Starting phenix.real_space_refine on Mon Jan 13 19:03:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyo_18760/01_2025/8qyo_18760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyo_18760/01_2025/8qyo_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/cci-nas-00/data/ceres_data/8qyo_18760/01_2025/8qyo_18760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyo_18760/01_2025/8qyo_18760.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyo_18760/01_2025/8qyo_18760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyo_18760/01_2025/8qyo_18760.cif" } 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. Time to flip 35 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 20.82, per 1000 atoms: 0.43 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 - 3.00 Amino acid : True - 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: 9.15 Conformation dependent library (CDL) restraints added in 4.7 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: 4.99 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: 18.63 Time building geometry restraints manager: 10.73 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: 0.00 - 1.72: 64068 1.72 - 3.43: 1566 3.43 - 5.15: 215 5.15 - 6.87: 27 6.87 - 8.58: 8 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 3.120 nonbonded pdb=" OD1 ASN M 83 " pdb=" NH2 ARG M 231 " model vdw 2.218 3.120 nonbonded pdb=" OG1 THR D 230 " pdb=" OE1 GLU D 233 " model vdw 2.250 3.040 nonbonded pdb=" OD2 ASP B 6 " pdb=" OH TYR C 3 " model vdw 2.265 3.040 nonbonded pdb=" OD2 ASP P 6 " pdb=" OH TYR Q 3 " model vdw 2.280 3.040 ... (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 Time spend for trying shortcut: 0.02 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: 0.850 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: 1.440 Check model and map are aligned: 0.270 Set scattering table: 0.340 Process input model: 82.910 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.300 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: 0.000 Load rotamer database and sin/cos tables:10.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.550 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 826 time to evaluate : 4.125 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: 1.5014 time to fit residues: 1493.4903 Evaluate side-chains 635 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 635 time to evaluate : 4.185 ------------------------------------------------------------------------------- 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: 0.9990 chunk 454 optimal weight: 6.9990 chunk 252 optimal weight: 0.0070 chunk 155 optimal weight: 0.1980 chunk 306 optimal weight: 3.9990 chunk 242 optimal weight: 10.0000 chunk 470 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 285 optimal weight: 6.9990 chunk 350 optimal weight: 0.8980 chunk 544 optimal weight: 0.9980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 189 HIS B 123 GLN D 104 ASN D 225 ASN I 157 ASN J 8 GLN K 144 ASN K 237 HIS P 109 GLN P 123 GLN P 235 GLN R 104 ASN R 225 ASN W 81 GLN ** X 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 144 ASN Y 237 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106935 restraints weight = 56001.341| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.87 r_work: 0.3129 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 48784 Z= 0.134 Angle : 0.494 13.128 65884 Z= 0.269 Chirality : 0.042 0.153 7404 Planarity : 0.004 0.068 8484 Dihedral : 4.265 25.409 6778 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.47 % Allowed : 8.34 % Favored : 90.20 % 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: 1.16 (0.11), residues: 6102 helix: 2.28 (0.11), residues: 2210 sheet: 0.77 (0.13), residues: 1496 loop : -0.68 (0.12), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 216 HIS 0.005 0.001 HIS D 186 PHE 0.022 0.001 PHE F 136 TYR 0.014 0.001 TYR X 117 ARG 0.003 0.000 ARG M 211 *********************** 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 793 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 718 time to evaluate : 4.159 Fit side-chains REVERT: A 102 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7119 (mp10) REVERT: A 203 MET cc_start: 0.8065 (ptm) cc_final: 0.7490 (ptp) REVERT: B 178 ASP cc_start: 0.6601 (m-30) cc_final: 0.6348 (m-30) REVERT: D 235 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6894 (mp0) REVERT: E 61 LYS cc_start: 0.7346 (mtpt) cc_final: 0.6930 (mttt) REVERT: E 100 ASP cc_start: 0.7889 (t70) cc_final: 0.7545 (t0) REVERT: E 167 SER cc_start: 0.7440 (OUTLIER) cc_final: 0.7212 (p) REVERT: F 115 ARG cc_start: 0.7474 (mtp85) cc_final: 0.7124 (mtp85) REVERT: F 181 GLN cc_start: 0.6972 (mp10) cc_final: 0.6405 (pp30) REVERT: F 182 MET cc_start: 0.7676 (pmm) cc_final: 0.7047 (pmm) REVERT: F 184 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6019 (pm20) REVERT: G 113 MET cc_start: 0.8503 (mmm) cc_final: 0.8186 (mmp) REVERT: G 174 GLU cc_start: 0.6269 (mp0) cc_final: 0.5901 (mm-30) REVERT: H 65 GLU cc_start: 0.7702 (tt0) cc_final: 0.7487 (tt0) REVERT: I 4 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7110 (mmm) REVERT: J 12 TYR cc_start: 0.8897 (p90) cc_final: 0.8598 (p90) REVERT: J 28 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8160 (mtp) REVERT: J 37 LYS cc_start: 0.8808 (tttt) cc_final: 0.8601 (tttm) REVERT: K 156 MET cc_start: 0.8346 (ptm) cc_final: 0.7912 (ptm) REVERT: K 178 ASN cc_start: 0.8860 (m-40) cc_final: 0.8219 (m110) REVERT: L 97 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: L 186 MET cc_start: 0.8709 (mtm) cc_final: 0.8484 (mtm) REVERT: M 50 MET cc_start: 0.7369 (mmt) cc_final: 0.7165 (mmm) REVERT: M 200 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: N 105 ASN cc_start: 0.8401 (t0) cc_final: 0.8188 (t0) REVERT: N 126 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: O 102 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7097 (mp10) REVERT: O 203 MET cc_start: 0.8037 (ptm) cc_final: 0.7584 (ptp) REVERT: P 151 ASP cc_start: 0.8055 (m-30) cc_final: 0.7854 (t0) REVERT: P 178 ASP cc_start: 0.6595 (m-30) cc_final: 0.6334 (m-30) REVERT: S 61 LYS cc_start: 0.7362 (mtpt) cc_final: 0.6915 (mttt) REVERT: S 100 ASP cc_start: 0.7665 (t0) cc_final: 0.7340 (t0) REVERT: S 167 SER cc_start: 0.7414 (OUTLIER) cc_final: 0.7186 (p) REVERT: T 33 ASN cc_start: 0.7370 (m110) cc_final: 0.6931 (m110) REVERT: T 94 GLU cc_start: 0.7284 (tp30) cc_final: 0.7059 (tp30) REVERT: T 115 ARG cc_start: 0.7544 (mtp85) cc_final: 0.7111 (mtp85) REVERT: U 74 GLU cc_start: 0.7306 (mp0) cc_final: 0.7045 (pm20) REVERT: U 113 MET cc_start: 0.8505 (mmm) cc_final: 0.8199 (mmp) REVERT: U 174 GLU cc_start: 0.6090 (mp0) cc_final: 0.5700 (mm-30) REVERT: V 157 TYR cc_start: 0.8588 (m-80) cc_final: 0.8373 (m-80) REVERT: W 48 ARG cc_start: 0.8461 (mtt90) cc_final: 0.8251 (mtt90) REVERT: W 155 GLU cc_start: 0.8310 (pt0) cc_final: 0.7918 (pt0) REVERT: X 12 TYR cc_start: 0.8900 (p90) cc_final: 0.8604 (p90) REVERT: Y 130 LYS cc_start: 0.8008 (mmmm) cc_final: 0.7659 (mtmm) REVERT: Y 178 ASN cc_start: 0.8866 (m-40) cc_final: 0.8223 (m110) REVERT: Z 146 LYS cc_start: 0.8005 (mttm) cc_final: 0.7786 (mttm) REVERT: a 200 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6755 (mp0) REVERT: b 105 ASN cc_start: 0.8229 (t0) cc_final: 0.7985 (t0) REVERT: b 126 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: b 179 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7803 (mt-10) outliers start: 75 outliers final: 17 residues processed: 753 average time/residue: 1.5053 time to fit residues: 1367.1539 Evaluate side-chains 661 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 632 time to evaluate : 4.