain W residue 183 MET Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 177 THR Chi-restraints excluded: chain X residue 185 LYS Chi-restraints excluded: chain Y residue 88 GLN Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 161 CYS Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Z residue 76 ASP Chi-restraints excluded: chain Z residue 151 SER Chi-restraints excluded: chain Z residue 226 VAL Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain a residue 243 GLU Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 144 GLN Chi-restraints excluded: chain b residue 199 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 539 optimal weight: 4.9990 chunk 410 optimal weight: 5.9990 chunk 283 optimal weight: 0.0770 chunk 60 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 366 optimal weight: 2.9990 chunk 547 optimal weight: 0.9990 chunk 579 optimal weight: 4.9990 chunk 286 optimal weight: 0.9990 chunk 519 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 123 GLN B 198 ASN B 240 HIS C 85 ASN C 175 ASN D 225 ASN H 134 GLN I 81 GLN I 157 ASN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 HIS O 42 ASN R 225 ASN T 222 ASN V 134 GLN W 40 GLN W 81 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 48784 Z= 0.211 Angle : 0.516 11.728 65884 Z= 0.280 Chirality : 0.043 0.145 7404 Planarity : 0.004 0.067 8484 Dihedral : 4.403 24.918 6778 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.41 % Allowed : 12.41 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.11), residues: 6102 helix: 2.28 (0.11), residues: 2202 sheet: 0.78 (0.13), residues: 1458 loop : -0.89 (0.11), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 100 HIS 0.007 0.001 HIS D 186 PHE 0.019 0.001 PHE F 136 TYR 0.014 0.001 TYR J 117 ARG 0.003 0.000 ARG O 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 660 time to evaluate : 4.389 Fit side-chains REVERT: A 102 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.6949 (mp10) REVERT: A 203 MET cc_start: 0.8286 (ptm) cc_final: 0.7736 (ptp) REVERT: B 218 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7834 (tpt-90) REVERT: B 238 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7322 (mppt) REVERT: D 186 HIS cc_start: 0.7723 (p-80) cc_final: 0.7332 (p90) REVERT: D 235 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7280 (mp0) REVERT: E 61 LYS cc_start: 0.7580 (mtpt) cc_final: 0.7152 (mttt) REVERT: E 100 ASP cc_start: 0.7419 (t70) cc_final: 0.7063 (t0) REVERT: E 122 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7302 (mtp85) REVERT: F 71 ASP cc_start: 0.7581 (t0) cc_final: 0.7062 (t0) REVERT: G 174 GLU cc_start: 0.6293 (mp0) cc_final: 0.5978 (mm-30) REVERT: H 65 GLU cc_start: 0.7230 (tt0) cc_final: 0.6994 (tt0) REVERT: H 225 LYS cc_start: 0.7872 (pttm) cc_final: 0.7670 (pttm) REVERT: I 155 GLU cc_start: 0.7864 (pt0) cc_final: 0.7613 (pt0) REVERT: K 152 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.6268 (mpt) REVERT: K 156 MET cc_start: 0.7801 (ptm) cc_final: 0.7566 (ptm) REVERT: K 159 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.7532 (mpp) REVERT: K 174 ASP cc_start: 0.8522 (p0) cc_final: 0.8312 (p0) REVERT: K 178 ASN cc_start: 0.8634 (m-40) cc_final: 0.8228 (m110) REVERT: L 101 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7392 (mttp) REVERT: M 50 MET cc_start: 0.7483 (mmt) cc_final: 0.7185 (mmm) REVERT: M 200 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: N 105 ASN cc_start: 0.8406 (t0) cc_final: 0.8135 (t0) REVERT: N 126 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: N 198 MET cc_start: 0.8612 (mtm) cc_final: 0.8137 (mtp) REVERT: O 102 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7024 (mp10) REVERT: O 203 MET cc_start: 0.8266 (ptm) cc_final: 0.7806 (ptp) REVERT: P 178 ASP cc_start: 0.6915 (m-30) cc_final: 0.6704 (m-30) REVERT: P 218 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7785 (tpt-90) REVERT: Q 99 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7607 (mm-30) REVERT: S 61 LYS cc_start: 0.7588 (mtpt) cc_final: 0.7155 (mttt) REVERT: S 100 ASP cc_start: 0.7434 (t0) cc_final: 0.6970 (t0) REVERT: S 122 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7304 (mtp85) REVERT: T 71 ASP cc_start: 0.7958 (t0) cc_final: 0.7476 (t0) REVERT: W 155 GLU cc_start: 0.7869 (pt0) cc_final: 0.7614 (pt0) REVERT: Y 159 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.7521 (mpp) REVERT: Y 174 ASP cc_start: 0.8463 (p0) cc_final: 0.8254 (p0) REVERT: Y 178 ASN cc_start: 0.8629 (m-40) cc_final: 0.8215 (m110) REVERT: a 164 GLU cc_start: 0.5803 (OUTLIER) cc_final: 0.5217 (pp20) REVERT: a 200 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: b 105 ASN cc_start: 0.8389 (t0) cc_final: 0.8122 (t0) REVERT: b 126 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: b 198 MET cc_start: 0.8627 (mtm) cc_final: 0.8133 (mtp) outliers start: 123 outliers final: 62 residues processed: 727 average time/residue: 1.8295 time to fit residues: 1605.6187 Evaluate side-chains 714 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 635 time to evaluate : 5.