Starting phenix.real_space_refine on Sun Nov 17 22:26:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0m_40944/11_2024/8t0m_40944.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0m_40944/11_2024/8t0m_40944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0m_40944/11_2024/8t0m_40944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0m_40944/11_2024/8t0m_40944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0m_40944/11_2024/8t0m_40944.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0m_40944/11_2024/8t0m_40944.cif" } resolution = 2.4 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= 0.004 sd= 0.183 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 152 5.16 5 C 30140 2.51 5 N 8050 2.21 5 O 9196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 47538 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1805 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "B" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1900 Classifications: {'peptide': 248} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 235} Chain: "C" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1861 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 2 Chain: "D" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1727 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 10, 'TRANS': 210} Chain breaks: 2 Chain: "E" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1750 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 4, 'TRANS': 222} Chain breaks: 1 Chain: "F" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1765 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "G" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1885 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain: "H" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1424 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain breaks: 2 Chain: "I" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1550 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 3 Chain: "J" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1551 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 192} Chain breaks: 1 Chain: "K" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "L" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1617 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 204} Chain breaks: 1 Chain: "M" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1737 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 212} Chain: "N" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1639 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "O" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1805 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "P" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1900 Classifications: {'peptide': 248} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 235} Chain: "Q" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1861 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 2 Chain: "R" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1727 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 10, 'TRANS': 210} Chain breaks: 2 Chain: "S" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1750 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 4, 'TRANS': 222} Chain breaks: 1 Chain: "T" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1765 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "U" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1885 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain: "V" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1424 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain breaks: 2 Chain: "W" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1550 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 3 Chain: "X" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1551 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 192} Chain breaks: 1 Chain: "Y" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "Z" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1617 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 204} Chain breaks: 1 Chain: "a" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1737 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 212} Chain: "b" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1639 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Time building chain proxies: 26.61, per 1000 atoms: 0.56 Number of scatterers: 47538 At special positions: 0 Unit cell: (177.02, 189.74, 135.68, 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 152 16.00 O 9196 8.00 N 8050 7.00 C 30140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 32 " - pdb=" SG CYS D 46 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 191 " distance=2.04 Simple disulfide: pdb=" SG CYS R 32 " - pdb=" SG CYS R 46 " distance=2.03 Simple disulfide: pdb=" SG CYS R 41 " - pdb=" SG CYS R 191 " distance=2.03 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: 11.70 Conformation dependent library (CDL) restraints added in 6.0 seconds 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11220 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 70 sheets defined 40.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.70 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 removed outlier: 3.953A pdb=" N ARG A 14 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 86 through 109 Processing helix chain 'A' and resid 113 through 131 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 199 through 215 Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'B' and resid 18 through 30 Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 78 through 96 Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 124 Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 184 through 200 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'C' and resid 2 through 7 removed outlier: 4.189A pdb=" N ARG C 5 " --> pdb=" O GLY C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 Processing helix chain 'C' and resid 80 through 103 Processing helix chain 'C' and resid 107 through 125 removed outlier: 3.573A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 231 through 243 Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 78 through 101 removed outlier: 3.509A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 167 through 179 Processing helix chain 'D' and resid 187 through 200 Processing helix chain 'D' and resid 225 through 236 Processing helix chain 'E' and resid 21 through 32 Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 81 through 104 removed outlier: 3.529A pdb=" N ALA E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 175 through 187 removed outlier: 3.818A pdb=" N ALA E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 208 Processing helix chain 'E' and resid 232 through 242 Processing helix chain 'F' and resid 19 through 31 Processing helix chain 'F' and resid 77 through 100 Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.971A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN F 121 " --> pdb=" O GLN F 117 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 180 removed outlier: 4.406A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASP F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N THR F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 199 Processing helix chain 'F' and resid 226 through 231 Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 81 through 103 Processing helix chain 'G' and resid 108 through 123 removed outlier: 3.512A pdb=" N HIS G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 183 Processing helix chain 'G' and resid 188 through 204 Processing helix chain 'G' and resid 205 through 208 removed outlier: 3.823A pdb=" N LYS G 208 " --> pdb=" O GLU G 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 233 through 248 removed outlier: 3.898A pdb=" N ASN G 248 " --> pdb=" O GLN G 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 90 Processing helix chain 'H' and resid 93 through 106 Processing helix chain 'H' and resid 150 through 152 No H-bonds generated for 'chain 'H' and resid 150 through 152' Processing helix chain 'H' and resid 153 through 161 Processing helix chain 'H' and resid 166 through 185 Processing helix chain 'H' and resid 208 through 213 Processing helix chain 'I' and resid 84 through 100 Processing helix chain 'I' and resid 104 through 119 Processing helix chain 'I' and resid 159 through 171 Processing helix chain 'I' and resid 176 through 195 Processing helix chain 'J' and resid 4 through 9 removed outlier: 4.388A pdb=" N ASN J 8 " --> pdb=" O PRO J 4 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 4 through 9' Processing helix chain 'J' and resid 57 through 80 Processing helix chain 'J' and resid 84 through 98 Processing helix chain 'J' and resid 143 through 155 Processing helix chain 'J' and resid 160 through 178 removed outlier: 3.698A pdb=" N ARG J 178 " --> pdb=" O ASN J 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 72 removed outlier: 4.690A pdb=" N VAL K 54 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN K 55 " --> pdb=" O GLY K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 93 removed outlier: 4.006A pdb=" N ARG K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 139 removed outlier: 4.095A pdb=" N GLY K 137 " --> pdb=" O GLY K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 148 Processing helix chain 'K' and resid 153 through 172 Processing helix chain 'L' and resid 123 through 146 Processing helix chain 'L' and resid 150 through 165 Processing helix chain 'L' and resid 207 through 219 Processing helix chain 'L' and resid 224 through 243 Processing helix chain 'L' and resid 268 through 280 removed outlier: 3.537A pdb=" N TRP L 273 " --> pdb=" O GLY L 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 99 Processing helix chain 'M' and resid 105 through 119 Processing helix chain 'M' and resid 162 through 165 Processing helix chain 'M' and resid 166 through 174 Processing helix chain 'M' and resid 196 through 215 Processing helix chain 'N' and resid 91 through 110 removed outlier: 3.539A pdb=" N TYR N 110 " --> pdb=" O THR N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 140 Processing helix chain 'N' and resid 179 through 191 removed outlier: 3.786A pdb=" N HIS N 183 " --> pdb=" O GLY N 179 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASN N 186 " --> pdb=" O ALA N 182 " (cutoff:3.500A) Proline residue: N 187 - end of helix Processing helix chain 'N' and resid 195 through 199 Processing helix chain 'N' and resid 203 through 222 Processing helix chain 'O' and resid 11 through 15 removed outlier: 4.007A pdb=" N ARG O 14 " --> pdb=" O GLY O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 34 Processing helix chain 'O' and resid 35 through 37 No H-bonds generated for 'chain 'O' and resid 35 through 37' Processing helix chain 'O' and