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 239 LYS 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 I residue 4 MET Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 185 LYS Chi-restraints excluded: chain K residue 155 SER Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 97 GLU 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 Q residue 134 VAL Chi-restraints excluded: chain R residue 239 LYS 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 V residue 172 SER Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 185 LYS Chi-restraints excluded: chain Y residue 155 SER Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 179 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 187 optimal weight: 0.7980 chunk 134 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 591 optimal weight: 4.9990 chunk 497 optimal weight: 0.8980 chunk 217 optimal weight: 6.9990 chunk 347 optimal weight: 0.0470 chunk 58 optimal weight: 6.9990 chunk 331 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.5280 ------------------------------------------------------------------------------- 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 D 204 GLN D 225 ASN H 123 ASN H 134 GLN I 81 GLN I 93 ASN K 148 GLN N 111 HIS N 144 GLN O 42 ASN P 109 GLN Q 175 ASN R 104 ASN R 204 GLN R 225 ASN V 123 ASN W 81 GLN W 93 ASN X 27 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.134025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.104692 restraints weight = 56481.494| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.88 r_work: 0.3077 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 48784 Z= 0.186 Angle : 0.500 13.130 65884 Z= 0.270 Chirality : 0.042 0.143 7404 Planarity : 0.004 0.064 8484 Dihedral : 4.209 24.238 6778 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.76 % Allowed : 10.67 % Favored : 87.57 % 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: 1.31 (0.11), residues: 6102 helix: 2.46 (0.11), residues: 2204 sheet: 0.80 (0.13), residues: 1518 loop : -0.61 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 216 HIS 0.006 0.001 HIS X 132 PHE 0.018 0.001 PHE V 79 TYR 0.016 0.001 TYR U 160 ARG 0.003 0.000 ARG L 239 *********************** 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 741 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 651 time to evaluate : 4.193 Fit side-chains revert: symmetry clash REVERT: A 102 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7047 (mp10) REVERT: A 203 MET cc_start: 0.8050 (ptm) cc_final: 0.7510 (ptp) REVERT: B 178 ASP cc_start: 0.6800 (m-30) cc_final: 0.6534 (m-30) REVERT: D 235 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6968 (mp0) REVERT: E 26 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.8021 (mtp) REVERT: E 61 LYS cc_start: 0.7372 (mtpt) cc_final: 0.6925 (mttt) REVERT: E 100 ASP cc_start: 0.7926 (t70) cc_final: 0.7582 (t0) REVERT: F 115 ARG cc_start: 0.7532 (mtp85) cc_final: 0.7172 (mtp85) REVERT: F 181 GLN cc_start: 0.7005 (mp10) cc_final: 0.6629 (pp30) REVERT: F 182 MET cc_start: 0.7698 (pmm) cc_final: 0.7112 (pmm) REVERT: F 184 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6124 (pm20) REVERT: G 174 GLU cc_start: 0.6278 (mp0) cc_final: 0.5933 (mm-30) REVERT: H 65 GLU cc_start: 0.7733 (tt0) cc_final: 0.7513 (tt0) REVERT: H 172 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.8282 (t) REVERT: I 4 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7322 (mmm) REVERT: I 40 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8839 (tt0) REVERT: I 155 GLU cc_start: 0.8229 (pt0) cc_final: 0.7806 (pt0) REVERT: J 28 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8285 (mtp) REVERT: K 152 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7160 (mpt) REVERT: K 156 MET cc_start: 0.8192 (ptm) cc_final: 0.7936 (ptm) REVERT: K 159 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8185 (mtp) REVERT: K 178 ASN cc_start: 0.8710 (m-40) cc_final: 0.8061 (m-40) REVERT: L 101 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7267 (mttp) REVERT: L 186 MET cc_start: 0.8765 (mtm) cc_final: 0.8521 (mtm) REVERT: M 50 MET cc_start: 0.7453 (mmt) cc_final: 0.7217 (mmm) REVERT: M 200 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: N 105 ASN cc_start: 0.8395 (t0) cc_final: 0.8160 (t0) REVERT: N 126 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: O 102 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.6975 (mp10) REVERT: O 143 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7110 (ptm-80) REVERT: O 203 MET cc_start: 0.7976 (ptm) cc_final: 0.7509 (ptp) REVERT: P 178 ASP cc_start: 0.6740 (m-30) cc_final: 0.6491 (m-30) REVERT: S 61 LYS cc_start: 0.7407 (mtpt) cc_final: 0.6949 (mttt) REVERT: S 100 ASP cc_start: 0.7809 (t0) cc_final: 0.7396 (t0) REVERT: T 33 ASN cc_start: 0.7424 (m110) cc_final: 0.6981 (m110) REVERT: T 115 ARG cc_start: 0.7593 (mtp85) cc_final: 0.7166 (mtp85) REVERT: T 242 GLU cc_start: 0.7571 (pt0) cc_final: 0.7346 (pt0) REVERT: U 74 GLU cc_start: 0.7422 (mp0) cc_final: 0.7135 (pm20) REVERT: U 174 GLU cc_start: 0.6262 (mp0) cc_final: 0.5940 (mm-30) REVERT: V 157 TYR cc_start: 0.8626 (m-80) cc_final: 0.8425 (m-80) REVERT: W 40 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8784 (tt0) REVERT: W 155 GLU cc_start: 0.8383 (pt0) cc_final: 0.7967 (pt0) REVERT: Y 130 LYS cc_start: 0.8035 (mmmm) cc_final: 0.7681 (mtmm) REVERT: Y 159 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8195 (mtp) REVERT: Y 178 ASN cc_start: 0.8738 (m-40) cc_final: 0.8107 (m110) REVERT: Z 146 LYS cc_start: 0.7994 (mttm) cc_final: 0.7783 (mttm) REVERT: a 200 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6944 (mp0) REVERT: a 243 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7297 (tt0) REVERT: a 245 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6935 (tp30) REVERT: b 105 ASN cc_start: 0.8367 (t0) cc_final: 0.8125 (t0) REVERT: b 126 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: b 179 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7655 (mp0) outliers start: 90 outliers final: 38 residues processed: 701 average time/residue: 1.5283 time to fit residues: 1287.2200 Evaluate side-chains 676 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 618 time to evaluate : 4.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 239 LYS Chi-restraints excluded: chain E residue 26 MET 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 28 MET Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 40 GLN Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 181 ARG Chi-restraints excluded: chain J residue 185 LYS Chi-restraints excluded: chain K residue 88 GLN Chi-restraints excluded: chain K residue 152 MET Chi-restraints excluded: chain K residue 155 SER 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 101 LYS Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain M residue 200 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 143 ARG Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain Q residue 163 ARG Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 239 LYS 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 215 SER Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain V residue 230 ARG Chi-restraints excluded: chain W residue 40 GLN Chi-restraints excluded: chain W residue 106 GLU Chi-restraints excluded: chain W residue 183 MET 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 176 LEU Chi-restraints excluded: chain a residue 243 GLU Chi-restraints excluded: chain a residue 245 GLU Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 129 MET Chi-restraints excluded: chain b residue 144 GLN Chi-restraints excluded: chain b residue 179 GLU 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 143 optimal weight: 0.0670 chunk 83 optimal weight: 5.9990 chunk 473 optimal weight: 0.5980 chunk 511 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 580 optimal weight: 8.9990 chunk 239 optimal weight: 5.9990 chunk 528 optimal weight: 1.9990 chunk 333 optimal weight: 0.9980 chunk 500 optimal weight: 8.