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 237 LYS Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 119 ASP Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 185 LYS Chi-restraints excluded: chain K residue 152 MET Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 226 VAL Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 218 MET Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain O residue 102 GLN Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 222 THR Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 218 ARG Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 99 GLU Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 163 ARG Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain S residue 122 ARG Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 91 ILE Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 237 LYS Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain W residue 106 GLU Chi-restraints excluded: chain W residue 183 MET Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 185 LYS Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 161 CYS Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Z residue 76 ASP Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain Z residue 226 VAL Chi-restraints excluded: chain a residue 164 GLU Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 144 GLN Chi-restraints excluded: chain b residue 199 GLU Chi-restraints excluded: chain b residue 219 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 483 optimal weight: 0.9990 chunk 329 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 431 optimal weight: 0.2980 chunk 239 optimal weight: 9.9990 chunk 494 optimal weight: 0.9990 chunk 400 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 296 optimal weight: 0.9990 chunk 520 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN C 175 ASN D 104 ASN F 181 GLN H 134 GLN I 40 GLN I 81 GLN J 27 GLN K 237 HIS O 42 ASN O 52 GLN P 100 GLN Q 85 ASN R 104 ASN R 225 ASN T 222 ASN W 81 GLN Y 88 GLN Y 237 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 48784 Z= 0.134 Angle : 0.460 9.791 65884 Z= 0.250 Chirality : 0.041 0.192 7404 Planarity : 0.004 0.062 8484 Dihedral : 4.085 22.186 6778 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.02 % Allowed : 13.74 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.11), residues: 6102 helix: 2.61 (0.11), residues: 2200 sheet: 0.89 (0.13), residues: 1500 loop : -0.73 (0.12), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 100 HIS 0.007 0.000 HIS D 186 PHE 0.015 0.001 PHE H 79 TYR 0.014 0.001 TYR J 117 ARG 0.006 0.000 ARG J 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 681 time to evaluate : 5.539 Fit side-chains REVERT: A 102 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.6900 (mp10) REVERT: A 143 ARG cc_start: 0.7529 (ptm-80) cc_final: 0.7321 (ptm-80) REVERT: A 203 MET cc_start: 0.8088 (ptm) cc_final: 0.7498 (ptp) REVERT: B 151 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7765 (t0) REVERT: B 238 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7305 (mppt) REVERT: D 186 HIS cc_start: 0.7703 (p-80) cc_final: 0.7285 (p90) REVERT: E 61 LYS cc_start: 0.7526 (mtpt) cc_final: 0.7103 (mttt) REVERT: E 100 ASP cc_start: 0.7295 (t70) cc_final: 0.6993 (t0) REVERT: G 174 GLU cc_start: 0.6284 (mp0) cc_final: 0.5997 (mm-30) REVERT: I 151 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7687 (mm-30) REVERT: I 183 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7978 (mtt) REVERT: K 152 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.6344 (mpt) REVERT: K 156 MET cc_start: 0.7794 (ptm) cc_final: 0.7570 (ptm) REVERT: K 159 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7426 (mpp) REVERT: K 174 ASP cc_start: 0.8446 (p0) cc_final: 0.8232 (p0) REVERT: K 178 ASN cc_start: 0.8619 (m-40) cc_final: 0.8189 (m110) REVERT: K 256 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6957 (mp0) REVERT: L 97 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: L 101 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7306 (mttp) REVERT: M 50 MET cc_start: 0.7409 (mmt) cc_final: 0.7067 (mmm) REVERT: M 200 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: N 126 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: N 198 MET cc_start: 0.8503 (mtm) cc_final: 0.8040 (mtm) REVERT: O 102 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.6897 (mp10) REVERT: O 143 ARG cc_start: 0.7610 (ptm-80) cc_final: 0.7377 (ptm-80) REVERT: O 203 MET cc_start: 0.8190 (ptm) cc_final: 0.7623 (ptp) REVERT: P 178 ASP cc_start: 0.6862 (m-30) cc_final: 0.6657 (m-30) REVERT: S 61 LYS cc_start: 0.7537 (mtpt) cc_final: 0.7075 (mttt) REVERT: S 100 ASP cc_start: 0.7386 (t0) cc_final: 0.6924 (t0) REVERT: W 134 ASP cc_start: 0.7631 (t70) cc_final: 0.7340 (t0) REVERT: W 151 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7651 (mm-30) REVERT: Y 159 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7395 (mpp) REVERT: Y 178 ASN cc_start: 0.8626 (m-40) cc_final: 0.8223 (m110) REVERT: b 105 ASN cc_start: 0.8152 (t0) cc_final: 0.7908 (t0) REVERT: b 126 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: b 198 MET cc_start: 0.8509 (mtm) cc_final: 0.8055 (mtm) outliers start: 103 outliers final: 45 residues processed: 728 average time/residue: 1.7956 time to fit residues: 1584.7686 Evaluate side-chains 701 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 643 time to evaluate : 5.