resid 65 through 69 Processing helix chain 'O' and resid 86 through 109 Processing helix chain 'O' and resid 113 through 131 Processing helix chain 'O' and resid 174 through 186 Processing helix chain 'O' and resid 199 through 215 Processing helix chain 'O' and resid 237 through 250 Processing helix chain 'P' and resid 18 through 30 Processing helix chain 'P' and resid 58 through 61 Processing helix chain 'P' and resid 78 through 96 Processing helix chain 'P' and resid 97 through 102 Processing helix chain 'P' and resid 106 through 124 Processing helix chain 'P' and resid 167 through 179 Processing helix chain 'P' and resid 184 through 200 removed outlier: 3.596A pdb=" N SER P 199 " --> pdb=" O THR P 195 " (cutoff:3.500A) Processing helix chain 'P' and resid 218 through 222 Processing helix chain 'P' and resid 239 through 249 Processing helix chain 'Q' and resid 2 through 7 removed outlier: 4.236A pdb=" N ARG Q 5 " --> pdb=" O GLY Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 30 Processing helix chain 'Q' and resid 80 through 103 Processing helix chain 'Q' and resid 107 through 125 removed outlier: 3.587A pdb=" N THR Q 123 " --> pdb=" O LYS Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 180 Processing helix chain 'Q' and resid 185 through 199 Processing helix chain 'Q' and resid 207 through 209 No H-bonds generated for 'chain 'Q' and resid 207 through 209' Processing helix chain 'Q' and resid 231 through 243 Processing helix chain 'R' and resid 17 through 29 Processing helix chain 'R' and resid 78 through 101 removed outlier: 3.755A pdb=" N ILE R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 121 Processing helix chain 'R' and resid 167 through 179 Processing helix chain 'R' and resid 187 through 200 Processing helix chain 'R' and resid 225 through 236 Processing helix chain 'S' and resid 21 through 32 removed outlier: 3.531A pdb=" N GLU S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE S 31 " --> pdb=" O SER S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 81 through 104 removed outlier: 3.600A pdb=" N ARG S 86 " --> pdb=" O THR S 82 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 118 Processing helix chain 'S' and resid 175 through 187 removed outlier: 3.892A pdb=" N ALA S 181 " --> pdb=" O GLU S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 208 Processing helix chain 'S' and resid 232 through 242 Processing helix chain 'T' and resid 19 through 31 removed outlier: 3.940A pdb=" N ILE T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS T 30 " --> pdb=" O LEU T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 100 Processing helix chain 'T' and resid 104 through 122 removed outlier: 4.098A pdb=" N ASN T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR T 120 " --> pdb=" O ALA T 116 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN T 121 " --> pdb=" O GLN T 117 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER T 122 " --> pdb=" O LYS T 118 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 180 removed outlier: 4.268A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASP T 177 " --> pdb=" O GLU T 173 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N THR T 178 " --> pdb=" O ARG T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 199 Processing helix chain 'T' and resid 226 through 231 Processing helix chain 'U' and resid 21 through 33 Processing helix chain 'U' and resid 81 through 103 Processing helix chain 'U' and resid 108 through 123 Processing helix chain 'U' and resid 168 through 183 Processing helix chain 'U' and resid 188 through 204 Processing helix chain 'U' and resid 205 through 208 removed outlier: 3.854A pdb=" N LYS U 208 " --> pdb=" O GLU U 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 205 through 208' Processing helix chain 'U' and resid 233 through 248 removed outlier: 3.963A pdb=" N ASN U 248 " --> pdb=" O GLN U 244 " (cutoff:3.500A) Processing helix chain 'V' and resid 73 through 90 Processing helix chain 'V' and resid 93 through 106 Processing helix chain 'V' and resid 150 through 152 No H-bonds generated for 'chain 'V' and resid 150 through 152' Processing helix chain 'V' and resid 153 through 161 Processing helix chain 'V' and resid 166 through 185 Processing helix chain 'V' and resid 208 through 213 Processing helix chain 'W' and resid 84 through 100 Processing helix chain 'W' and resid 104 through 119 Processing helix chain 'W' and resid 159 through 171 Processing helix chain 'W' and resid 176 through 195 Processing helix chain 'X' and resid 4 through 9 removed outlier: 4.398A pdb=" N ASN X 8 " --> pdb=" O PRO X 4 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY X 9 " --> pdb=" O SER X 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 4 through 9' Processing helix chain 'X' and resid 57 through 80 Processing helix chain 'X' and resid 84 through 98 Processing helix chain 'X' and resid 143 through 155 Processing helix chain 'X' and resid 160 through 178 removed outlier: 3.553A pdb=" N ARG X 178 " --> pdb=" O ASN X 174 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 72 Processing helix chain 'Y' and resid 76 through 92 Processing helix chain 'Y' and resid 134 through 139 removed outlier: 4.068A pdb=" N GLY Y 137 " --> pdb=" O GLY Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 140 through 148 Processing helix chain 'Y' and resid 153 through 172 Processing helix chain 'Z' and resid 123 through 146 Processing helix chain 'Z' and resid 150 through 165 Processing helix chain 'Z' and resid 207 through 219 Processing helix chain 'Z' and resid 224 through 243 Processing helix chain 'Z' and resid 268 through 280 removed outlier: 3.569A pdb=" N TRP Z 273 " --> pdb=" O GLY Z 269 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 99 Processing helix chain 'a' and resid 105 through 119 Processing helix chain 'a' and resid 162 through 165 Processing helix chain 'a' and resid 166 through 174 Processing helix chain 'a' and resid 196 through 215 Processing helix chain 'b' and resid 91 through 110 removed outlier: 3.605A pdb=" N TYR b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 140 Processing helix chain 'b' and resid 180 through 191 removed outlier: 4.626A pdb=" N ASN b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) Proline residue: b 187 - end of helix Processing helix chain 'b' and resid 195 through 199 Processing helix chain 'b' and resid 203 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 74 removed outlier: 4.066A pdb=" N ILE A 154 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY A 165 " --> pdb=" O MET B 57 " (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 68 removed outlier: 6.550A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.703A pdb=" N ASN I 218 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL I 202 " --> pdb=" O ASN I 218 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N THR I 31 " --> pdb=" O ASP I 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.727A pdb=" N GLY C 43 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 66 through 68 removed outlier: 4.061A pdb=" N LEU C 148 " --> pdb=" O TRP C 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 161 through 165 Processing sheet with id=AA9, first strand: chain 'D' and resid 65 through 66 Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 172 Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.423A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR E 165 " --> pdb=" O HIS E 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 65 Processing sheet with id=AB5, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AB6, first strand: chain 'G' and resid 68 through 70 Processing sheet with id=AB7, first strand: chain 'H' and resid 143 through 146 Processing sheet with id=AB8, first strand: chain 'H' and resid 39 through 41 removed outlier: 6.629A pdb=" N THR H 41 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE H 45 " --> pdb=" O THR H 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 54 through 57 removed outlier: 6.689A pdb=" N ILE H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL H 129 " --> pdb=" O LEU H 141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 49 through 51 removed outlier: 6.690A pdb=" N SER I 49 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 63 through 67 removed outlier: 6.461A pdb=" N ILE I 70 " --> pdb=" O ILE I 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 241 through 247 removed outlier: 3.531A pdb=" N LYS I 243 " --> pdb=" O TYR J 200 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL J 196 " --> pdb=" O VAL I 247 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA J 186 " --> pdb=" O LEU J 201 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE J 12 " --> pdb=" O ASP J 27 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 30 through 32 removed outlier: 6.263A pdb=" N SER J 32 " --> pdb=" O GLY J 36 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLY J 36 " --> pdb=" O SER J 32 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 44 through 47 Processing sheet with id=AC6, first strand: chain 'K' and resid 130 through 132 removed outlier: 4.135A pdb=" N VAL K 181 " --> pdb=" O VAL K 192 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 21 through 23 removed outlier: 6.797A pdb=" N ARG K 23 " --> pdb=" O VAL K 27 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL K 27 " --> pdb=" O ARG K 23 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.456A pdb=" N THR K 42 " --> pdb=" O LEU K 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 201 through 205 removed outlier: 6.169A pdb=" N VAL L 250 " --> pdb=" O ASN L 265 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN L 265 " --> pdb=" O VAL L 250 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU L 252 " --> pdb=" O HIS L 263 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.831A pdb=" N ALA L 95 " --> pdb=" O ALA L 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 109 through 113 removed outlier: 6.369A pdb=" N LEU L 116 " --> pdb=" O ILE L 112 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET L 175 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE L 187 " --> pdb=" O GLY L 199 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 156 through 160 removed outlier: 5.430A pdb=" N THR M 31 " --> pdb=" O ASP M 46 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 49 through 51 removed outlier: 6.199A pdb=" N THR M 51 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE M 55 " --> pdb=" O THR M 51 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 64 through 65 removed outlier: 3.536A pdb=" N THR M 129 " --> pdb=" O PHE M 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL M 142 " --> pdb=" O GLU M 154 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 67 through 70 removed outlier: 3.616A pdb=" N ARG N 69 " --> pdb=" O GLY N 62 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY N 62 " --> pdb=" O ARG N 69 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 67 through 70 removed outlier: 3.616A pdb=" N ARG N 69 " --> pdb=" O GLY N 62 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY N 62 " --> pdb=" O ARG N 69 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 175 through 177 removed outlier: 5.759A pdb=" N PHE N 229 " --> pdb=" O ASN N 245 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN N 245 " --> pdb=" O PHE N 229 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 168 through 171 Processing sheet with id=AE1, first strand: chain 'O' and resid 72 through 74 removed outlier: 4.065A pdb=" N ILE O 154 " --> pdb=" O TYR O 166 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY O 165 " --> pdb=" O MET P 57 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 161 through 164 Processing sheet with id=AE3, first strand: chain 'P' and resid 65 through 68 removed outlier: 6.553A pdb=" N ILE P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 224 through 225 removed outlier: 3.722A pdb=" N ASN W 218 " --> pdb=" O VAL W 202 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL W 202 " --> pdb=" O ASN W 218 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N THR W 31 " --> pdb=" O ASP W 46 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 162 through 165 Processing sheet with id=AE6, first strand: chain 'Q' and resid 66 through 68 removed outlier: 4.062A pdb=" N LEU Q 148 " --> pdb=" O TRP Q 160 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 161 through 165 Processing sheet with id=AE8, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AE9, first strand: chain 'S' and resid 169 through 172 Processing sheet with id=AF1, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.433A pdb=" N ILE S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR S 165 " --> pdb=" O HIS S 157 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 158 through 161 Processing sheet with id=AF3, first strand: chain 'T' and resid 63 through 65 Processing sheet with id=AF4, first strand: chain 'U' and resid 162 through 165 Processing sheet with id=AF5, first strand: chain 'U' and resid 68 through 70 removed outlier: 3.508A pdb=" N TRP U 158 " --> pdb=" O MET U 150 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 143 through 146 Processing sheet with id=AF7, first strand: chain 'V' and resid 39 through 41 removed outlier: 6.625A pdb=" N THR V 41 " --> pdb=" O ILE V 45 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE V 45 " --> pdb=" O THR V 41 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 54 through 57 removed outlier: 6.692A pdb=" N ILE V 60 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL V 129 " --> pdb=" O LEU V 141 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 49 through 51 removed outlier: 6.695A pdb=" N SER W 49 " --> pdb=" O ALA W 56 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 63 through 67 removed outlier: 6.475A pdb=" N ILE W 70 " --> pdb=" O ILE W 66 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 241 through 247 removed outlier: 3.517A pdb=" N LYS W 243 " --> pdb=" O TYR X 200 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL X 196 " --> pdb=" O VAL W 247 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA X 186 " --> pdb=" O LEU X 201 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ILE X 12 " --> pdb=" O ASP X 27 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 30 through 32 removed outlier: 6.257A pdb=" N SER X 32 " --> pdb=" O GLY X 36 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLY X 36 " --> pdb=" O SER X 32 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 44 through 47 Processing sheet with id=AG5, first strand: chain 'Y' and resid 130 through 132 removed outlier: 4.187A pdb=" N VAL Y 181 " --> pdb=" O VAL Y 192 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 21 through 23 removed outlier: 6.808A pdb=" N ARG Y 23 " --> pdb=" O VAL Y 27 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 35 through 39 removed outlier: 6.453A pdb=" N THR Y 42 " --> pdb=" O LEU Y 38 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 201 through 205 removed outlier: 6.183A pdb=" N VAL Z 250 " --> pdb=" O ASN Z 265 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN Z 265 " --> pdb=" O VAL Z 250 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU Z 252 " --> pdb=" O HIS Z 263 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 95 through 97 removed outlier: 6.828A pdb=" N ALA Z 95 " --> pdb=" O ALA Z 102 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 109 through 113 removed outlier: 6.391A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 112 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET Z 175 " --> pdb=" O THR Z 119 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE Z 187 " --> pdb=" O GLY Z 199 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'a' and resid 156 through 160 removed outlier: 5.281A pdb=" N THR a 31 " --> pdb=" O ASP a 46 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 49 through 51 removed outlier: 6.196A pdb=" N THR a 51 " --> pdb=" O ILE a 55 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE a 55 " --> pdb=" O THR a 51 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'a' and resid 64 through 65 removed outlier: 3.536A pdb=" N THR a 129 " --> pdb=" O PHE a 145 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL a 142 " --> pdb=" O GLU a 154 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 67 through 70 removed outlier: 3.611A pdb=" N ARG b 69 " --> pdb=" O GLY b 62 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY b 62 " --> pdb=" O ARG b 69 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 67 through 70 removed outlier: 3.611A pdb=" N ARG b 69 " --> pdb=" O GLY b 62 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY b 62 " --> pdb=" O ARG b 69 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 175 through 177 removed outlier: 5.764A pdb=" N PHE b 229 " --> pdb=" O ASN b 245 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN b 245 " --> pdb=" O PHE b 229 " (cutoff:3.500A) 2809 hydrogen bonds defined for protein. 7953 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: 21.66 Time building geometry restraints manager: 13.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 15637 1.35 - 1.47: 11288 1.47 - 1.59: 21235 1.59 - 1.71: 0 1.71 - 1.84: 236 Bond restraints: 48396 Sorted by residual: bond pdb=" N ARG K 171 " pdb=" CA ARG K 171 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.29e-02 6.01e+03 8.77e+00 bond pdb=" N MET K 172 " pdb=" CA MET K 172 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.53e-02 4.27e+03 3.25e+00 bond pdb=" CA GLY Y 105 " pdb=" C GLY Y 105 " ideal model delta sigma weight residual 1.520 1.509 0.011 7.30e-03 1.88e+04 2.20e+00 bond pdb=" N LYS K 170 " pdb=" CA LYS K 170 " ideal model delta sigma weight residual 1.458 1.476 -0.017 1.26e-02 6.30e+03 1.86e+00 bond pdb=" CA GLY K 105 " pdb=" C GLY K 105 " ideal model delta sigma weight residual 1.520 1.510 0.010 7.30e-03 1.88e+04 1.82e+00 ... (remaining 48391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 64773 2.20 - 4.40: 608 4.40 - 6.60: 55 6.60 - 8.80: 7 8.80 - 11.00: 1 Bond angle restraints: 65444 Sorted by residual: angle pdb=" C ASP F 183 " pdb=" CA ASP F 183 " pdb=" CB ASP F 183 " ideal model delta sigma weight residual 116.63 110.25 6.38 1.16e+00 7.43e-01 3.03e+01 angle pdb=" C ASP T 183 " pdb=" CA ASP T 183 " pdb=" CB ASP T 183 " ideal model delta sigma weight residual 116.63 110.28 6.35 1.16e+00 7.43e-01 3.00e+01 angle pdb=" N SER b 44 " pdb=" CA SER b 44 " pdb=" C SER b 44 " ideal model delta sigma weight residual 110.24 115.78 -5.54 1.30e+00 5.92e-01 1.81e+01 angle pdb=" N SER N 44 " pdb=" CA SER N 44 " pdb=" C SER N 44 " ideal model delta sigma weight residual 110.24 115.59 -5.35 1.41e+00 5.03e-01 1.44e+01 angle pdb=" C ARG Y 171 " pdb=" N MET Y 172 " pdb=" CA MET Y 172 " ideal model delta sigma weight residual 120.69 109.69 11.00 2.95e+00 1.15e-01 1.39e+01 ... (remaining 65439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 25767 18.00 - 36.00: 2383 36.00 - 53.99: 609 53.99 - 71.99: 170 71.99 - 89.99: 83 Dihedral angle restraints: 29012 sinusoidal: 11446 harmonic: 17566 Sorted by residual: dihedral pdb=" CA VAL P 132 " pdb=" C VAL P 132 " pdb=" N SER P 133 " pdb=" CA SER P 133 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLY J 102 " pdb=" C GLY J 102 " pdb=" N PRO J 103 " pdb=" CA PRO J 103 " ideal model delta harmonic sigma weight residual -180.00 -158.19 -21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA VAL B 132 " pdb=" C VAL B 132 " pdb=" N SER B 133 " pdb=" CA SER B 133 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 29009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 4890 0.035 - 0.070: 1639 0.070 - 0.104: 655 0.104 - 0.139: 202 0.139 - 0.174: 6 Chirality restraints: 7392 Sorted by residual: chirality pdb=" CB THR A 180 " pdb=" CA THR A 180 " pdb=" OG1 THR A 180 " pdb=" CG2 THR A 180 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CB ILE F 180 " pdb=" CA ILE F 180 " pdb=" CG1 ILE F 180 " pdb=" CG2 ILE F 180 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CA ILE B 214 " pdb=" N ILE B 214 " pdb=" C ILE B 214 " pdb=" CB ILE B 214 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 7389 not shown) Planarity restraints: 8412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 149 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO K 150 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO K 150 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO K 150 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG Y 149 " 0.050 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PRO Y 150 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO Y 150 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO Y 150 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP M 146 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO M 147 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO M 147 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO M 147 " -0.030 5.00e-02 4.00e+02 ... (remaining 8409 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 2245 2.73 - 3.27: 47047 3.27 - 3.81: 85377 3.81 - 4.36: 107302 4.36 - 4.90: 179148 Nonbonded interactions: 421119 Sorted by model distance: nonbonded pdb=" O ARG L 82 " pdb=" OH TYR L 219 " model vdw 2.184 3.040 nonbonded pdb=" O GLY D 154 " pdb=" NH2 ARG E 86 " model vdw 2.195 3.120 nonbonded pdb=" O GLY V 190 " pdb=" OH TYR V 212 " model vdw 2.196 3.040 nonbonded pdb=" O GLY H 190 " pdb=" OH TYR H 212 " model vdw 2.197 3.040 nonbonded pdb=" O ARG Z 82 " pdb=" OH TYR Z 219 " model vdw 2.197 3.040 ... (remaining 421114 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: 0.00 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: 2.020 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: 0.030 Extract box with map and model: 1.730 Check model and map are aligned: 0.340 Set scattering table: 0.430 Process input model: 104.370 Find NCS groups from input model: 3.720 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.003 0.048 48396 Z= 0.204 Angle : 0.564 11.003 65444 Z= 0.321 Chirality : 0.043 0.174 7392 Planarity : 0.004 0.079 8412 Dihedral : 16.138 89.991 17780 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.17 % Allowed : 15.89 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.11), residues: 5994 helix: 1.52 (0.10), residues: 2220 sheet: 0.64 (0.13), residues: 1528 loop : 0.34 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 187 HIS 0.008 0.001 HIS B 94 PHE 0.024 0.002 PHE K 142 TYR 0.018 0.001 TYR D 156 ARG 0.008 0.000 ARG C 4 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 691 time to evaluate : 5.