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- 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 225 ASN I 81 GLN I 93 ASN K 148 GLN O 42 ASN Q 175 ASN R 225 ASN V 134 GLN W 81 GLN W 93 ASN X 27 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.133946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.104547 restraints weight = 56072.026| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.87 r_work: 0.3092 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 48784 Z= 0.184 Angle : 0.492 11.606 65884 Z= 0.266 Chirality : 0.042 0.142 7404 Planarity : 0.004 0.064 8484 Dihedral : 4.152 23.671 6778 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.11 % Allowed : 11.49 % Favored : 86.40 % 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: 2.54 (0.11), residues: 2204 sheet: 0.86 (0.13), residues: 1514 loop : -0.63 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 216 HIS 0.005 0.001 HIS X 132 PHE 0.020 0.001 PHE T 136 TYR 0.014 0.001 TYR U 160 ARG 0.003 0.000 ARG B 218 *********************** 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 768 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 660 time to evaluate : 4.270 Fit side-chains revert: symmetry clash REVERT: A 102 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: A 143 ARG cc_start: 0.7440 (ptm-80) cc_final: 0.7152 (ptm-80) REVERT: A 203 MET cc_start: 0.8027 (ptm) cc_final: 0.7535 (ptp) REVERT: B 87 THR cc_start: 0.8497 (m) cc_final: 0.8224 (p) REVERT: B 178 ASP cc_start: 0.6803 (m-30) cc_final: 0.6548 (m-30) REVERT: D 235 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7019 (mp0) REVERT: E 61 LYS cc_start: 0.7459 (mtpt) cc_final: 0.6960 (mttt) REVERT: E 100 ASP cc_start: 0.7957 (t70) cc_final: 0.7609 (t0) REVERT: F 71 ASP cc_start: 0.7802 (t0) cc_final: 0.7345 (t0) REVERT: F 115 ARG cc_start: 0.7541 (mtp85) cc_final: 0.7203 (mtp85) REVERT: F 181 GLN cc_start: 0.6973 (mp10) cc_final: 0.6614 (pp30) REVERT: F 182 MET cc_start: 0.7718 (pmm) cc_final: 0.7207 (pmm) REVERT: F 184 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6124 (pm20) REVERT: G 131 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7437 (pmm) REVERT: G 174 GLU cc_start: 0.6332 (mp0) cc_final: 0.6009 (mm-30) REVERT: H 65 GLU cc_start: 0.7793 (tt0) cc_final: 0.7558 (tt0) REVERT: I 40 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8867 (tt0) REVERT: I 155 GLU cc_start: 0.8222 (pt0) cc_final: 0.7791 (pt0) REVERT: J 28 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8286 (mtp) REVERT: K 152 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7158 (mpt) REVERT: K 156 MET cc_start: 0.8205 (ptm) cc_final: 0.7943 (ptm) REVERT: K 159 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8360 (mtp) REVERT: K 256 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: L 97 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: L 101 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7285 (mttp) REVERT: L 186 MET cc_start: 0.8774 (mtm) cc_final: 0.8549 (mtm) REVERT: M 50 MET cc_start: 0.7480 (mmt) cc_final: 0.7231 (mmm) REVERT: M 200 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: M 243 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: N 105 ASN cc_start: 0.8399 (t0) cc_final: 0.8169 (t0) REVERT: N 126 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: N 198 MET cc_start: 0.8554 (mtp) cc_final: 0.8019 (mtp) REVERT: O 102 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.6921 (mp10) REVERT: O 203 MET cc_start: 0.7995 (ptm) cc_final: 0.7576 (ptp) REVERT: P 178 ASP cc_start: 0.6724 (m-30) cc_final: 0.6472 (m-30) REVERT: P 218 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7519 (tpt-90) REVERT: S 61 LYS cc_start: 0.7473 (mtpt) cc_final: 0.6964 (mttt) REVERT: S 100 ASP cc_start: 0.7898 (t0) cc_final: 0.7485 (t0) REVERT: T 115 ARG cc_start: 0.7571 (mtp85) cc_final: 0.7206 (mtp85) REVERT: U 74 GLU cc_start: 0.7501 (mp0) cc_final: 0.7204 (pm20) REVERT: U 131 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7561 (pmm) REVERT: U 174 GLU cc_start: 0.6316 (mp0) cc_final: 0.5997 (mm-30) REVERT: V 157 TYR cc_start: 0.8621 (m-80) cc_final: 0.8416 (m-80) REVERT: W 40 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8851 (tt0) REVERT: W 155 GLU cc_start: 0.8356 (pt0) cc_final: 0.7935 (pt0) REVERT: X 111 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7286 (tm-30) REVERT: Y 130 LYS cc_start: 0.8016 (mmmm) cc_final: 0.7645 (mtmm) REVERT: Y 159 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8212 (mtp) REVERT: a 200 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6901 (mp0) REVERT: a 245 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6915 (tp30) REVERT: b 105 ASN cc_start: 0.8360 (t0) cc_final: 0.8121 (t0) REVERT: b 126 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: b 179 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: b 198 MET cc_start: 0.8561 (mtp) cc_final: 0.8096 (mtp) outliers start: 108 outliers final: 50 residues processed: 713 average time/residue: 1.5296 time to fit residues: 1313.1401 Evaluate side-chains 692 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 621 time to evaluate : 4.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN 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 239 LYS 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 28 MET Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain H residue 230 ARG Chi-restraints excluded: chain I residue 40 GLN 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 165 GLU Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 181 ARG Chi-restraints excluded: chain K residue 88 GLN 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 K residue 256 GLU Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 101 LYS 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 200 GLU Chi-restraints excluded: chain M residue 243 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 P residue 218 ARG 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 U residue 131 MET Chi-restraints excluded: chain V residue 230 ARG Chi-restraints excluded: chain W residue 40 GLN 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 1 MET Chi-restraints excluded: chain X residue 165 GLU 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 161 ASP Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 226 VAL 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 179 GLU Chi-restraints excluded: chain b residue 199 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 15 optimal weight: 0.9990 chunk 527 optimal weight: 0.2980 chunk 160 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 240 optimal weight: 0.9980 chunk 310 optimal weight: 5.9990 chunk 251 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 295 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 394 optimal weight: 10.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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** H 134 GLN I 81 GLN I 93 ASN K 148 GLN O 42 ASN O 71 HIS Q 175 ASN R 104 ASN R 225 ASN U 75 ASN V 134 GLN W 81 GLN W 93 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.107129 restraints weight = 56164.432| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.88 r_work: 0.3127 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 48784 Z= 0.130 Angle : 0.457 10.192 65884 Z= 0.248 Chirality : 0.041 0.143 7404 Planarity : 0.004 0.060 8484 Dihedral : 3.978 23.886 6778 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.11 % Allowed : 12.02 % Favored : 85.87 % 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: 1.56 (0.11), residues: 6102 helix: 2.72 (0.11), residues: 2204 sheet: 0.95 (0.13), residues: 1512 loop : -0.55 (0.12), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 100 HIS 0.008 0.000 HIS D 186 PHE 0.017 0.001 PHE F 136 TYR 0.013 0.001 TYR X 117 ARG 0.004 0.000 ARG U 228 *********************** 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 763 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 655 time to evaluate : 4.178 Fit side-chains REVERT: A 102 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.6912 (mp10) REVERT: A 203 MET cc_start: 0.7810 (ptm) cc_final: 0.7263 (ptp) REVERT: B 151 ASP cc_start: 0.8364 (t0) cc_final: 0.8159 (t0) REVERT: B 178 ASP cc_start: 0.6756 (m-30) cc_final: 0.6481 (m-30) REVERT: B 238 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7138 (mppt) REVERT: D 29 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7052 (tp30) REVERT: D 186 HIS cc_start: 0.7355 (p-80) cc_final: 0.6993 (p90) REVERT: D 235 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7186 (mm-30) REVERT: E 39 LYS cc_start: 0.8968 (pttt) cc_final: 0.8613 (pttt) REVERT: E 61 LYS cc_start: 0.7430 (mtpt) cc_final: 0.6938 (mttt) REVERT: E 94 ASP cc_start: 0.7854 (m-30) cc_final: 0.7640 (m-30) REVERT: E 100 ASP cc_start: 0.7894 (t70) cc_final: 0.7549 (t0) REVERT: E 122 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7577 (mtp85) REVERT: E 167 SER cc_start: 0.7441 (OUTLIER) cc_final: 0.7184 (p) REVERT: F 115 ARG cc_start: 0.7502 (mtp85) cc_final: 0.7171 (mtp85) REVERT: F 181 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6571 (pp30) REVERT: F 182 MET cc_start: 0.7687 (pmm) cc_final: 0.7111 (pmm) REVERT: F 184 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6062 (pm20) REVERT: G 113 MET cc_start: 0.8480 (mmm) cc_final: 0.8258 (mmp) REVERT: G 131 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7444 (pmm) REVERT: G 174 GLU cc_start: 0.6498 (mp0) cc_final: 0.6180 (mm-30) REVERT: J 12 TYR cc_start: 0.8867 (p90) cc_final: 0.8643 (p90) REVERT: J 28 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8307 (mtp) REVERT: K 152 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7217 (mpt) REVERT: K 156 MET cc_start: 0.8096 (ptm) cc_final: 0.7857 (ptm) REVERT: K 159 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8229 (mtp) REVERT: K 256 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: L 97 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: L 101 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7214 (mttp) REVERT: M 50 MET cc_start: 0.7388 (mmt) cc_final: 0.7120 (mmm) REVERT: M 200 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: N 105 ASN cc_start: 0.8223 (t0) cc_final: 0.8020 (t0) REVERT: N 120 MET cc_start: 0.8007 (ttt) cc_final: 0.7677 (mtp) REVERT: N 126 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: N 198 MET cc_start: 0.8498 (mtp) cc_final: 0.8027 (mtm) REVERT: O 102 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.6903 (mp10) REVERT: O 143 ARG cc_start: 0.7370 (ptm-80) cc_final: 0.7139 (ptm-80) REVERT: O 182 LEU cc_start: 0.6943 (mt) cc_final: 0.6621 (OUTLIER) REVERT: O 203 MET cc_start: 0.7880 (ptm) cc_final: 0.7338 (ptp) REVERT: P 151 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8095 (t0) REVERT: P 178 ASP cc_start: 0.6704 (m-30) cc_final: 0.6423 (m-30) REVERT: R 29 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7031 (tp30) REVERT: R 235 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: S 61 LYS cc_start: 0.7445 (mtpt) cc_final: 0.6944 (mttt) REVERT: S 94 ASP cc_start: 0.7853 (m-30) cc_final: 0.7636 (m-30) REVERT: S 100 ASP cc_start: 0.7866 (t0) cc_final: 0.7437 (t0) REVERT: S 122 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7563 (mtp85) REVERT: T 33 ASN cc_start: 0.7133 (m110) cc_final: 0.6780 (m110) REVERT: T 71 ASP cc_start: 0.8313 (t0) cc_final: 0.7785 (t0) REVERT: T 94 GLU cc_start: 0.7360 (tp30) cc_final: 0.6656 (tt0) REVERT: T 115 ARG cc_start: 0.7596 (mtp85) cc_final: 0.7221 (mtp85) REVERT: T 203 ASP cc_start: 0.7375 (t0) cc_final: 0.7139 (t0) REVERT: T 204 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.7051 (pm20) REVERT: U 74 GLU cc_start: 0.7511 (mp0) cc_final: 0.7193 (pm20) REVERT: U 108 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: U 113 MET cc_start: 0.8485 (mmm) cc_final: 0.8182 (mmp) REVERT: U 131 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7379 (pmm) REVERT: U 174 GLU cc_start: 0.6295 (mp0) cc_final: 0.5959 (mm-30) REVERT: W 40 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8816 (tt0) REVERT: W 45 MET cc_start: 0.8701 (mmt) cc_final: 0.8481 (mmp) REVERT: X 12 TYR cc_start: 0.8886 (p90) cc_final: 0.8644 (p90) REVERT: X 111 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7258 (tm-30) REVERT: Y 130 LYS cc_start: 0.8003 (mmmm) cc_final: 0.7661 (mtmm) REVERT: Y 159 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8468 (mtp) REVERT: Z 97 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7620 (mp0) REVERT: a 200 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6885 (mp0) REVERT: b 105 ASN cc_start: 0.8142 (t0) cc_final: 0.7922 (t0) REVERT: b 126 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: b 179 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: b 198 MET cc_start: 0.8479 (mtp) cc_final: 0.8015 (mtm) outliers start: 108 outliers final: 46 residues processed: 713 average time/residue: 1.5074 time to fit residues: 1296.6338 Evaluate side-chains 679 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 608 time to evaluate : 4.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN 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 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 181 GLN Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 230 ARG Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain K residue 152 MET Chi-restraints excluded: chain K residue 155 SER 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 K residue 256 GLU Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 226 VAL Chi-restraints excluded: chain M residue 200 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 P residue 81 SER Chi-restraints excluded: chain P residue 151 ASP 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 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 204 GLU Chi-restraints excluded: chain U residue 108 GLU Chi-restraints excluded: chain U residue 131 MET Chi-restraints excluded: chain V residue 230 ARG Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 40 GLN Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 106 GLU Chi-restraints excluded: chain X residue 165 GLU 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 151 SER Chi-restraints excluded: chain Z residue 161 ASP Chi-restraints excluded: chain Z residue 226 VAL Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 144 GLN Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 199 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 595 optimal weight: 6.9990 chunk 361 optimal weight: 6.9990 chunk 357 optimal weight: 4.9990 chunk 554 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 410 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 313 optimal weight: 0.9980 chunk 304 optimal weight: 0.7980 chunk 173 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** H 134 GLN I 81 GLN I 93 ASN K 148 GLN O 42 ASN O 52 GLN Q 175 ASN R 225 ASN V 134 GLN W 81 GLN W 93 ASN Y 88 GLN a 114 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107256 restraints weight = 56054.390| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.87 r_work: 0.3134 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 48784 Z= 0.133 Angle : 0.456 10.364 65884 Z= 0.247 Chirality : 0.041 0.140 7404 Planarity : 0.004 0.065 8484 Dihedral : 3.916 23.301 6778 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.15 % Allowed : 12.90 % Favored : 84.95 % 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: 1.64 (0.11), residues: 6102 helix: 2.80 (0.11), residues: 2202 sheet: 0.98 (0.13), residues: 1512 loop : -0.50 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 100 HIS 0.008 0.000 HIS D 186 PHE 0.019 0.001 PHE T 136 TYR 0.020 0.001 TYR N 95 ARG 0.003 0.000 ARG G 228 *********************** 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 750 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 640 time to evaluate : 4.196 Fit side-chains REVERT: A 102 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.6897 (mp10) REVERT: A 143 ARG cc_start: 0.7410 (ptm-80) cc_final: 0.7171 (ptm-80) REVERT: A 203 MET cc_start: 0.7782 (ptm) cc_final: 0.7223 (ptp) REVERT: B 151 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.8015 (t0) REVERT: B 178 ASP cc_start: 0.6757 (m-30) cc_final: 0.6508 (m-30) REVERT: B 238 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7147 (mppt) REVERT: D 29 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7059 (tp30) REVERT: D 186 HIS cc_start: 0.7374 (p-80) cc_final: 0.6997 (p90) REVERT: D 235 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7109 (mm-30) REVERT: E 39 LYS cc_start: 0.8974 (pttt) cc_final: 0.8601 (pttt) REVERT: E 61 LYS cc_start: 0.7432 (mtpt) cc_final: 0.6940 (mttt) REVERT: E 100 ASP cc_start: 0.7908 (t70) cc_final: 0.7549 (t0) REVERT: E 167 SER cc_start: 0.7436 (OUTLIER) cc_final: 0.7183 (p) REVERT: F 33 ASN cc_start: 0.7054 (m110) cc_final: 0.6732 (m110) REVERT: F 115 ARG cc_start: 0.7506 (mtp85) cc_final: 0.7173 (mtp85) REVERT: F 181 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6582 (pp30) REVERT: F 182 MET cc_start: 0.7648 (pmm) cc_final: 0.7050 (pmm) REVERT: G 131 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7458 (pmm) REVERT: G 174 GLU cc_start: 0.6433 (mp0) cc_final: 0.6052 (mm-30) REVERT: I 4 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7253 (mpp) REVERT: I 134 ASP cc_start: 0.8141 (t70) cc_final: 0.7705 (t0) REVERT: J 12 TYR cc_start: 0.8860 (p90) cc_final: 0.8592 (p90) REVERT: J 28 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8288 (mtp) REVERT: K 152 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7208 (mpt) REVERT: K 156 MET cc_start: 0.8094 (ptm) cc_final: 0.7862 (ptm) REVERT: K 159 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8165 (mtp) REVERT: L 97 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: L 101 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7197 (mttp) REVERT: M 200 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: N 126 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: N 198 MET cc_start: 0.8434 (mtp) cc_final: 0.7963 (mtm) REVERT: O 102 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.6891 (mp10) REVERT: O 182 LEU cc_start: 0.6845 (mt) cc_final: 0.6585 (pp) REVERT: O 203 MET cc_start: 0.7920 (ptm) cc_final: 0.7441 (ptp) REVERT: P 151 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8058 (t0) REVERT: P 178 ASP cc_start: 0.6700 (m-30) cc_final: 0.6420 (m-30) REVERT: R 29 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7040 (tp30) REVERT: R 235 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6142 (mp0) REVERT: S 26 MET cc_start: 0.8317 (mtp) cc_final: 0.7516 (mtp) REVERT: S 61 LYS cc_start: 0.7444 (mtpt) cc_final: 0.6939 (mttt) REVERT: S 94 ASP cc_start: 0.7855 (m-30) cc_final: 0.7630 (m-30) REVERT: S 100 ASP cc_start: 0.7875 (t0) cc_final: 0.7424 (t0) REVERT: S 122 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7575 (mtp85) REVERT: T 33 ASN cc_start: 0.7099 (m110) cc_final: 0.6768 (m110) REVERT: T 115 ARG cc_start: 0.7596 (mtp85) cc_final: 0.7221 (mtp85) REVERT: T 204 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6989 (pm20) REVERT: U 74 GLU cc_start: 0.7509 (mp0) cc_final: 0.7185 (pm20) REVERT: U 108 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: U 131 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7467 (pmm) REVERT: U 174 GLU cc_start: 0.6461 (mp0) cc_final: 0.6054 (mm-30) REVERT: V 172 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8300 (t) REVERT: V 227 ASP cc_start: 0.7798 (m-30) cc_final: 0.7490 (m-30) REVERT: W 40 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8820 (tt0) REVERT: X 70 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6944 (mtt180) REVERT: X 111 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7254 (tm-30) REVERT: Y 130 LYS cc_start: 0.8000 (mmmm) cc_final: 0.7665 (mtmm) REVERT: Y 159 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8273 (mtp) REVERT: Z 97 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7615 (mp0) REVERT: a 200 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6952 (mp0) REVERT: a 245 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6877 (tp30) REVERT: b 105 ASN cc_start: 0.8107 (t0) cc_final: 0.7888 (t0) REVERT: b 126 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: b 179 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: b 198 MET cc_start: 0.8451 (mtp) cc_final: 0.7934 (mtm) outliers start: 110 outliers final: 53 residues processed: 698 average time/residue: 1.4782 time to fit residues: 1248.9902 Evaluate side-chains 703 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 622 time to evaluate : 4.202 ------------------------------------------------------------------------------- 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 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 181 GLN Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain H residue 230 ARG Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 152 MET Chi-restraints excluded: chain K residue 155 SER 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 97 GLU Chi-restraints excluded: chain L residue 101 LYS 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 66 VAL Chi-restraints excluded: chain M residue 172 MET 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 P residue 151 ASP 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 209 LYS Chi-restraints excluded: chain R residue 224 GLN Chi-restraints excluded: chain R residue 228 MET 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 176 MET Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 204 GLU Chi-restraints excluded: chain U residue 108 GLU Chi-restraints excluded: chain U residue 131 MET Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 230 ARG Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 40 GLN Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 70 ARG Chi-restraints excluded: chain X residue 165 GLU 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 151 SER Chi-restraints excluded: chain Z residue 161 ASP Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 226 VAL 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 179 GLU Chi-restraints excluded: chain b residue 199 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 132 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 512 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 chunk 281 optimal weight: 9.9990 chunk 414 optimal weight: 9.9990 chunk 483 optimal weight: 6.9990 chunk 489 optimal weight: 5.9990 chunk 273 optimal weight: 0.9990 chunk 572 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN B 240 HIS C 175 ASN ** D 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN I 93 ASN K 88 GLN O 42 ASN O 52 GLN Q 175 ASN R 225 ASN V 134 GLN W 81 GLN W 93 ASN Y 88 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.130793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.101205 restraints weight = 56509.457| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.88 r_work: 0.3043 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 48784 Z= 0.323 Angle : 0.578 11.379 65884 Z= 0.308 Chirality : 0.045 0.164 7404 Planarity : 0.005 0.067 8484 Dihedral : 4.344 23.947 6778 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.25 % Allowed : 13.35 % Favored : 84.40 % 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: 1.31 (0.11), residues: 6102 helix: 2.45 (0.11), residues: 2200 sheet: 0.93 (0.13), residues: 1492 loop : -0.70 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 101 HIS 0.008 0.001 HIS a 134 PHE 0.027 0.002 PHE V 79 TYR 0.021 0.002 TYR P 136 ARG 0.004 0.000 ARG E 101 *********************** 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 759 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 644 time to evaluate : 4.186 Fit side-chains REVERT: A 102 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7093 (mp10) REVERT: A 203 MET cc_start: 0.7849 (ptm) cc_final: 0.7460 (ptp) REVERT: B 178 ASP cc_start: 0.6766 (m-30) cc_final: 0.6523 (m-30) REVERT: B 238 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7111 (mppt) REVERT: D 186 HIS cc_start: 0.7335 (p-80) cc_final: 0.6881 (p90) REVERT: D 235 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7105 (mm-30) REVERT: E 61 LYS cc_start: 0.7509 (mtpt) cc_final: 0.6932 (mttt) REVERT: E 100 ASP cc_start: 0.8104 (t70) cc_final: 0.7700 (t0) REVERT: E 186 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7182 (mt-10) REVERT: F 33 ASN cc_start: 0.7187 (m110) cc_final: 0.6911 (m110) REVERT: F 71 ASP cc_start: 0.7951 (t0) cc_final: 0.7498 (t0) REVERT: F 115 ARG cc_start: 0.7610 (mtp85) cc_final: 0.7233 (mtp85) REVERT: F 181 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6477 (pp30) REVERT: F 182 MET cc_start: 0.7638 (pmm) cc_final: 0.7069 (pmm) REVERT: F 184 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6258 (pm20) REVERT: G 174 GLU cc_start: 0.6359 (mp0) cc_final: 0.6020 (mm-30) REVERT: H 71 ASP cc_start: 0.7977 (t0) cc_final: 0.7755 (t0) REVERT: H 100 GLN cc_start: 0.8370 (mt0) cc_final: 0.8031 (mt0) REVERT: I 4 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7531 (mpp) REVERT: I 98 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8022 (mptt) REVERT: I 155 GLU cc_start: 0.8416 (pt0) cc_final: 0.7987 (pt0) REVERT: I 183 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8193 (mtt) REVERT: J 28 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8430 (mtp) REVERT: K 152 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7002 (mpt) REVERT: K 159 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8311 (mtp) REVERT: M 200 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: M 245 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6847 (tp30) REVERT: N 120 MET cc_start: 0.8204 (ttt) cc_final: 0.7994 (ttm) REVERT: N 126 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: N 198 MET cc_start: 0.8556 (mtp) cc_final: 0.8132 (mtm) REVERT: O 96 GLN cc_start: 0.8383 (mt0) cc_final: 0.8105 (mt0) REVERT: O 102 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7118 (mp10) REVERT: O 203 MET cc_start: 0.7913 (ptm) cc_final: 0.7406 (ptp) REVERT: P 178 ASP cc_start: 0.6675 (m-30) cc_final: 0.6434 (m-30) REVERT: R 235 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6105 (mp0) REVERT: S 26 MET cc_start: 0.8346 (mtp) cc_final: 0.7583 (mtp) REVERT: S 61 LYS cc_start: 0.7518 (mtpt) cc_final: 0.6917 (mttt) REVERT: S 100 ASP cc_start: 0.8077 (t0) cc_final: 0.7589 (t0) REVERT: S 122 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7618 (mtp85) REVERT: T 33 ASN cc_start: 0.7124 (m110) cc_final: 0.6748 (m110) REVERT: T 115 ARG cc_start: 0.7668 (mtp85) cc_final: 0.7267 (mtp85) REVERT: U 74 GLU cc_start: 0.7659 (mp0) cc_final: 0.7275 (pm20) REVERT: U 108 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: U 174 GLU cc_start: 0.6348 (mp0) cc_final: 0.6013 (mm-30) REVERT: V 100 GLN cc_start: 0.8414 (mt0) cc_final: 0.8080 (mt0) REVERT: V 172 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8339 (t) REVERT: V 227 ASP cc_start: 0.7842 (m-30) cc_final: 0.7577 (m-30) REVERT: W 40 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8921 (tt0) REVERT: W 155 GLU cc_start: 0.8414 (pt0) cc_final: 0.7988 (pt0) REVERT: X 111 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7329 (tm-30) REVERT: Y 89 THR cc_start: 0.8521 (p) cc_final: 0.8207 (m) REVERT: Y 159 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8296 (mtp) REVERT: a 164 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5343 (pp20) REVERT: a 200 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7104 (mp0) REVERT: b 105 ASN cc_start: 0.8415 (t0) cc_final: 0.8173 (t0) REVERT: b 126 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: b 154 MET cc_start: 0.8614 (ttp) cc_final: 0.8303 (ttt) REVERT: b 179 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: b 198 MET cc_start: 0.8534 (mtp) cc_final: 0.8017 (mtm) outliers start: 115 outliers final: 54 residues processed: 708 average time/residue: 1.5148 time to fit residues: 1293.2171 Evaluate side-chains 696 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 619 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN 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 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 28 MET Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 230 ARG Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 58 THR 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 165 GLU Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain K residue 88 GLN Chi-restraints excluded: chain K residue 152 MET Chi-restraints excluded: chain K residue 155 SER 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 151 SER Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 226 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 245 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 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 224 GLN 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 U residue 50 ILE Chi-restraints excluded: chain U residue 108 GLU Chi-restraints excluded: chain U residue 131 MET 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 40 GLN Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 106 GLU Chi-restraints excluded: chain X residue 165 GLU 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 151 SER Chi-restraints excluded: chain Z residue 226 VAL Chi-restraints excluded: chain a residue 164 GLU Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 199 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 327 optimal weight: 4.9990 chunk 444 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 526 optimal weight: 0.0270 chunk 395 optimal weight: 5.9990 chunk 544 optimal weight: 0.4980 chunk 565 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 257 optimal weight: 0.8980 chunk 521 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 overall best weight: 1.4240 ------------------------------------------------------------------------------- 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 B 198 ASN B 240 HIS C 175 ASN ** D 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN I 81 GLN I 93 ASN K 88 GLN O 42 ASN O 52 GLN Q 175 ASN T 102 ASN V 134 GLN W 81 GLN W 93 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.104330 restraints weight = 56003.241| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.88 r_work: 0.3089 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 48784 Z= 0.179 Angle : 0.494 10.964 65884 Z= 0.267 Chirality : 0.042 0.144 7404 Planarity : 0.004 0.066 8484 Dihedral : 4.145 23.641 6778 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.84 % Allowed : 14.29 % Favored : 83.87 % 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: 1.45 (0.11), residues: 6102 helix: 2.63 (0.11), residues: 2202 sheet: 0.92 (0.13), residues: 1514 loop : -0.64 (0.12), residues: 2386 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 0.017 0.001 PHE H 79 TYR 0.024 0.001 TYR N 95 ARG 0.004 0.000 ARG P 218 *********************** 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 736 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 642 time to evaluate : 4.159 Fit side-chains REVERT: A 102 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.6835 (mp10) REVERT: A 203 MET cc_start: 0.7741 (ptm) cc_final: 0.7287 (ptp) REVERT: B 87 THR cc_start: 0.8496 (m) cc_final: 0.8256 (p) REVERT: B 151 ASP cc_start: 0.8411 (t0) cc_final: 0.8194 (t0) REVERT: B 178 ASP cc_start: 0.6774 (m-30) cc_final: 0.6528 (m-30) REVERT: B 238 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7153 (mppt) REVERT: C 23 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7555 (mt0) REVERT: D 186 HIS cc_start: 0.7262 (p-80) cc_final: 0.6860 (p90) REVERT: D 235 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7117 (mm-30) REVERT: E 39 LYS cc_start: 0.9088 (pttt) cc_final: 0.8688 (pttt) REVERT: E 61 LYS cc_start: 0.7501 (mtpt) cc_final: 0.6934 (mttt) REVERT: E 100 ASP cc_start: 0.8032 (t70) cc_final: 0.7626 (t0) REVERT: F 71 ASP cc_start: 0.7821 (t0) cc_final: 0.7380 (t0) REVERT: F 115 ARG cc_start: 0.7575 (mtp85) cc_final: 0.7213 (mtp85) REVERT: F 181 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6542 (pp30) REVERT: F 182 MET cc_start: 0.7567 (pmm) cc_final: 0.7095 (pmm) REVERT: G 113 MET cc_start: 0.8553 (mmm) cc_final: 0.8207 (mmp) REVERT: G 131 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7400 (pmm) REVERT: G 174 GLU cc_start: 0.6407 (mp0) cc_final: 0.6084 (mm-30) REVERT: I 4 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7545 (mpp) REVERT: I 40 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8894 (tt0) REVERT: I 155 GLU cc_start: 0.8335 (pt0) cc_final: 0.7893 (pt0) REVERT: I 183 MET cc_start: 0.8560 (mtm) cc_final: 0.8167 (mtt) REVERT: J 28 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8360 (mtp) REVERT: K 89 THR cc_start: 0.8545 (p) cc_final: 0.8249 (m) REVERT: K 152 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7138 (mpt) REVERT: K 159 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8214 (mtp) REVERT: L 101 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7271 (mtmp) REVERT: M 50 MET cc_start: 0.7407 (mmt) cc_final: 0.7192 (mmm) REVERT: M 200 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: M 245 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6797 (tp30) REVERT: N 120 MET cc_start: 0.8040 (ttt) cc_final: 0.7725 (mtp) REVERT: N 126 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: N 198 MET cc_start: 0.8502 (mtp) cc_final: 0.8075 (mtm) REVERT: O 102 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.6844 (mp10) REVERT: O 143 ARG cc_start: 0.7534 (ptm-80) cc_final: 0.7306 (ptm-80) REVERT: O 203 MET cc_start: 0.7845 (ptm) cc_final: 0.7391 (ptp) REVERT: P 17 ARG cc_start: 0.7826 (mtp180) cc_final: 0.7622 (mtp85) REVERT: P 87 THR cc_start: 0.8493 (m) cc_final: 0.8236 (p) REVERT: P 151 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8172 (t0) REVERT: P 178 ASP cc_start: 0.6657 (m-30) cc_final: 0.6432 (m-30) REVERT: R 235 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6363 (mt-10) REVERT: S 26 MET cc_start: 0.8356 (mtp) cc_final: 0.7562 (mtp) REVERT: S 61 LYS cc_start: 0.7507 (mtpt) cc_final: 0.6928 (mttt) REVERT: S 100 ASP cc_start: 0.7992 (t0) cc_final: 0.7514 (t0) REVERT: T 33 ASN cc_start: 0.7047 (m110) cc_final: 0.6694 (m110) REVERT: T 115 ARG cc_start: 0.7582 (mtp85) cc_final: 0.7205 (mtp85) REVERT: U 74 GLU cc_start: 0.7587 (mp0) cc_final: 0.7218 (pm20) REVERT: U 108 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: U 174 GLU cc_start: 0.6534 (mp0) cc_final: 0.6226 (mm-30) REVERT: W 40 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8861 (tt0) REVERT: W 155 GLU cc_start: 0.8346 (pt0) cc_final: 0.7916 (pt0) REVERT: X 12 TYR cc_start: 0.8861 (p90) cc_final: 0.8626 (p90) REVERT: X 70 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7119 (mtt180) REVERT: X 111 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7310 (tm-30) REVERT: Y 89 THR cc_start: 0.8499 (p) cc_final: 0.8247 (m) REVERT: Y 159 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8204 (mtp) REVERT: a 200 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7005 (mp0) REVERT: b 95 TYR cc_start: 0.8431 (t80) cc_final: 0.8212 (t80) REVERT: b 105 ASN cc_start: 0.8331 (t0) cc_final: 0.8091 (t0) REVERT: b 126 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: b 179 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: b 198 MET cc_start: 0.8490 (mtp) cc_final: 0.8004 (mtm) outliers start: 94 outliers final: 49 residues processed: 696 average time/residue: 1.4918 time to fit residues: 1257.7481 Evaluate side-chains 690 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 619 time to evaluate : 4.