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 237 LYS Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 119 ASP Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 185 LYS Chi-restraints excluded: chain K residue 152 MET Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 172 MET Chi-restraints excluded: chain M residue 184 THR Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain O residue 102 GLN Chi-restraints excluded: chain O residue 222 THR Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 163 ARG Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 176 MET Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain V residue 230 ARG Chi-restraints excluded: chain V residue 237 LYS Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 183 MET Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 119 ASP Chi-restraints excluded: chain Y residue 88 GLN Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 161 CYS Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain Z residue 215 VAL Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 144 GLN Chi-restraints excluded: chain b residue 204 SER Chi-restraints excluded: chain b residue 219 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 195 optimal weight: 0.8980 chunk 522 optimal weight: 0.0000 chunk 114 optimal weight: 9.9990 chunk 340 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 580 optimal weight: 6.9990 chunk 481 optimal weight: 10.0000 chunk 268 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 304 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 ASN ** D 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN I 81 GLN I 93 ASN J 27 GLN N 144 GLN O 42 ASN O 52 GLN P 240 HIS R 225 ASN V 134 GLN W 81 GLN W 93 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 48784 Z= 0.167 Angle : 0.474 10.601 65884 Z= 0.257 Chirality : 0.042 0.142 7404 Planarity : 0.004 0.065 8484 Dihedral : 4.075 23.768 6778 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.11 % Allowed : 14.79 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.11), residues: 6102 helix: 2.65 (0.11), residues: 2202 sheet: 0.91 (0.13), residues: 1504 loop : -0.71 (0.12), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 100 HIS 0.007 0.001 HIS D 186 PHE 0.018 0.001 PHE T 136 TYR 0.014 0.001 TYR J 117 ARG 0.004 0.000 ARG J 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 664 time to evaluate : 5.701 Fit side-chains revert: symmetry clash REVERT: A 102 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.6907 (mp10) REVERT: A 203 MET cc_start: 0.8080 (ptm) cc_final: 0.7485 (ptp) REVERT: B 151 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7786 (t0) REVERT: B 238 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7310 (mppt) REVERT: D 186 HIS cc_start: 0.7662 (p-80) cc_final: 0.7206 (p90) REVERT: E 61 LYS cc_start: 0.7543 (mtpt) cc_final: 0.7103 (mttt) REVERT: E 100 ASP cc_start: 0.7337 (t70) cc_final: 0.7035 (t0) REVERT: G 174 GLU cc_start: 0.6293 (mp0) cc_final: 0.6013 (mm-30) REVERT: H 258 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6429 (ptpt) REVERT: I 4 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7181 (mpp) REVERT: I 155 GLU cc_start: 0.7839 (pt0) cc_final: 0.7575 (pt0) REVERT: I 183 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7999 (mtt) REVERT: J 28 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7988 (mtp) REVERT: K 152 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.6323 (mpt) REVERT: K 156 MET cc_start: 0.7785 (ptm) cc_final: 0.7556 (ptm) REVERT: K 159 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.7394 (mpp) REVERT: K 174 ASP cc_start: 0.8414 (p0) cc_final: 0.8191 (p0) REVERT: K 178 ASN cc_start: 0.8625 (m-40) cc_final: 0.8194 (m110) REVERT: L 146 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7920 (mttm) REVERT: M 50 MET cc_start: 0.7409 (mmt) cc_final: 0.7061 (mmm) REVERT: M 200 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: M 245 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6358 (tp30) REVERT: N 126 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: N 198 MET cc_start: 0.8509 (mtm) cc_final: 0.7991 (mtm) REVERT: O 102 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.6917 (mp10) REVERT: O 203 MET cc_start: 0.8210 (ptm) cc_final: 0.7705 (ptp) REVERT: P 178 ASP cc_start: 0.6873 (m-30) cc_final: 0.6672 (m-30) REVERT: R 235 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: S 61 LYS cc_start: 0.7539 (mtpt) cc_final: 0.7069 (mttt) REVERT: S 100 ASP cc_start: 0.7414 (t0) cc_final: 0.6968 (t0) REVERT: U 174 GLU cc_start: 0.6436 (mp0) cc_final: 0.6169 (mm-30) REVERT: V 233 THR cc_start: 0.8533 (m) cc_final: 0.8252 (p) REVERT: W 151 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7685 (mm-30) REVERT: Y 159 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7375 (mpp) REVERT: Y 178 ASN cc_start: 0.8603 (m-40) cc_final: 0.8098 (m110) REVERT: a 201 LYS cc_start: 0.7660 (mtmt) cc_final: 0.7417 (mttp) REVERT: b 105 ASN cc_start: 0.8236 (t0) cc_final: 0.7995 (t0) REVERT: b 126 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: b 198 MET cc_start: 0.8513 (mtm) cc_final: 0.8006 (mtm) outliers start: 108 outliers final: 65 residues processed: 715 average time/residue: 1.8560 time to fit residues: 1616.9303 Evaluate side-chains 725 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 643 time to evaluate : 5.