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.8012 (tpp80) cc_final: 0.7690 (tpt90) REVERT: D 39 LYS cc_start: 0.7477 (mtmm) cc_final: 0.7108 (ptmm) REVERT: D 177 LYS cc_start: 0.7161 (mttm) cc_final: 0.6761 (mttp) REVERT: F 31 GLN cc_start: 0.7715 (mp10) cc_final: 0.7448 (mm110) REVERT: F 86 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8360 (t0) REVERT: N 102 LYS cc_start: 0.8431 (mtmt) cc_final: 0.7996 (mmpt) REVERT: O 120 ARG cc_start: 0.8116 (tpp80) cc_final: 0.7780 (tpt90) REVERT: T 61 LYS cc_start: 0.8231 (ttmm) cc_final: 0.7500 (tptp) REVERT: U 195 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8364 (mm-40) outliers start: 60 outliers final: 43 residues processed: 740 average time/residue: 1.7143 time to fit residues: 1546.2580 Evaluate side-chains 711 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 667 time to evaluate : 5.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain R residue 41 CYS Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 140 SER Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain Z residue 156 LYS Chi-restraints excluded: chain Z residue 217 SER Chi-restraints excluded: chain a residue 129 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 506 optimal weight: 1.9990 chunk 454 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 306 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 470 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 chunk 350 optimal weight: 6.9990 chunk 544 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 GLN H 81 HIS H 88 GLN I 223 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 185 ASN ** S 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 99 HIS S 147 HIS U 237 GLN V 81 HIS V 88 GLN W 223 ASN Z 164 GLN a 100 ASN a 114 GLN a 185 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 48396 Z= 0.452 Angle : 0.686 10.844 65444 Z= 0.372 Chirality : 0.051 0.226 7392 Planarity : 0.006 0.059 8412 Dihedral : 6.427 57.783 6701 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.30 % Allowed : 14.02 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.10), residues: 5994 helix: 1.56 (0.10), residues: 2224 sheet: 0.51 (0.13), residues: 1522 loop : 0.25 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP V 184 HIS 0.012 0.002 HIS A 209 PHE 0.027 0.003 PHE b 127 TYR 0.021 0.003 TYR Q 20 ARG 0.010 0.001 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 683 time to evaluate : 4.213 Fit side-chains REVERT: A 120 ARG cc_start: 0.8180 (tpp80) cc_final: 0.7826 (tpt90) REVERT: B 237 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8351 (ttmt) REVERT: B 241 GLN cc_start: 0.8059 (tp40) cc_final: 0.7695 (tp-100) REVERT: C 177 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: D 41 CYS cc_start: 0.6437 (OUTLIER) cc_final: 0.6171 (p) REVERT: D 55 GLN cc_start: 0.8952 (mt0) cc_final: 0.8739 (mm-40) REVERT: D 102 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8107 (t70) REVERT: E 52 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.6030 (mptm) REVERT: E 197 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: F 30 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7425 (mmmt) REVERT: F 31 GLN cc_start: 0.7571 (mp10) cc_final: 0.7322 (mm110) REVERT: F 86 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8364 (t0) REVERT: G 101 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.6722 (tppt) REVERT: G 152 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7861 (mm-30) REVERT: G 195 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7836 (mp10) REVERT: G 205 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: K 5 LEU cc_start: 0.8919 (mm) cc_final: 0.8707 (mt) REVERT: K 7 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8711 (tp) REVERT: K 23 ARG cc_start: 0.6741 (ttt-90) cc_final: 0.6441 (ttt180) REVERT: L 142 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6725 (tp30) REVERT: L 164 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7557 (pt0) REVERT: L 274 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7841 (ttmt) REVERT: M 136 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6509 (pm20) REVERT: N 102 LYS cc_start: 0.8553 (mtmt) cc_final: 0.8089 (mmpt) REVERT: O 120 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7735 (tpt90) REVERT: P 237 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8333 (ttmt) REVERT: P 241 GLN cc_start: 0.8118 (tp40) cc_final: 0.7872 (tp-100) REVERT: Q 231 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7811 (mppt) REVERT: R 39 LYS cc_start: 0.7646 (mtmm) cc_final: 0.7357 (mtmm) REVERT: R 55 GLN cc_start: 0.8948 (mt0) cc_final: 0.8739 (mm-40) REVERT: R 102 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8109 (t70) REVERT: R 122 GLN cc_start: 0.8126 (pt0) cc_final: 0.7838 (tt0) REVERT: S 52 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.6090 (mptm) REVERT: S 197 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.6898 (mm-30) REVERT: S 211 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6540 (tttm) REVERT: U 152 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7998 (mm-30) REVERT: W 72 CYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7509 (p) REVERT: Y 7 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8723 (tp) REVERT: Z 274 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7795 (ttmt) REVERT: a 136 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6470 (pm20) REVERT: a 154 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7269 (mt-10) REVERT: b 102 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8097 (mmpt) REVERT: b 191 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8407 (mtpt) outliers start: 169 outliers final: 67 residues processed: 795 average time/residue: 1.7086 time to fit residues: 1652.6608 Evaluate side-chains 752 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 655 time to evaluate : 5.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain G residue 101 LYS Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 195 GLN Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 210 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 164 GLN Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain L residue 274 LYS Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain N residue 44 SER Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain P residue 57 MET Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 237 LYS Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 197 GLU Chi-restraints excluded: chain S residue 211 LYS Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 140 SER Chi-restraints excluded: chain U residue 152 GLU Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 148 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 78 LYS Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain Y residue 2 ASP Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 274 LYS Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 102 LYS Chi-restraints excluded: chain b residue 134 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 302 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 453 optimal weight: 4.9990 chunk 371 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 chunk 545 optimal weight: 0.7980 chunk 589 optimal weight: 1.9990 chunk 486 optimal weight: 4.9990 chunk 541 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 437 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN C 156 ASN E 154 GLN G 237 GLN H 88 GLN I 115 HIS I 223 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 ASN M 100 ASN M 185 ASN O 181 ASN Q 156 ASN ** S 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 154 GLN U 237 GLN V 88 GLN W 95 HIS W 115 HIS W 170 HIS W 223 ASN ** Y 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 164 GLN a 75 ASN a 100 ASN a 185 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 48396 Z= 0.213 Angle : 0.535 7.582 65444 Z= 0.293 Chirality : 0.044 0.163 7392 Planarity : 0.004 0.051 8412 Dihedral : 5.713 55.178 6680 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.85 % Allowed : 15.00 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.11), residues: 5994 helix: 2.02 (0.10), residues: 2230 sheet: 0.52 (0.13), residues: 1490 loop : 0.23 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 199 HIS 0.008 0.001 HIS A 209 PHE 0.023 0.002 PHE T 179 TYR 0.018 0.001 TYR X 70 ARG 0.006 0.000 ARG C 4 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 713 time to evaluate : 5.361 Fit side-chains REVERT: A 120 ARG cc_start: 0.8163 (tpp80) cc_final: 0.7714 (tpt90) REVERT: B 241 GLN cc_start: 0.8054 (tp40) cc_final: 0.7754 (tp-100) REVERT: C 60 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.6423 (m-30) REVERT: C 109 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8352 (tm-30) REVERT: C 231 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7761 (mppt) REVERT: D 41 CYS cc_start: 0.6303 (OUTLIER) cc_final: 0.6037 (p) REVERT: D 55 GLN cc_start: 0.8923 (mt0) cc_final: 0.8714 (mm-40) REVERT: D 177 LYS cc_start: 0.7074 (mttm) cc_final: 0.6673 (mttp) REVERT: E 52 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.5951 (mptm) REVERT: E 197 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7165 (mt-10) REVERT: F 9 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6840 (m-30) REVERT: F 30 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7283 (mmmt) REVERT: F 31 GLN cc_start: 0.7586 (mp10) cc_final: 0.7346 (mm110) REVERT: F 61 LYS cc_start: 0.8274 (ttmm) cc_final: 0.7565 (tptp) REVERT: G 195 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7826 (mp10) REVERT: G 205 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: K 7 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8669 (tp) REVERT: K 93 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.8059 (mpt-90) REVERT: L 142 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6800 (tp30) REVERT: L 172 MET cc_start: 0.4792 (OUTLIER) cc_final: 0.3744 (ppp) REVERT: M 136 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6631 (mt-10) REVERT: M 