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN 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 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 28 MET Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 230 ARG Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 40 GLN Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 152 SER 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 K residue 152 MET Chi-restraints excluded: chain K residue 155 SER 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 101 LYS Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 226 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 201 LYS Chi-restraints excluded: chain M residue 245 GLU Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain N residue 129 MET 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 P residue 151 ASP 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 U residue 108 GLU Chi-restraints excluded: chain V residue 237 LYS Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 40 GLN Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 70 ARG Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 177 THR 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 151 SER Chi-restraints excluded: chain Z residue 226 VAL Chi-restraints excluded: chain a residue 243 GLU Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 199 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 429 optimal weight: 6.9990 chunk 517 optimal weight: 2.9990 chunk 285 optimal weight: 10.0000 chunk 496 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 416 optimal weight: 6.9990 chunk 516 optimal weight: 1.9990 chunk 574 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 406 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 B 198 ASN B 240 HIS C 175 ASN D 104 ASN ** D 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN I 81 GLN I 93 ASN O 42 ASN O 52 GLN Q 175 ASN R 104 ASN W 81 GLN W 93 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.101112 restraints weight = 56236.381| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.87 r_work: 0.3045 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 48784 Z= 0.326 Angle : 0.580 11.718 65884 Z= 0.310 Chirality : 0.045 0.165 7404 Planarity : 0.005 0.070 8484 Dihedral : 4.380 24.448 6778 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.82 % Allowed : 14.54 % Favored : 83.64 % 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: 1.19 (0.11), residues: 6102 helix: 2.37 (0.11), residues: 2202 sheet: 0.86 (0.13), residues: 1478 loop : -0.78 (0.11), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP U 101 HIS 0.008 0.001 HIS a 134 PHE 0.024 0.002 PHE H 79 TYR 0.019 0.002 TYR P 136 ARG 0.004 0.000 ARG B 91 *********************** 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 717 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 624 time to evaluate : 4.210 Fit side-chains REVERT: A 102 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7096 (mp10) REVERT: A 203 MET cc_start: 0.7861 (ptm) cc_final: 0.7448 (ptp) REVERT: B 178 ASP cc_start: 0.6773 (m-30) cc_final: 0.6544 (m-30) REVERT: B 238 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7097 (mppt) REVERT: C 23 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7581 (mt0) REVERT: C 100 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8460 (t0) REVERT: D 186 HIS cc_start: 0.7288 (p-80) cc_final: 0.6874 (p90) REVERT: D 235 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7101 (mm-30) REVERT: E 61 LYS cc_start: 0.7488 (mtpt) cc_final: 0.6879 (mttt) REVERT: E 100 ASP cc_start: 0.8114 (t70) cc_final: 0.7711 (t0) REVERT: E 186 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7197 (mt-10) REVERT: F 115 ARG cc_start: 0.7632 (mtp85) cc_final: 0.7239 (mtp85) REVERT: F 182 MET cc_start: 0.7604 (pmm) cc_final: 0.7106 (pmm) REVERT: G 174 GLU cc_start: 0.6361 (mp0) cc_final: 0.6022 (mm-30) REVERT: H 100 GLN cc_start: 0.8366 (mt0) cc_final: 0.8030 (mt0) REVERT: H 258 LYS cc_start: 0.6591 (OUTLIER) cc_final: 0.5985 (ptpt) REVERT: I 4 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7559 (mpp) REVERT: I 40 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8936 (tt0) REVERT: I 155 GLU cc_start: 0.8406 (pt0) cc_final: 0.7981 (pt0) REVERT: I 183 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8286 (mtt) REVERT: J 12 TYR cc_start: 0.8868 (p90) cc_final: 0.8621 (p90) REVERT: J 28 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8385 (mtp) REVERT: K 89 THR cc_start: 0.8532 (p) cc_final: 0.8322 (m) REVERT: K 152 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.6933 (mpt) REVERT: K 159 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8287 (mtp) REVERT: M 200 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: M 245 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6837 (tp30) REVERT: N 120 MET cc_start: 0.8221 (ttt) cc_final: 0.8001 (ttm) REVERT: N 126 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: N 198 MET cc_start: 0.8574 (mtp) cc_final: 0.8160 (mtm) REVERT: O 96 GLN cc_start: 0.8351 (mt0) cc_final: 0.8064 (mt0) REVERT: O 102 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7165 (mp10) REVERT: O 203 MET cc_start: 0.7920 (ptm) cc_final: 0.7418 (ptp) REVERT: P 17 ARG cc_start: 0.7748 (mtp180) cc_final: 0.7527 (mtp85) REVERT: P 178 ASP cc_start: 0.6729 (m-30) cc_final: 0.6494 (m-30) REVERT: R 235 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6089 (mp0) REVERT: S 26 MET cc_start: 0.8422 (mtp) cc_final: 0.7706 (mtp) REVERT: S 61 LYS cc_start: 0.7493 (mtpt) cc_final: 0.6879 (mttt) REVERT: S 100 ASP cc_start: 0.8092 (t0) cc_final: 0.7606 (t0) REVERT: T 33 ASN cc_start: 0.7082 (m110) cc_final: 0.6789 (m110) REVERT: T 115 ARG cc_start: 0.7707 (mtp85) cc_final: 0.7313 (mtp85) REVERT: U 74 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7308 (pm20) REVERT: U 108 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: U 174 GLU cc_start: 0.6349 (mp0) cc_final: 0.6019 (mm-30) REVERT: V 100 GLN cc_start: 0.8362 (mt0) cc_final: 0.8032 (mt0) REVERT: V 172 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8339 (t) REVERT: W 40 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8915 (tt0) REVERT: W 155 GLU cc_start: 0.8420 (pt0) cc_final: 0.8020 (pt0) REVERT: X 111 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7338 (tm-30) REVERT: Y 89 THR cc_start: 0.8517 (p) cc_final: 0.8311 (m) REVERT: Y 159 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8271 (mtp) REVERT: b 105 ASN cc_start: 0.8363 (t0) cc_final: 0.8108 (t0) REVERT: b 126 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: b 179 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: b 198 MET cc_start: 0.8556 (mtp) cc_final: 0.7982 (mtm) outliers start: 93 outliers final: 56 residues processed: 679 average time/residue: 1.5686 time to fit residues: 1294.0989 Evaluate side-chains 695 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 617 time to evaluate : 4.