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain H residue 237 LYS Chi-restraints excluded: chain H residue 258 LYS Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 185 LYS Chi-restraints excluded: chain K residue 152 MET Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 226 VAL Chi-restraints excluded: chain M residue 172 MET Chi-restraints excluded: chain M residue 184 THR Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 245 GLU Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain O residue 102 GLN Chi-restraints excluded: chain O residue 222 THR Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 163 ARG Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 176 MET Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 215 SER Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 230 ARG Chi-restraints excluded: chain V residue 237 LYS Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 183 MET Chi-restraints excluded: chain X residue 119 ASP Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 185 LYS Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 161 CYS Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 76 ASP Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain Z residue 215 VAL Chi-restraints excluded: chain Z residue 226 VAL Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 127 ASP Chi-restraints excluded: chain b residue 144 GLN Chi-restraints excluded: chain b residue 199 GLU Chi-restraints excluded: chain b residue 204 SER Chi-restraints excluded: chain b residue 219 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 559 optimal weight: 4.9990 chunk 65 optimal weight: 0.3980 chunk 330 optimal weight: 0.8980 chunk 423 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 488 optimal weight: 0.9980 chunk 324 optimal weight: 1.9990 chunk 578 optimal weight: 3.9990 chunk 361 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 chunk 266 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 52 GLN C 175 ASN D 104 ASN ** D 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN I 81 GLN I 93 ASN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 GLN O 42 ASN O 52 GLN O 71 HIS P 198 ASN P 240 HIS R 225 ASN W 81 GLN W 93 ASN Y 88 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 48784 Z= 0.194 Angle : 0.497 10.683 65884 Z= 0.268 Chirality : 0.042 0.181 7404 Planarity : 0.004 0.065 8484 Dihedral : 4.116 24.415 6778 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.49 % Allowed : 14.79 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.11), residues: 6102 helix: 2.64 (0.11), residues: 2202 sheet: 0.90 (0.13), residues: 1498 loop : -0.72 (0.12), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 100 HIS 0.007 0.001 HIS D 186 PHE 0.018 0.001 PHE H 79 TYR 0.025 0.001 TYR b 95 ARG 0.007 0.000 ARG U 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 658 time to evaluate : 5.131 Fit side-chains REVERT: A 102 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.6914 (mp10) REVERT: A 143 ARG cc_start: 0.7596 (ptm-80) cc_final: 0.7375 (ptm-80) REVERT: A 203 MET cc_start: 0.8022 (ptm) cc_final: 0.7554 (ptp) REVERT: B 151 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7835 (t0) REVERT: B 238 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7316 (mppt) REVERT: D 235 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: E 61 LYS cc_start: 0.7488 (mtpt) cc_final: 0.7024 (mttt) REVERT: E 100 ASP cc_start: 0.7332 (t70) cc_final: 0.7031 (t0) REVERT: F 185 MET cc_start: 0.8808 (ptt) cc_final: 0.8579 (ptt) REVERT: G 113 MET cc_start: 0.8500 (mmm) cc_final: 0.8047 (mmp) REVERT: G 174 GLU cc_start: 0.6302 (mp0) cc_final: 0.6026 (mm-30) REVERT: H 258 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6447 (ptpt) REVERT: I 4 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7232 (mpp) REVERT: I 155 GLU cc_start: 0.7848 (pt0) cc_final: 0.7582 (pt0) REVERT: I 183 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7996 (mtt) REVERT: J 28 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8006 (mtp) REVERT: K 159 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.7414 (mpp) REVERT: K 174 ASP cc_start: 0.8400 (p0) cc_final: 0.8173 (p0) REVERT: K 178 ASN cc_start: 0.8629 (m-40) cc_final: 0.8197 (m110) REVERT: M 50 MET cc_start: 0.7414 (mmt) cc_final: 0.7073 (mmm) REVERT: M 200 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: M 245 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6376 (tp30) REVERT: N 120 MET cc_start: 0.8083 (ttt) cc_final: 0.7789 (mtp) REVERT: N 126 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: N 198 MET cc_start: 0.8524 (mtm) cc_final: 0.7865 (mtm) REVERT: O 102 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.6869 (mp10) REVERT: O 143 ARG cc_start: 0.7699 (ptm-80) cc_final: 0.7461 (ptm-80) REVERT: O 203 MET cc_start: 0.8221 (ptm) cc_final: 0.7666 (ptp) REVERT: S 26 MET cc_start: 0.8149 (mtp) cc_final: 0.7418 (mtp) REVERT: S 61 LYS cc_start: 0.7496 (mtpt) cc_final: 0.7033 (mttt) REVERT: S 100 ASP cc_start: 0.7475 (t0) cc_final: 0.7002 (t0) REVERT: W 134 ASP cc_start: 0.7745 (t70) cc_final: 0.7430 (t0) REVERT: W 151 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7698 (mm-30) REVERT: W 155 GLU cc_start: 0.7845 (pt0) cc_final: 0.7560 (pt0) REVERT: Y 159 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.7400 (mpp) REVERT: a 201 LYS cc_start: 0.7677 (mtmt) cc_final: 0.7433 (mttp) REVERT: b 105 ASN cc_start: 0.8251 (t0) cc_final: 0.8005 (t0) REVERT: b 126 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: b 198 MET cc_start: 0.8526 (mtm) cc_final: 0.7944 (mtm) outliers start: 127 outliers final: 77 residues processed: 725 average time/residue: 1.8636 time to fit residues: 1669.1288 Evaluate side-chains 730 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 638 time to evaluate : 5.