146 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7452 (t0) REVERT: N 102 LYS cc_start: 0.8495 (mtmt) cc_final: 0.8048 (mmpt) REVERT: N 191 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8403 (mtpt) REVERT: O 120 ARG cc_start: 0.8124 (tpp80) cc_final: 0.7733 (tpt90) REVERT: P 4 ARG cc_start: 0.7257 (mpt180) cc_final: 0.6088 (pmt170) REVERT: P 241 GLN cc_start: 0.8053 (tp40) cc_final: 0.7561 (tp-100) REVERT: Q 109 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8327 (tm-30) REVERT: Q 231 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7801 (mtmt) REVERT: R 55 GLN cc_start: 0.8914 (mt0) cc_final: 0.8714 (mm-40) REVERT: R 122 GLN cc_start: 0.7974 (pt0) cc_final: 0.7762 (tt0) REVERT: R 193 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7529 (ttpp) REVERT: S 52 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.5968 (mptm) REVERT: S 197 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6958 (mm-30) REVERT: S 229 LYS cc_start: 0.8032 (mmpt) cc_final: 0.7587 (ptpp) REVERT: T 9 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6822 (m-30) REVERT: T 61 LYS cc_start: 0.8150 (ttmm) cc_final: 0.7514 (tptp) REVERT: T 106 GLU cc_start: 0.7960 (mp0) cc_final: 0.7696 (mp0) REVERT: U 195 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8525 (mm-40) REVERT: Y 7 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8669 (tp) REVERT: a 136 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6660 (mt-10) REVERT: b 102 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8090 (mmpt) REVERT: b 140 LYS cc_start: 0.7172 (mtpm) cc_final: 0.6836 (mtpt) outliers start: 146 outliers final: 44 residues processed: 814 average time/residue: 1.7622 time to fit residues: 1750.3825 Evaluate side-chains 726 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 659 time to evaluate : 6.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 195 GLN Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 193 LYS Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 197 GLU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 140 SER Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 78 LYS Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 136 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 539 optimal weight: 10.0000 chunk 410 optimal weight: 0.0270 chunk 283 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 260 optimal weight: 5.9990 chunk 366 optimal weight: 9.9990 chunk 547 optimal weight: 6.9990 chunk 579 optimal weight: 0.0020 chunk 286 optimal weight: 3.9990 chunk 519 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 overall best weight: 3.0052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN C 156 ASN G 237 GLN H 88 GLN I 86 GLN I 115 HIS I 223 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 ASN M 100 ASN M 185 ASN N 136 GLN ** O 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN Q 124 GLN Q 156 ASN U 237 GLN V 88 GLN W 115 HIS W 223 ASN ** Y 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 164 GLN a 100 ASN a 178 ASN a 185 ASN b 136 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 48396 Z= 0.371 Angle : 0.621 7.451 65444 Z= 0.337 Chirality : 0.048 0.200 7392 Planarity : 0.005 0.050 8412 Dihedral : 5.908 56.827 6668 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.14 % Allowed : 15.19 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.10), residues: 5994 helix: 1.86 (0.10), residues: 2224 sheet: 0.46 (0.13), residues: 1520 loop : 0.18 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP V 184 HIS 0.011 0.002 HIS O 209 PHE 0.024 0.003 PHE N 127 TYR 0.019 0.002 TYR C 20 ARG 0.009 0.001 ARG P 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 673 time to evaluate : 5.116 Fit side-chains REVERT: A 120 ARG cc_start: 0.8225 (tpp80) cc_final: 0.7757 (tpt90) REVERT: A 242 GLU cc_start: 0.7879 (tp30) cc_final: 0.7664 (tp30) REVERT: B 241 GLN cc_start: 0.8048 (tp40) cc_final: 0.7573 (tp-100) REVERT: C 109 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8381 (tm-30) REVERT: C 177 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: D 41 CYS cc_start: 0.6475 (OUTLIER) cc_final: 0.6176 (p) REVERT: D 55 GLN cc_start: 0.8943 (mt0) cc_final: 0.8729 (mm-40) REVERT: D 177 LYS cc_start: 0.7110 (mttm) cc_final: 0.6694 (mttp) REVERT: E 52 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.5974 (mptm) REVERT: E 197 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: F 9 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.7042 (m-30) REVERT: F 30 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7426 (mmmt) REVERT: F 61 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7564 (tptp) REVERT: F 86 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8359 (t0) REVERT: G 195 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7848 (mp10) REVERT: G 205 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: I 164 MET cc_start: 0.9073 (tpp) cc_final: 0.8857 (tpp) REVERT: J 27 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8616 (p0) REVERT: K 7 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8684 (tp) REVERT: L 92 ASP cc_start: 0.8721 (p0) cc_final: 0.8436 (p0) REVERT: L 142 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6799 (tp30) REVERT: L 172 MET cc_start: 0.5016 (OUTLIER) cc_final: 0.3975 (ppp) REVERT: L 274 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7741 (ttmt) REVERT: M 136 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6503 (pm20) REVERT: M 146 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7352 (t0) REVERT: N 102 LYS cc_start: 0.8543 (mtmt) cc_final: 0.8085 (mmpt) REVERT: N 191 LYS cc_start: 0.8633 (mtpp) cc_final: 0.8416 (mtpt) REVERT: O 120 ARG cc_start: 0.8120 (tpp80) cc_final: 0.7681 (tpt90) REVERT: P 241 GLN cc_start: 0.8037 (tp40) cc_final: 0.7687 (tp-100) REVERT: Q 109 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8325 (tm-30) REVERT: Q 231 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7845 (mtmt) REVERT: R 41 CYS cc_start: 0.6383 (OUTLIER) cc_final: 0.6023 (p) REVERT: R 55 GLN cc_start: 0.8938 (mt0) cc_final: 0.8731 (mm-40) REVERT: R 122 GLN cc_start: 0.8073 (pt0) cc_final: 0.7862 (tt0) REVERT: R 193 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7589 (ttpp) REVERT: S 52 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.6000 (mptm) REVERT: S 197 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.6993 (mm-30) REVERT: S 229 LYS cc_start: 0.8087 (mmpt) cc_final: 0.7604 (ptpp) REVERT: T 9 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6845 (m-30) REVERT: T 61 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7529 (tptp) REVERT: T 86 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8370 (t0) REVERT: U 152 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8074 (mm-30) REVERT: U 195 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8417 (mm-40) REVERT: W 246 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8538 (mm) REVERT: X 27 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8605 (p0) REVERT: Y 7 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8701 (tp) REVERT: Z 172 MET cc_start: 0.5126 (OUTLIER) cc_final: 0.4233 (ppp) REVERT: Z 274 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7751 (ttmt) REVERT: a 136 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6703 (mt-10) REVERT: a 146 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7361 (t0) REVERT: a 154 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7201 (mt-10) REVERT: b 102 LYS cc_start: 0.8543 (mtmt) cc_final: 0.8133 (mmpt) outliers start: 161 outliers final: 70 residues processed: 777 average time/residue: 1.7726 time to fit residues: 1677.6438 Evaluate side-chains 748 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 644 time to evaluate : 5.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 195 GLN Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 211 GLU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain L residue 274 LYS Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain P residue 57 MET Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 41 CYS Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 193 LYS Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 76 CYS Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 197 GLU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 86 ASN Chi-restraints excluded: chain T residue 140 SER Chi-restraints excluded: chain U residue 152 GLU Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain W residue 148 THR Chi-restraints excluded: chain W residue 246 ILE Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 27 ASP Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 76 LYS Chi-restraints excluded: chain X residue 78 LYS Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 274 LYS Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain a residue 146 ASP Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 134 MET Chi-restraints excluded: chain b residue 173 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 483 optimal weight: 0.6980 chunk 329 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 431 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 494 optimal weight: 2.9990 chunk 400 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 520 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN C 156 ASN G 237 GLN H 88 GLN I 86 GLN I 115 HIS I 223 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 ASN M 90 ASN M 100 ASN M 185 ASN O 181 ASN O 221 ASN Q 156 ASN R 118 GLN U 170 GLN V 88 GLN W 223 ASN ** Y 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 164 GLN a 75 ASN a 100 ASN a 185 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 48396 Z= 0.184 Angle : 0.511 6.738 65444 Z= 0.279 Chirality : 0.043 0.158 7392 Planarity : 0.004 0.050 8412 Dihedral : 5.408 55.279 6668 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.79 % Allowed : 16.03 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.11), residues: 5994 helix: 2.24 (0.10), residues: 2236 sheet: 0.49 (0.13), residues: 1514 loop : 0.21 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 199 HIS 0.007 0.001 HIS O 209 PHE 0.021 0.002 PHE T 179 TYR 0.017 0.001 TYR X 70 ARG 0.005 0.000 ARG P 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 710 time to evaluate : 5.584 Fit side-chains revert: symmetry clash REVERT: A 120 ARG cc_start: 0.8154 (tpp80) cc_final: 0.7743 (tpt90) REVERT: B 4 ARG cc_start: 0.7220 (mpt180) cc_final: 0.6039 (pmt170) REVERT: B 241 GLN cc_start: 0.7989 (tp40) cc_final: 0.7728 (tp-100) REVERT: C 109 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: C 231 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7746 (mppt) REVERT: D 41 CYS cc_start: 0.6167 (OUTLIER) cc_final: 0.5903 (p) REVERT: D 55 GLN cc_start: 0.8932 (mt0) cc_final: 0.8725 (mm-40) REVERT: D 177 LYS cc_start: 0.7037 (mttm) cc_final: 0.6617 (mttp) REVERT: E 32 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7779 (mttm) REVERT: E 115 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.8040 (t) REVERT: E 197 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7248 (mt-10) REVERT: F 30 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7290 (mmmt) REVERT: F 61 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7518 (tptp) REVERT: F 106 GLU cc_start: 0.8006 (mp0) cc_final: 0.7788 (mp0) REVERT: G 195 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7843 (mp10) REVERT: I 164 MET cc_start: 0.9060 (tpp) cc_final: 0.8831 (tpp) REVERT: K 7 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8650 (tp) REVERT: L 92 ASP cc_start: 0.8631 (p0) cc_final: 0.8423 (p0) REVERT: L 142 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6848 (tp30) REVERT: M 136 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6681 (mt-10) REVERT: M 146 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7332 (t0) REVERT: N 90 ASP cc_start: 0.8508 (t70) cc_final: 0.8291 (t70) REVERT: N 102 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8044 (mmpt) REVERT: O 120 ARG cc_start: 0.8095 (tpp80) cc_final: 0.7711 (tpt90) REVERT: P 4 ARG cc_start: 0.7215 (mpt180) cc_final: 0.6090 (pmt170) REVERT: P 177 LYS cc_start: 0.8225 (mtpp) cc_final: 0.8004 (mttp) REVERT: P 241 GLN cc_start: 0.7983 (tp40) cc_final: 0.7735 (tp-100) REVERT: Q 109 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8319 (tm-30) REVERT: R 193 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7502 (ttpp) REVERT: S 197 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6877 (mm-30) REVERT: S 229 LYS cc_start: 0.8047 (mmpt) cc_final: 0.7596 (ptpp) REVERT: T 9 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6799 (m-30) REVERT: T 61 LYS cc_start: 0.8170 (ttmm) cc_final: 0.7517 (tptp) REVERT: T 93 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7793 (t0) REVERT: T 106 GLU cc_start: 0.7990 (mp0) cc_final: 0.7763 (mp0) REVERT: U 195 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8387 (mm-40) REVERT: Y 7 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8652 (tp) REVERT: a 146 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7307 (t0) REVERT: b 90 ASP cc_start: 0.8460 (t70) cc_final: 0.8232 (t70) REVERT: b 102 LYS cc_start: 0.8491 (mtmt) cc_final: 0.8090 (mmpt) REVERT: b 140 LYS cc_start: 0.7171 (mtpm) cc_final: 0.6877 (mtpt) outliers start: 143 outliers final: 53 residues processed: 813 average time/residue: 1.7204 time to fit residues: 1713.5155 Evaluate side-chains 734 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 661 time to evaluate : 5.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 195 GLN Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 193 LYS Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 197 GLU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 93 ASN Chi-restraints excluded: chain T residue 140 SER Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 76 LYS Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain Y residue 2 ASP Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 146 ASP Chi-restraints excluded: chain b residue 38 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 195 optimal weight: 10.0000 chunk 522 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 340 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 580 optimal weight: 0.6980 chunk 481 optimal weight: 3.9990 chunk 268 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 304 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN B 123 GLN C 156 ASN D 122 GLN G 237 GLN H 88 GLN I 86 GLN I 115 HIS I 223 ASN K 146 HIS ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 265 ASN M 90 ASN M 100 ASN M 185 ASN O 39 ASN O 181 ASN P 123 GLN Q 156 ASN R 117 GLN R 118 GLN R 122 GLN U 170 GLN V 88 GLN W 115 HIS W 223 ASN ** Y 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 164 GLN a 100 ASN a 114 GLN a 185 ASN b 136 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 48396 Z= 0.174 Angle : 0.502 9.238 65444 Z= 0.273 Chirality : 0.043 0.156 7392 Planarity : 0.004 0.050 8412 Dihedral : 5.142 54.270 6660 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.57 % Allowed : 16.40 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.11), residues: 5994 helix: 2.41 (0.11), residues: 2234 sheet: 0.52 (0.13), residues: 1514 loop : 0.22 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 199 HIS 0.007 0.001 HIS A 209 PHE 0.019 0.001 PHE K 142 TYR 0.017 0.001 TYR X 70 ARG 0.004 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 676 time to evaluate : 5.698 Fit side-chains REVERT: A 120 ARG cc_start: 0.8160 (tpp80) cc_final: 0.7742 (tpt90) REVERT: B 4 ARG cc_start: 0.7190 (mpt180) cc_final: 0.6010 (pmt170) REVERT: B 241 GLN cc_start: 0.7911 (tp40) cc_final: 0.7680 (tp-100) REVERT: C 109 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8383 (tm-30) REVERT: C 231 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7746 (mppt) REVERT: D 55 GLN cc_start: 0.8927 (mt0) cc_final: 0.8725 (mm-40) REVERT: D 177 LYS cc_start: 0.7016 (mttm) cc_final: 0.6663 (mtmp) REVERT: E 32 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7781 (mttm) REVERT: E 115 SER cc_start: 0.8298 (OUTLIER) cc_final: 0.8054 (m) REVERT: E 188 HIS cc_start: 0.7486 (p90) cc_final: 0.7084 (p90) REVERT: E 197 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: F 30 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7330 (mmmt) REVERT: F 61 LYS cc_start: 0.8193 (ttmm) cc_final: 0.7517 (tptp) REVERT: F 86 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8296 (t0) REVERT: F 106 GLU cc_start: 0.7994 (mp0) cc_final: 0.7787 (mp0) REVERT: F 123 TYR cc_start: 0.7873 (t80) cc_final: 0.7481 (t80) REVERT: G 195 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: G 205 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: I 164 MET cc_start: 0.9050 (tpp) cc_final: 0.8811 (tpp) REVERT: K 169 GLU cc_start: 0.6549 (mt-10) cc_final: 0.6227 (pt0) REVERT: L 107 LYS cc_start: 0.8447 (mmmt) cc_final: 0.7864 (mmpt) REVERT: L 142 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6841 (tp30) REVERT: L 172 MET cc_start: 0.4637 (OUTLIER) cc_final: 0.4060 (tmm) REVERT: L 179 TYR cc_start: 0.8083 (t80) cc_final: 0.7855 (t80) REVERT: M 136 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6677 (mt-10) REVERT: M 146 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7402 (t0) REVERT: N 90 ASP cc_start: 0.8488 (t70) cc_final: 0.8241 (t70) REVERT: N 102 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8039 (mmpt) REVERT: N 140 LYS cc_start: 0.7178 (mtpm) cc_final: 0.6883 (mtpt) REVERT: O 120 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7653 (tpt90) REVERT: P 4 ARG cc_start: 0.7248 (mpt180) cc_final: 0.6095 (pmt170) REVERT: P 241 GLN cc_start: 0.7900 (tp40) cc_final: 0.7671 (tp-100) REVERT: Q 109 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8295 (tm-30) REVERT: Q 231 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7777 (mppt) REVERT: R 142 ASP cc_start: 0.7228 (t0) cc_final: 0.6983 (t0) REVERT: S 89 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8287 (mt) REVERT: S 197 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6892 (mm-30) REVERT: S 229 LYS cc_start: 0.8016 (mmpt) cc_final: 0.7644 (ptpt) REVERT: T 9 ASP cc_start: 0.7029 (OUTLIER) cc_final: 0.6781 (m-30) REVERT: T 61 LYS cc_start: 0.8146 (ttmm) cc_final: 0.7493 (tptp) REVERT: T 86 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8313 (t0) REVERT: T 93 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7756 (t0) REVERT: T 106 GLU cc_start: 0.7982 (mp0) cc_final: 0.7772 (mp0) REVERT: W 164 MET cc_start: 0.9018 (tpp) cc_final: 0.8755 (tpp) REVERT: X 177 ASP cc_start: 0.8666 (m-30) cc_final: 0.8391 (m-30) REVERT: Z 172 MET cc_start: 0.4793 (OUTLIER) cc_final: 0.4035 (ppp) REVERT: a 87 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7964 (mmm-85) REVERT: a 146 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7287 (t0) REVERT: b 90 ASP cc_start: 0.8426 (t70) cc_final: 0.8217 (t70) REVERT: b 102 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8086 (mmpt) REVERT: b 140 LYS cc_start: 0.7158 (mtpm) cc_final: 0.6873 (mtpt) outliers start: 132 outliers final: 49 residues processed: 767 average time/residue: 1.8231 time to fit residues: 1714.8986 Evaluate side-chains 713 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 642 time to evaluate : 5.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 195 GLN Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 211 GLU Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 88 MET Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 197 GLU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 86 ASN Chi-restraints excluded: chain T residue 93 ASN Chi-restraints excluded: chain T residue 140 SER Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 76 LYS Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 146 ASP Chi-restraints excluded: chain b residue 38 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 559 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 330 optimal weight: 0.8980 chunk 423 optimal weight: 4.9990 chunk 328 optimal weight: 2.9990 chunk 488 optimal weight: 6.9990 chunk 324 optimal weight: 5.9990 chunk 578 optimal weight: 2.9990 chunk 361 optimal weight: 5.9990 chunk 352 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN G 170 GLN H 72 GLN H 88 GLN I 223 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 ASN M 100 ASN M 185 ASN ** O 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 ASN U 170 GLN V 72 GLN V 88 GLN W 115 HIS W 223 ASN Y 146 HIS ** Y 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 164 GLN Z 265 ASN a 100 ASN a 114 GLN a 185 ASN b 136 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 48396 Z= 0.310 Angle : 0.585 7.496 65444 Z= 0.317 Chirality : 0.046 0.180 7392 Planarity : 0.005 0.049 8412 Dihedral : 5.410 55.853 6651 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.65 % Allowed : 16.38 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.11), residues: 5994 helix: 2.16 (0.10), residues: 2228 sheet: 0.47 (0.13), residues: 1518 loop : 0.19 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Z 100 HIS 0.010 0.001 HIS A 209 PHE 0.026 0.002 PHE Y 142 TYR 0.023 0.002 TYR b 125 ARG 0.007 0.000 ARG P 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 668 time to evaluate : 5.621 Fit side-chains REVERT: A 120 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7734 (tpt90) REVERT: A 242 GLU cc_start: 0.7820 (tp30) cc_final: 0.7602 (tp30) REVERT: B 4 ARG cc_start: 0.7327 (mpt180) cc_final: 0.6034 (pmt170) REVERT: B 241 GLN cc_start: 0.7907 (tp40) cc_final: 0.7660 (tp-100) REVERT: C 109 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8356 (tm-30) REVERT: C 231 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7757 (mppt) REVERT: D 55 GLN cc_start: 0.8945 (mt0) cc_final: 0.8731 (mm-40) REVERT: D 177 LYS cc_start: 0.7031 (mttm) cc_final: 0.6604 (mttp) REVERT: E 32 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7810 (mttm) REVERT: E 115 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7988 (m) REVERT: E 197 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7318 (mt-10) REVERT: F 30 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7413 (mmmt) REVERT: F 61 LYS cc_start: 0.8190 (ttmm) cc_final: 0.7462 (tptp) REVERT: F 86 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8336 (t0) REVERT: G 195 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: G 205 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: I 164 MET cc_start: 0.9093 (tpp) cc_final: 0.8844 (tpp) REVERT: K 7 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8684 (tp) REVERT: L 142 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6842 (tp30) REVERT: L 172 MET cc_start: 0.4857 (OUTLIER) cc_final: 0.4246 (ppp) REVERT: M 87 ARG cc_start: 0.8140 (mtp180) cc_final: 0.7936 (mmm-85) REVERT: M 136 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6698 (mt-10) REVERT: M 146 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7376 (t0) REVERT: N 140 LYS cc_start: 0.7243 (mtpm) cc_final: 0.6948 (mtpt) REVERT: O 120 ARG cc_start: 0.8102 (tpp80) cc_final: 0.7666 (tpt90) REVERT: P 4 ARG cc_start: 0.7267 (mpt180) cc_final: 0.6077 (pmt170) REVERT: Q 109 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8334 (tm-30) REVERT: Q 231 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7801 (mppt) REVERT: R 142 ASP cc_start: 0.7165 (t0) cc_final: 0.6902 (t0) REVERT: S 197 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.6917 (mm-30) REVERT: T 9 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6807 (m-30) REVERT: T 61 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7464 (tptp) REVERT: T 86 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8348 (t0) REVERT: T 93 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7805 (t0) REVERT: T 106 GLU cc_start: 0.8009 (mp0) cc_final: 0.7765 (mp0) REVERT: W 164 MET cc_start: 0.9118 (tpp) cc_final: 0.8894 (tpp) REVERT: X 177 ASP cc_start: 0.8675 (m-30) cc_final: 0.8415 (m-30) REVERT: Y 7 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8706 (tp) REVERT: Z 172 MET cc_start: 0.5007 (OUTLIER) cc_final: 0.4768 (ppp) REVERT: a 146 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7273 (t0) REVERT: a 154 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7139 (mt-10) REVERT: b 102 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8126 (mmpt) REVERT: b 140 LYS cc_start: 0.7219 (mtpm) cc_final: 0.6931 (mtpt) outliers start: 136 outliers final: 66 residues processed: 752 average time/residue: 1.8043 time to fit residues: 1646.1960 Evaluate side-chains 733 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 643 time to evaluate : 5.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 195 GLN Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 194 ASP Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 57 MET Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 211 GLU Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 197 GLU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 86 ASN Chi-restraints excluded: chain T residue 93 ASN Chi-restraints excluded: chain T residue 140 SER Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 76 LYS Chi-restraints excluded: chain X residue 78 LYS Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain Y residue 2 ASP Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 146 ASP Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 38 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 357 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 345 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 367 optimal weight: 7.9990 chunk 393 optimal weight: 6.9990 chunk 285 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 454 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN C 156 ASN D 117 GLN G 170 GLN H 72 GLN H 88 GLN I 115 HIS I 223 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 185 ASN ** O 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 ASN R 117 GLN R 122 GLN U 170 GLN V 72 GLN V 88 GLN W 115 HIS W 223 ASN ** Y 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 164 GLN a 100 ASN a 114 GLN a 185 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 48396 Z= 0.264 Angle : 0.560 7.718 65444 Z= 0.304 Chirality : 0.045 0.173 7392 Planarity : 0.004 0.049 8412 Dihedral : 5.349 55.845 6651 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.48 % Allowed : 16.79 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.11), residues: 5994 helix: 2.17 (0.10), residues: 2228 sheet: 0.45 (0.13), residues: 1522 loop : 0.18 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Z 100 HIS 0.009 0.001 HIS O 209 PHE 0.026 0.002 PHE K 142 TYR 0.025 0.002 TYR M 151 ARG 0.006 0.000 ARG P 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 663 time to evaluate : 5.799 Fit side-chains REVERT: A 120 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7704 (tpt90) REVERT: B 4 ARG cc_start: 0.7229 (mpt180) cc_final: 0.5980 (pmt170) REVERT: B 241 GLN cc_start: 0.7847 (tp40) cc_final: 0.7610 (tp-100) REVERT: C 109 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: C 231 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7749 (mppt) REVERT: D 41 CYS cc_start: 0.6294 (OUTLIER) cc_final: 0.6026 (p) REVERT: D 55 GLN cc_start: 0.8944 (mt0) cc_final: 0.8730 (mm-40) REVERT: D 177 LYS cc_start: 0.7042 (mttm) cc_final: 0.6605 (mttp) REVERT: E 32 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7797 (mttm) REVERT: E 197 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: F 30 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7399 (mmmt) REVERT: F 61 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7457 (tptp) REVERT: F 86 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8324 (t0) REVERT: F 106 GLU cc_start: 0.8043 (mp0) cc_final: 0.7807 (mp0) REVERT: G 195 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: G 205 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: I 164 MET cc_start: 0.9093 (tpp) cc_final: 0.8842 (tpp) REVERT: K 7 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8669 (tp) REVERT: L 142 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6834 (tp30) REVERT: L 172 MET cc_start: 0.4793 (OUTLIER) cc_final: 0.4343 (ppp) REVERT: M 87 ARG cc_start: 0.8150 (mtp180) cc_final: 0.7934 (mmm-85) REVERT: M 136 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6693 (mt-10) REVERT: M 146 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7341 (t0) REVERT: N 102 LYS cc_start: 0.8529 (mtmt) cc_final: 0.8161 (mmpt) REVERT: N 140 LYS cc_start: 0.7229 (mtpm) cc_final: 0.6935 (mtpt) REVERT: O 120 ARG cc_start: 0.8059 (tpp80) cc_final: 0.7676 (tpt90) REVERT: P 4 ARG cc_start: 0.7285 (mpt180) cc_final: 0.6088 (pmt170) REVERT: Q 109 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8320 (tm-30) REVERT: Q 231 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7799 (mppt) REVERT: R 142 ASP cc_start: 0.7166 (t0) cc_final: 0.6908 (t0) REVERT: S 197 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.6913 (mm-30) REVERT: T 9 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6797 (m-30) REVERT: T 61 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7439 (tptp) REVERT: T 86 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8333 (t0) REVERT: T 93 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7769 (t0) REVERT: T 106 GLU cc_start: 0.8022 (mp0) cc_final: 0.7786 (mp0) REVERT: W 164 MET cc_start: 0.9131 (tpp) cc_final: 0.8896 (tpp) REVERT: X 177 ASP cc_start: 0.8677 (m-30) cc_final: 0.8410 (m-30) REVERT: Y 7 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8675 (tp) REVERT: Z 172 MET cc_start: 0.5015 (OUTLIER) cc_final: 0.4769 (ppp) REVERT: a 87 ARG cc_start: 0.8246 (mtp180) cc_final: 0.7970 (mmm-85) REVERT: a 146 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7282 (t0) REVERT: a 154 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7175 (mt-10) REVERT: b 102 LYS cc_start: 0.8514 (mtmt) cc_final: 0.8111 (mmpt) REVERT: b 140 LYS cc_start: 0.7212 (mtpm) cc_final: 0.6924 (mtpt) outliers start: 127 outliers final: 71 residues processed: 748 average time/residue: 1.7821 time to fit residues: 1625.9632 Evaluate side-chains 737 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 642 time to evaluate : 5.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 195 GLN Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 211 GLU Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 197 GLU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 86 ASN Chi-restraints excluded: chain T residue 93 ASN Chi-restraints excluded: chain T residue 140 SER Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 76 LYS Chi-restraints excluded: chain X residue 78 LYS Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain Y residue 2 ASP Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 146 ASP Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 134 MET Chi-restraints excluded: chain b residue 173 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 526 optimal weight: 8.9990 chunk 554 optimal weight: 6.9990 chunk 505 optimal weight: 0.9990 chunk 538 optimal weight: 3.9990 chunk 553 optimal weight: 3.9990 chunk 324 optimal weight: 5.9990 chunk 234 optimal weight: 6.9990 chunk 423 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 486 optimal weight: 5.9990 chunk 509 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN D 122 GLN G 170 GLN H 72 GLN H 88 GLN I 115 HIS I 223 ASN M 90 ASN M 100 ASN M 185 ASN U 170 GLN V 72 GLN V 88 GLN W 115 HIS W 223 ASN ** Y 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 164 GLN a 100 ASN a 114 GLN a 185 ASN b 136 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 48396 Z= 0.392 Angle : 0.639 7.648 65444 Z= 0.345 Chirality : 0.048 0.213 7392 Planarity : 0.005 0.050 8412 Dihedral : 5.647 55.656 6651 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.69 % Allowed : 16.77 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.10), residues: 5994 helix: 1.89 (0.10), residues: 2224 sheet: 0.42 (0.13), residues: 1520 loop : 0.15 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 221 HIS 0.011 0.002 HIS O 209 PHE 0.031 0.003 PHE Y 142 TYR 0.033 0.002 TYR N 125 ARG 0.009 0.001 ARG P 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 655 time to evaluate : 5.570 Fit side-chains revert: symmetry clash REVERT: A 120 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7715 (tpt90) REVERT: B 241 GLN cc_start: 0.7858 (tp40) cc_final: 0.7623 (tp-100) REVERT: C 109 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8372 (tm-30) REVERT: C 177 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: D 41 CYS cc_start: 0.6439 (OUTLIER) cc_final: 0.6127 (p) REVERT: D 55 GLN cc_start: 0.8946 (mt0) cc_final: 0.8734 (mt0) REVERT: D 177 LYS cc_start: 0.7034 (mttm) cc_final: 0.6604 (mttp) REVERT: E 32 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7835 (mttm) REVERT: E 197 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: F 30 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7319 (mmmt) REVERT: F 61 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7527 (tptp) REVERT: F 86 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8342 (t0) REVERT: G 190 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7856 (mtt-85) REVERT: G 195 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7828 (mp10) REVERT: G 205 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: K 7 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8702 (tp) REVERT: L 92 ASP cc_start: 0.8725 (p0) cc_final: 0.8379 (p0) REVERT: L 172 MET cc_start: 0.4935 (OUTLIER) cc_final: 0.4729 (ppp) REVERT: M 87 ARG cc_start: 0.8164 (mtp180) cc_final: 0.7942 (mmm-85) REVERT: M 136 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6716 (mt-10) REVERT: M 146 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7316 (t0) REVERT: N 102 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8132 (mmpt) REVERT: N 140 LYS cc_start: 0.7201 (mtpm) cc_final: 0.6900 (mtpt) REVERT: O 120 ARG cc_start: 0.8103 (tpp80) cc_final: 0.7659 (tpt90) REVERT: P 241 GLN cc_start: 0.8072 (tp40) cc_final: 0.7845 (tp-100) REVERT: Q 109 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8325 (tm-30) REVERT: Q 231 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7826 (mtmt) REVERT: R 142 ASP cc_start: 0.7059 (t0) cc_final: 0.6855 (t0) REVERT: S 197 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.6975 (mm-30) REVERT: T 9 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.7030 (m-30) REVERT: T 61 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7474 (tptp) REVERT: T 86 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8375 (t0) REVERT: T 106 GLU cc_start: 0.8046 (mp0) cc_final: 0.7782 (mp0) REVERT: W 164 MET cc_start: 0.9155 (tpp) cc_final: 0.8934 (tpp) REVERT: X 177 ASP cc_start: 0.8678 (m-30) cc_final: 0.8431 (m-30) REVERT: Y 7 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8717 (tp) REVERT: Z 172 MET cc_start: 0.5125 (OUTLIER) cc_final: 0.4802 (ppp) REVERT: a 38 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7390 (mt-10) REVERT: a 87 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7973 (mmm-85) REVERT: a 146 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7285 (t0) REVERT: a 154 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7140 (mt-10) REVERT: b 140 LYS cc_start: 0.7194 (mtpm) cc_final: 0.6900 (mtpt) outliers start: 138 outliers final: 84 residues processed: 751 average time/residue: 1.7837 time to fit residues: 1632.4042 Evaluate side-chains 755 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 648 time to evaluate : 5.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 195 GLN Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 194 ASP Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain P residue 57 MET Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 216 ILE Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 211 GLU Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 197 GLU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 86 ASN Chi-restraints excluded: chain T residue 140 SER Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 76 LYS Chi-restraints excluded: chain X residue 78 LYS Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain Y residue 2 ASP Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 146 ASP Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 134 MET Chi-restraints excluded: chain b residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 537 optimal weight: 1.9990 chunk 353 optimal weight: 4.9990 chunk 569 optimal weight: 5.9990 chunk 347 optimal weight: 3.9990 chunk 270 optimal weight: 9.9990 chunk 396 optimal weight: 4.9990 chunk 597 optimal weight: 0.5980 chunk 550 optimal weight: 4.9990 chunk 475 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 367 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN G 170 GLN H 72 GLN H 88 GLN I 115 HIS I 223 ASN M 100 ASN M 185 ASN ** O 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 221 ASN Q 156 ASN U 170 GLN V 72 GLN V 88 GLN W 115 HIS W 223 ASN ** Y 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 164 GLN a 100 ASN a 114 GLN a 185 ASN b 136 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 48396 Z= 0.304 Angle : 0.595 7.695 65444 Z= 0.323 Chirality : 0.046 0.183 7392 Planarity : 0.005 0.051 8412 Dihedral : 5.515 55.409 6651 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.40 % Allowed : 17.12 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.10), residues: 5994 helix: 1.99 (0.10), residues: 2226 sheet: 0.41 (0.13), residues: 1526 loop : 0.13 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 221 HIS 0.009 0.001 HIS O 209 PHE 0.032 0.002 PHE Y 142 TYR 0.031 0.002 TYR N 125 ARG 0.007 0.000 ARG P 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 640 time to evaluate : 5.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.8117 (tpp80) cc_final: 0.7718 (tpt90) REVERT: B 4 ARG cc_start: 0.7241 (mpt180) cc_final: 0.5991 (pmt170) REVERT: B 241 GLN cc_start: 0.7838 (tp40) cc_final: 0.7610 (tp-100) REVERT: C 109 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8375 (tm-30) REVERT: C 231 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7750 (mppt) REVERT: D 41 CYS cc_start: 0.6350 (OUTLIER) cc_final: 0.6039 (p) REVERT: D 55 GLN cc_start: 0.8943 (mt0) cc_final: 0.8722 (mm-40) REVERT: D 177 LYS cc_start: 0.7036 (mttm) cc_final: 0.6611 (mttp) REVERT: E 32 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7807 (mttm) REVERT: E 197 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7397 (mt-10) REVERT: F 30 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7316 (mmmt) REVERT: F 61 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7517 (tptp) REVERT: F 86 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8326 (t0) REVERT: G 190 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7836 (mtt-85) REVERT: G 195 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7827 (mp10) REVERT: G 205 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: K 7 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8667 (tp) REVERT: M 87 ARG cc_start: 0.8155 (mtp180) cc_final: 0.7928 (mmm-85) REVERT: M 136 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6707 (mt-10) REVERT: M 146 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7302 (t0) REVERT: N 102 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8175 (mmpt) REVERT: N 140 LYS cc_start: 0.7156 (mtpm) cc_final: 0.6865 (mtpt) REVERT: O 120 ARG cc_start: 0.8084 (tpp80) cc_final: 0.7704 (tpt90) REVERT: P 4 ARG cc_start: 0.7296 (mpt180) cc_final: 0.5959 (pmt170) REVERT: P 241 GLN cc_start: 0.8061 (tp40) cc_final: 0.7797 (tp-100) REVERT: Q 109 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: Q 231 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7821 (mtmt) REVERT: R 142 ASP cc_start: 0.7049 (t0) cc_final: 0.6845 (t0) REVERT: S 88 MET cc_start: 0.8376 (mtm) cc_final: 0.8141 (mtm) REVERT: S 197 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.6943 (mm-30) REVERT: S 229 LYS cc_start: 0.8018 (mmpt) cc_final: 0.7583 (ptpp) REVERT: T 9 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6817 (m-30) REVERT: T 61 LYS cc_start: 0.8147 (ttmm) cc_final: 0.7441 (tptp) REVERT: T 86 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8334 (t0) REVERT: T 93 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7857 (t0) REVERT: T 106 GLU cc_start: 0.8026 (mp0) cc_final: 0.7779 (mp0) REVERT: W 164 MET cc_start: 0.9128 (tpp) cc_final: 0.8876 (tpp) REVERT: X 177 ASP cc_start: 0.8661 (m-30) cc_final: 0.8394 (m-30) REVERT: Y 7 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8706 (tp) REVERT: Z 172 MET cc_start: 0.5049 (OUTLIER) cc_final: 0.4773 (ppp) REVERT: a 87 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7977 (mmm-85) REVERT: a 146 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7264 (t0) REVERT: a 154 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: b 102 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8141 (mmpt) REVERT: b 140 LYS cc_start: 0.7182 (mtpm) cc_final: 0.6892 (mtpt) outliers start: 123 outliers final: 79 residues processed: 722 average time/residue: 1.7961 time to fit residues: 1581.0230 Evaluate side-chains 735 residues out of total 5128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 633 time to evaluate : 5.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 195 GLN Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain I residue 51 GLN Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 194 ASP Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 211 GLU Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 197 GLU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 86 ASN Chi-restraints excluded: chain T residue 93 ASN Chi-restraints excluded: chain T residue 140 SER Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 76 LYS Chi-restraints excluded: chain X residue 78 LYS Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain Y residue 2 ASP Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 146 ASP Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 134 MET Chi-restraints excluded: chain b residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 291 optimal weight: 0.8980 chunk 378 optimal weight: 0.8980 chunk 507 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 438 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 476 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 489 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN G 170 GLN H 72 GLN H 88 GLN I 115 HIS I 223 ASN M 100 ASN M 185 ASN O 181 ASN O 221 ASN U 170 GLN U 237 GLN V 72 GLN V 88 GLN W 115 HIS W 223 ASN ** Y 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 164 GLN a 100 ASN a 114 GLN a 185 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.148220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.117604 restraints weight = 48093.755| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.78 r_work: 0.3119 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 48396 Z= 0.230 Angle : 0.557 8.190 65444 Z= 0.302 Chirality : 0.044 0.174 7392 Planarity : 0.004 0.050 8412 Dihedral : 5.315 54.809 6651 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.24 % Allowed : 17.34 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.11), residues: 5994 helix: 2.18 (0.10), residues: 2228 sheet: 0.43 (0.13), residues: 1516 loop : 0.15 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 221 HIS 0.007 0.001 HIS O 209 PHE 0.028 0.002 PHE K 142 TYR 0.031 0.002 TYR N 125 ARG 0.006 0.000 ARG P 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22772.69 seconds wall clock time: 399 minutes 42.34 seconds (23982.34 seconds total)