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 100 ASP 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 224 GLN 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 28 MET Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 230 ARG Chi-restraints excluded: chain H residue 258 LYS Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 40 GLN 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 165 GLU Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain K residue 152 MET Chi-restraints excluded: chain K residue 155 SER 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 226 VAL Chi-restraints excluded: chain M residue 66 VAL 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 126 GLU Chi-restraints excluded: chain N residue 129 MET 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 224 GLN 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 U residue 74 GLU Chi-restraints excluded: chain U residue 108 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 40 GLN 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 X residue 165 GLU Chi-restraints excluded: chain X residue 177 THR 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 151 SER Chi-restraints excluded: chain Z residue 226 VAL Chi-restraints excluded: chain a residue 243 GLU Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 129 MET Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 199 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 285 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 448 optimal weight: 4.9990 chunk 585 optimal weight: 4.9990 chunk 388 optimal weight: 0.5980 chunk 443 optimal weight: 2.9990 chunk 383 optimal weight: 0.6980 chunk 357 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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** H 134 GLN I 93 ASN O 42 ASN O 52 GLN Q 175 ASN T 222 ASN W 81 GLN W 93 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.102708 restraints weight = 56326.925| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.89 r_work: 0.3065 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 48784 Z= 0.233 Angle : 0.532 11.584 65884 Z= 0.286 Chirality : 0.043 0.144 7404 Planarity : 0.005 0.068 8484 Dihedral : 4.286 24.136 6778 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.60 % Allowed : 14.97 % Favored : 83.42 % 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: 1.27 (0.11), residues: 6102 helix: 2.47 (0.11), residues: 2204 sheet: 0.87 (0.13), residues: 1508 loop : -0.76 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 100 HIS 0.007 0.001 HIS D 186 PHE 0.019 0.002 PHE H 79 TYR 0.027 0.001 TYR N 95 ARG 0.003 0.000 ARG P 218 ********************** 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 713 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 631 time to evaluate : 4.599 Fit side-chains REVERT: A 102 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.6805 (mp10) REVERT: A 203 MET cc_start: 0.7814 (ptm) cc_final: 0.7383 (ptp) REVERT: B 87 THR cc_start: 0.8532 (m) cc_final: 0.8295 (p) REVERT: B 178 ASP cc_start: 0.6793 (m-30) cc_final: 0.6550 (m-30) REVERT: B 238 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7194 (mppt) REVERT: C 23 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7571 (mt0) REVERT: C 100 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8474 (t0) REVERT: D 235 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7106 (mm-30) REVERT: E 61 LYS cc_start: 0.7536 (mtpt) cc_final: 0.6943 (mttt) REVERT: E 100 ASP cc_start: 0.8071 (t70) cc_final: 0.7659 (t0) REVERT: E 186 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7174 (mt-10) REVERT: F 71 ASP cc_start: 0.7847 (t0) cc_final: 0.7372 (t0) REVERT: F 115 ARG cc_start: 0.7571 (mtp85) cc_final: 0.7197 (mtp85) REVERT: F 182 MET cc_start: 0.7578 (pmm) cc_final: 0.7132 (pmm) REVERT: G 174 GLU cc_start: 0.6391 (mp0) cc_final: 0.6057 (mm-30) REVERT: I 4 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7578 (mpp) REVERT: I 155 GLU cc_start: 0.8375 (pt0) cc_final: 0.7950 (pt0) REVERT: I 183 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8381 (mtt) REVERT: J 28 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8290 (mtp) REVERT: K 152 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7037 (mpt) REVERT: K 159 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8273 (mtp) REVERT: L 101 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7443 (mtmp) REVERT: M 200 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: M 245 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6878 (tp30) REVERT: N 126 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: N 198 MET cc_start: 0.8539 (mtp) cc_final: 0.8077 (mtm) REVERT: O 102 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.6822 (mp10) REVERT: O 203 MET cc_start: 0.7907 (ptm) cc_final: 0.7467 (ptp) REVERT: P 17 ARG cc_start: 0.7773 (mtp180) cc_final: 0.7537 (mtp85) REVERT: P 87 THR cc_start: 0.8525 (m) cc_final: 0.8268 (p) REVERT: P 178 ASP cc_start: 0.6706 (m-30) cc_final: 0.6464 (m-30) REVERT: R 235 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6374 (mt-10) REVERT: S 26 MET cc_start: 0.8342 (mtp) cc_final: 0.7576 (mtp) REVERT: S 61 LYS cc_start: 0.7525 (mtpt) cc_final: 0.6919 (mttt) REVERT: S 100 ASP cc_start: 0.8057 (t0) cc_final: 0.7576 (t0) REVERT: T 115 ARG cc_start: 0.7650 (mtp85) cc_final: 0.7272 (mtp85) REVERT: U 108 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: U 174 GLU cc_start: 0.6376 (mp0) cc_final: 0.6052 (mm-30) REVERT: V 172 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8325 (t) REVERT: W 40 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8888 (tt0) REVERT: W 155 GLU cc_start: 0.8355 (pt0) cc_final: 0.7918 (pt0) REVERT: W 183 MET cc_start: 0.8483 (mtm) cc_final: 0.8218 (mtt) REVERT: X 12 TYR cc_start: 0.8848 (p90) cc_final: 0.8607 (p90) REVERT: X 111 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7321 (tm-30) REVERT: Y 89 THR cc_start: 0.8525 (p) cc_final: 0.8275 (m) REVERT: Y 159 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8236 (mtp) REVERT: Z 47 ASP cc_start: 0.8352 (p0) cc_final: 0.7990 (p0) REVERT: a 200 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7063 (mp0) REVERT: b 95 TYR cc_start: 0.8580 (t80) cc_final: 0.8366 (t80) REVERT: b 105 ASN cc_start: 0.8395 (t0) cc_final: 0.8119 (t0) REVERT: b 126 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: b 179 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: b 198 MET cc_start: 0.8497 (mtp) cc_final: 0.8046 (mtm) REVERT: b 230 LYS cc_start: 0.6764 (mmtt) cc_final: 0.6493 (mmtt) outliers start: 82 outliers final: 52 residues processed: 680 average time/residue: 1.5715 time to fit residues: 1299.6636 Evaluate side-chains 679 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 607 time to evaluate : 4.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 100 ASP 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 224 GLN 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 28 MET Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 230 ARG 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 1 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 K residue 152 MET Chi-restraints excluded: chain K residue 155 SER 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 101 LYS Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 226 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 245 GLU Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain N residue 129 MET 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 224 GLN 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 U residue 108 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 40 GLN Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 152 SER Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 177 THR 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 151 SER Chi-restraints excluded: chain Z residue 226 VAL Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 199 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 225 optimal weight: 6.9990 chunk 578 optimal weight: 0.0170 chunk 267 optimal weight: 2.9990 chunk 323 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 250 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 190 optimal weight: 0.9980 chunk 277 optimal weight: 3.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- 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 186 HIS I 81 GLN I 93 ASN O 42 ASN Q 175 ASN T 222 ASN W 93 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.134957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.105563 restraints weight = 55931.735| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.88 r_work: 0.3107 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 48784 Z= 0.161 Angle : 0.483 10.950 65884 Z= 0.262 Chirality : 0.042 0.141 7404 Planarity : 0.004 0.066 8484 Dihedral : 4.083 24.256 6778 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.53 % Allowed : 15.23 % Favored : 83.25 % 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: 1.45 (0.11), residues: 6102 helix: 2.69 (0.11), residues: 2204 sheet: 0.89 (0.13), residues: 1508 loop : -0.68 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 100 HIS 0.006 0.001 HIS D 186 PHE 0.015 0.001 PHE V 79 TYR 0.015 0.001 TYR U 160 ARG 0.004 0.000 ARG P 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28950.38 seconds wall clock time: 495 minutes 9.27 seconds (29709.27 seconds total)