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain H residue 237 LYS Chi-restraints excluded: chain H residue 258 LYS Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 119 ASP Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 185 LYS Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 226 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 172 MET Chi-restraints excluded: chain M residue 184 THR Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 245 GLU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain O residue 102 GLN Chi-restraints excluded: chain O residue 222 THR Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 163 ARG Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 206 MET Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 176 MET Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 215 SER Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 230 ARG Chi-restraints excluded: chain V residue 237 LYS Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 106 GLU Chi-restraints excluded: chain W residue 152 SER Chi-restraints excluded: chain W residue 183 MET Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 119 ASP Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 185 LYS Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 161 CYS Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain Z residue 215 VAL Chi-restraints excluded: chain Z residue 226 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 127 ASP Chi-restraints excluded: chain b residue 144 GLN Chi-restraints excluded: chain b residue 199 GLU Chi-restraints excluded: chain b residue 204 SER Chi-restraints excluded: chain b residue 219 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 357 optimal weight: 0.4980 chunk 230 optimal weight: 5.9990 chunk 345 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 367 optimal weight: 3.9990 chunk 393 optimal weight: 0.0770 chunk 285 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 454 optimal weight: 9.9990 overall best weight: 2.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 52 GLN C 175 ASN ** D 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN I 93 ASN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 GLN O 42 ASN O 52 GLN R 104 ASN R 225 ASN W 81 GLN W 93 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 48784 Z= 0.284 Angle : 0.552 11.601 65884 Z= 0.296 Chirality : 0.044 0.153 7404 Planarity : 0.005 0.069 8484 Dihedral : 4.332 24.631 6778 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.39 % Allowed : 15.17 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.11), residues: 6102 helix: 2.45 (0.11), residues: 2200 sheet: 0.86 (0.13), residues: 1502 loop : -0.82 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP U 101 HIS 0.007 0.001 HIS D 186 PHE 0.024 0.002 PHE H 79 TYR 0.018 0.002 TYR P 136 ARG 0.007 0.000 ARG U 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 642 time to evaluate : 5.258 Fit side-chains revert: symmetry clash REVERT: A 102 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7046 (mp10) REVERT: A 203 MET cc_start: 0.8079 (ptm) cc_final: 0.7623 (ptp) REVERT: B 238 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7367 (mppt) REVERT: D 186 HIS cc_start: 0.7835 (p-80) cc_final: 0.7527 (p90) REVERT: D 235 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: E 61 LYS cc_start: 0.7558 (mtpt) cc_final: 0.7052 (mttt) REVERT: E 100 ASP cc_start: 0.7412 (t70) cc_final: 0.7076 (t0) REVERT: E 186 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7171 (mt-10) REVERT: F 184 GLU cc_start: 0.7637 (pm20) cc_final: 0.6962 (pm20) REVERT: G 131 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7146 (pmm) REVERT: G 174 GLU cc_start: 0.6322 (mp0) cc_final: 0.6022 (mm-30) REVERT: H 100 GLN cc_start: 0.8330 (mt0) cc_final: 0.7937 (mt0) REVERT: H 225 LYS cc_start: 0.7611 (pttm) cc_final: 0.7361 (ttpt) REVERT: H 258 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6465 (ptpt) REVERT: I 4 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7245 (mpp) REVERT: I 155 GLU cc_start: 0.7881 (pt0) cc_final: 0.7611 (pt0) REVERT: I 183 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8116 (mtt) REVERT: J 28 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7912 (mtp) REVERT: K 159 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.7425 (mpp) REVERT: K 174 ASP cc_start: 0.8397 (p0) cc_final: 0.8160 (p0) REVERT: K 178 ASN cc_start: 0.8621 (m-40) cc_final: 0.8198 (m110) REVERT: M 200 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: M 245 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6416 (tp30) REVERT: N 120 MET cc_start: 0.8118 (ttt) cc_final: 0.7825 (ttm) REVERT: N 126 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: N 198 MET cc_start: 0.8552 (mtm) cc_final: 0.7984 (mtm) REVERT: O 102 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.6883 (mp10) REVERT: O 203 MET cc_start: 0.8136 (ptm) cc_final: 0.7581 (ptp) REVERT: Q 23 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7811 (mt0) REVERT: R 235 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6753 (mt-10) REVERT: S 26 MET cc_start: 0.8201 (mtp) cc_final: 0.7430 (mtp) REVERT: S 61 LYS cc_start: 0.7561 (mtpt) cc_final: 0.7053 (mttt) REVERT: S 100 ASP cc_start: 0.7496 (t0) cc_final: 0.6998 (t0) REVERT: W 155 GLU cc_start: 0.7891 (pt0) cc_final: 0.7602 (pt0) REVERT: Y 159 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7408 (mpp) REVERT: Y 178 ASN cc_start: 0.8728 (m-40) cc_final: 0.8260 (m-40) REVERT: b 105 ASN cc_start: 0.8353 (t0) cc_final: 0.8095 (t0) REVERT: b 126 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: b 198 MET cc_start: 0.8552 (mtm) cc_final: 0.7993 (mtm) outliers start: 122 outliers final: 82 residues processed: 717 average time/residue: 1.8241 time to fit residues: 1580.5414 Evaluate side-chains 740 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 642 time to evaluate : 5.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 237 LYS Chi-restraints excluded: chain H residue 258 LYS Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 119 ASP Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 185 LYS Chi-restraints excluded: chain K residue 88 GLN Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 226 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 184 THR Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 243 GLU Chi-restraints excluded: chain M residue 245 GLU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain O residue 102 GLN Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 222 THR Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 239 LYS Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 163 ARG Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 206 MET Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 176 MET Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 215 SER Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 237 LYS Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 106 GLU Chi-restraints excluded: chain W residue 152 SER Chi-restraints excluded: chain W residue 183 MET Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 119 ASP Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 177 THR Chi-restraints excluded: chain X residue 185 LYS Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 161 CYS Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain Z residue 215 VAL Chi-restraints excluded: chain Z residue 226 VAL Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 127 ASP Chi-restraints excluded: chain b residue 129 MET Chi-restraints excluded: chain b residue 144 GLN Chi-restraints excluded: chain b residue 199 GLU Chi-restraints excluded: chain b residue 204 SER Chi-restraints excluded: chain b residue 219 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 526 optimal weight: 1.9990 chunk 554 optimal weight: 5.9990 chunk 505 optimal weight: 5.9990 chunk 538 optimal weight: 4.9990 chunk 553 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 423 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 486 optimal weight: 0.9990 chunk 509 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 52 GLN C 175 ASN D 186 HIS J 27 GLN O 42 ASN R 186 HIS R 225 ASN T 222 ASN W 81 GLN W 93 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 48784 Z= 0.208 Angle : 0.515 11.788 65884 Z= 0.278 Chirality : 0.043 0.174 7404 Planarity : 0.004 0.067 8484 Dihedral : 4.234 24.374 6778 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.09 % Allowed : 15.77 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.11), residues: 6102 helix: 2.53 (0.11), residues: 2200 sheet: 0.89 (0.13), residues: 1502 loop : -0.80 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 100 HIS 0.007 0.001 HIS D 186 PHE 0.018 0.001 PHE V 79 TYR 0.026 0.001 TYR N 95 ARG 0.007 0.000 ARG U 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 647 time to evaluate : 5.393 Fit side-chains revert: symmetry clash REVERT: A 102 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.6839 (mp10) REVERT: A 203 MET cc_start: 0.8034 (ptm) cc_final: 0.7553 (ptp) REVERT: B 238 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7361 (mppt) REVERT: C 23 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7771 (mt0) REVERT: D 235 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: E 61 LYS cc_start: 0.7593 (mtpt) cc_final: 0.7045 (mmtp) REVERT: E 100 ASP cc_start: 0.7377 (t70) cc_final: 0.7077 (t0) REVERT: G 113 MET cc_start: 0.8499 (mmm) cc_final: 0.8065 (mmp) REVERT: G 131 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7024 (pmm) REVERT: G 174 GLU cc_start: 0.6282 (mp0) cc_final: 0.6002 (mm-30) REVERT: H 225 LYS cc_start: 0.7608 (pttm) cc_final: 0.7190 (pttt) REVERT: H 233 THR cc_start: 0.8553 (m) cc_final: 0.8297 (p) REVERT: H 258 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6458 (ptpt) REVERT: I 4 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7232 (mpp) REVERT: I 155 GLU cc_start: 0.7851 (pt0) cc_final: 0.7581 (pt0) REVERT: I 183 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8037 (mtt) REVERT: J 28 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8006 (mtp) REVERT: K 159 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7352 (mpp) REVERT: K 174 ASP cc_start: 0.8402 (p0) cc_final: 0.8163 (p0) REVERT: K 178 ASN cc_start: 0.8648 (m-40) cc_final: 0.8202 (m110) REVERT: L 97 GLU cc_start: 0.7380 (mp0) cc_final: 0.7103 (mm-30) REVERT: M 200 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: M 245 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6391 (tp30) REVERT: N 120 MET cc_start: 0.8022 (ttt) cc_final: 0.7711 (mtp) REVERT: N 126 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: N 198 MET cc_start: 0.8500 (mtm) cc_final: 0.7869 (mtm) REVERT: O 102 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.6831 (mp10) REVERT: O 143 ARG cc_start: 0.7726 (ptm-80) cc_final: 0.7522 (ptm-80) REVERT: O 203 MET cc_start: 0.8135 (ptm) cc_final: 0.7506 (ptp) REVERT: Q 23 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7776 (mt0) REVERT: R 235 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6551 (mt-10) REVERT: S 26 MET cc_start: 0.8191 (mtp) cc_final: 0.7423 (mtp) REVERT: S 61 LYS cc_start: 0.7598 (mtpt) cc_final: 0.7098 (mttt) REVERT: S 100 ASP cc_start: 0.7488 (t0) cc_final: 0.6991 (t0) REVERT: T 234 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6329 (mp0) REVERT: U 43 ARG cc_start: 0.8027 (ptt180) cc_final: 0.7697 (ptt90) REVERT: U 59 LYS cc_start: 0.7600 (ttpp) cc_final: 0.7386 (ttpp) REVERT: V 233 THR cc_start: 0.8478 (m) cc_final: 0.8213 (p) REVERT: W 155 GLU cc_start: 0.7856 (pt0) cc_final: 0.7568 (pt0) REVERT: Y 159 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7330 (mpp) REVERT: a 201 LYS cc_start: 0.7704 (mtmt) cc_final: 0.7461 (mttp) REVERT: b 105 ASN cc_start: 0.8291 (t0) cc_final: 0.8034 (t0) REVERT: b 126 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: b 198 MET cc_start: 0.8502 (mtm) cc_final: 0.7951 (mtm) outliers start: 107 outliers final: 79 residues processed: 712 average time/residue: 1.7850 time to fit residues: 1537.0496 Evaluate side-chains 725 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 629 time to evaluate : 5.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 237 LYS Chi-restraints excluded: chain H residue 258 LYS Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 119 ASP Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 185 LYS Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 226 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 184 THR Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 243 GLU Chi-restraints excluded: chain M residue 245 GLU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain O residue 102 GLN Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 222 THR Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 239 LYS Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 163 ARG Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 176 MET Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 215 SER Chi-restraints excluded: chain T residue 234 GLU Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 237 LYS Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 106 GLU Chi-restraints excluded: chain W residue 152 SER Chi-restraints excluded: chain W residue 183 MET Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 119 ASP Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 177 THR Chi-restraints excluded: chain X residue 185 LYS Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 161 CYS Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain Z residue 215 VAL Chi-restraints excluded: chain Z residue 226 VAL Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 127 ASP Chi-restraints excluded: chain b residue 144 GLN Chi-restraints excluded: chain b residue 199 GLU Chi-restraints excluded: chain b residue 204 SER Chi-restraints excluded: chain b residue 219 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 537 optimal weight: 7.9990 chunk 353 optimal weight: 8.9990 chunk 569 optimal weight: 3.9990 chunk 347 optimal weight: 0.3980 chunk 270 optimal weight: 2.9990 chunk 396 optimal weight: 1.9990 chunk 597 optimal weight: 3.9990 chunk 550 optimal weight: 0.0970 chunk 475 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 367 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN C 175 ASN D 104 ASN H 134 GLN J 27 GLN K 88 GLN O 42 ASN R 225 ASN T 222 ASN V 134 GLN W 81 GLN W 93 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 48784 Z= 0.216 Angle : 0.517 11.954 65884 Z= 0.279 Chirality : 0.043 0.167 7404 Planarity : 0.004 0.067 8484 Dihedral : 4.222 24.425 6778 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.05 % Allowed : 15.83 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.11), residues: 6102 helix: 2.54 (0.11), residues: 2200 sheet: 0.85 (0.13), residues: 1510 loop : -0.79 (0.12), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 100 HIS 0.006 0.001 HIS X 132 PHE 0.019 0.001 PHE H 79 TYR 0.015 0.001 TYR P 136 ARG 0.006 0.000 ARG U 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 633 time to evaluate : 5.059 Fit side-chains revert: symmetry clash REVERT: A 102 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.6843 (mp10) REVERT: A 203 MET cc_start: 0.8038 (ptm) cc_final: 0.7560 (ptp) REVERT: B 238 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7362 (mppt) REVERT: C 23 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7795 (mt0) REVERT: D 235 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: E 61 LYS cc_start: 0.7598 (mtpt) cc_final: 0.7087 (mttt) REVERT: E 100 ASP cc_start: 0.7411 (t70) cc_final: 0.7076 (t0) REVERT: G 113 MET cc_start: 0.8501 (mmm) cc_final: 0.8019 (mmp) REVERT: G 131 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7024 (pmm) REVERT: G 174 GLU cc_start: 0.6216 (mp0) cc_final: 0.5963 (mm-30) REVERT: H 225 LYS cc_start: 0.7574 (pttm) cc_final: 0.7150 (pttt) REVERT: H 233 THR cc_start: 0.8560 (m) cc_final: 0.8302 (p) REVERT: H 258 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6478 (ptpt) REVERT: I 4 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7231 (mpp) REVERT: I 155 GLU cc_start: 0.7848 (pt0) cc_final: 0.7578 (pt0) REVERT: I 183 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8018 (mtt) REVERT: J 28 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7996 (mtp) REVERT: K 159 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7416 (mpp) REVERT: K 174 ASP cc_start: 0.8394 (p0) cc_final: 0.8156 (p0) REVERT: K 178 ASN cc_start: 0.8650 (m-40) cc_final: 0.8212 (m110) REVERT: L 97 GLU cc_start: 0.7358 (mp0) cc_final: 0.7093 (mm-30) REVERT: M 200 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: M 245 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6402 (tp30) REVERT: N 120 MET cc_start: 0.8080 (ttt) cc_final: 0.7804 (ttm) REVERT: N 126 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: N 198 MET cc_start: 0.8508 (mtm) cc_final: 0.7900 (mtm) REVERT: O 102 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.6863 (mp10) REVERT: O 143 ARG cc_start: 0.7703 (ptm-80) cc_final: 0.7501 (ptm-80) REVERT: O 203 MET cc_start: 0.8139 (ptm) cc_final: 0.7515 (ptp) REVERT: Q 23 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7694 (mt0) REVERT: R 235 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6633 (mt-10) REVERT: S 26 MET cc_start: 0.8200 (mtp) cc_final: 0.7432 (mtp) REVERT: S 61 LYS cc_start: 0.7605 (mtpt) cc_final: 0.7091 (mttt) REVERT: S 100 ASP cc_start: 0.7473 (t0) cc_final: 0.6962 (t0) REVERT: T 234 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6330 (mp0) REVERT: U 43 ARG cc_start: 0.8036 (ptt180) cc_final: 0.7691 (ptt90) REVERT: U 59 LYS cc_start: 0.7605 (ttpp) cc_final: 0.7390 (ttpp) REVERT: V 233 THR cc_start: 0.8487 (m) cc_final: 0.8224 (p) REVERT: W 81 GLN cc_start: 0.8065 (mt0) cc_final: 0.7785 (mt0) REVERT: W 155 GLU cc_start: 0.7856 (pt0) cc_final: 0.7569 (pt0) REVERT: Y 159 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.7305 (mpp) REVERT: Y 178 ASN cc_start: 0.8642 (m-40) cc_final: 0.8240 (m110) REVERT: b 105 ASN cc_start: 0.8272 (t0) cc_final: 0.8017 (t0) REVERT: b 126 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: b 198 MET cc_start: 0.8491 (mtm) cc_final: 0.7874 (mtm) outliers start: 105 outliers final: 82 residues processed: 698 average time/residue: 1.8707 time to fit residues: 1581.8898 Evaluate side-chains 726 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 627 time to evaluate : 5.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 237 LYS Chi-restraints excluded: chain H residue 258 LYS Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 119 ASP Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 185 LYS Chi-restraints excluded: chain K residue 88 GLN Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 226 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 184 THR Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 243 GLU Chi-restraints excluded: chain M residue 245 GLU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain O residue 102 GLN Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 222 THR Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 239 LYS Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 163 ARG Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 176 MET Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 215 SER Chi-restraints excluded: chain T residue 234 GLU Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 237 LYS Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 106 GLU Chi-restraints excluded: chain W residue 183 MET Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 119 ASP Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 177 THR Chi-restraints excluded: chain X residue 185 LYS Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 161 CYS Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain Z residue 215 VAL Chi-restraints excluded: chain Z residue 226 VAL Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain a residue 243 GLU Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 127 ASP Chi-restraints excluded: chain b residue 144 GLN Chi-restraints excluded: chain b residue 199 GLU Chi-restraints excluded: chain b residue 204 SER Chi-restraints excluded: chain b residue 219 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 291 optimal weight: 0.9980 chunk 378 optimal weight: 0.6980 chunk 507 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 438 optimal weight: 0.0170 chunk 70 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 476 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 489 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN C 175 ASN I 93 ASN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 ASN O 52 GLN R 225 ASN T 222 ASN W 93 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.138331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109471 restraints weight = 55711.486| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.85 r_work: 0.3160 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 48784 Z= 0.132 Angle : 0.463 11.500 65884 Z= 0.252 Chirality : 0.041 0.162 7404 Planarity : 0.004 0.066 8484 Dihedral : 3.990 24.417 6778 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.64 % Allowed : 16.36 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.11), residues: 6102 helix: 2.76 (0.11), residues: 2206 sheet: 0.93 (0.13), residues: 1506 loop : -0.67 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 100 HIS 0.004 0.000 HIS X 132 PHE 0.018 0.001 PHE F 136 TYR 0.026 0.001 TYR N 95 ARG 0.007 0.000 ARG U 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21829.52 seconds wall clock time: 384 minutes 4.70 seconds (23044.70 seconds total)