Starting phenix.real_space_refine on Mon Mar 25 08:46:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0m_40944/03_2024/8t0m_40944.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0m_40944/03_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_40944/03_2024/8t0m_40944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0m_40944/03_2024/8t0m_40944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0m_40944/03_2024/8t0m_40944.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0m_40944/03_2024/8t0m_40944.pdb" } 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 Residue "A GLU 204": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "G GLU 152": "OE1" <-> "OE2" Residue "G GLU 191": "OE1" <-> "OE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H GLU 128": "OE1" <-> "OE2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H GLU 203": "OE1" <-> "OE2" Residue "H GLU 213": "OE1" <-> "OE2" Residue "I GLU 93": "OE1" <-> "OE2" Residue "I GLU 102": "OE1" <-> "OE2" Residue "I GLU 179": "OE1" <-> "OE2" Residue "I GLU 208": "OE1" <-> "OE2" Residue "I GLU 226": "OE1" <-> "OE2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "K GLU 58": "OE1" <-> "OE2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "K GLU 115": "OE1" <-> "OE2" Residue "K GLU 127": "OE1" <-> "OE2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K GLU 169": "OE1" <-> "OE2" Residue "L GLU 131": "OE1" <-> "OE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "L GLU 147": "OE1" <-> "OE2" Residue "L GLU 183": "OE1" <-> "OE2" Residue "L GLU 257": "OE1" <-> "OE2" Residue "L GLU 270": "OE1" <-> "OE2" Residue "L GLU 277": "OE1" <-> "OE2" Residue "L GLU 279": "OE1" <-> "OE2" Residue "M TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 154": "OE1" <-> "OE2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N GLU 98": "OE1" <-> "OE2" Residue "N GLU 107": "OE1" <-> "OE2" Residue "N GLU 119": "OE1" <-> "OE2" Residue "N GLU 208": "OE1" <-> "OE2" Residue "O GLU 204": "OE1" <-> "OE2" Residue "P GLU 184": "OE1" <-> "OE2" Residue "Q GLU 104": "OE1" <-> "OE2" Residue "Q GLU 109": "OE1" <-> "OE2" Residue "S GLU 44": "OE1" <-> "OE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S GLU 177": "OE1" <-> "OE2" Residue "S GLU 197": "OE1" <-> "OE2" Residue "S GLU 238": "OE1" <-> "OE2" Residue "T GLU 23": "OE1" <-> "OE2" Residue "T GLU 55": "OE1" <-> "OE2" Residue "T GLU 68": "OE1" <-> "OE2" Residue "T GLU 106": "OE1" <-> "OE2" Residue "T GLU 146": "OE1" <-> "OE2" Residue "T GLU 173": "OE1" <-> "OE2" Residue "T GLU 188": "OE1" <-> "OE2" Residue "T GLU 228": "OE1" <-> "OE2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U GLU 191": "OE1" <-> "OE2" Residue "U GLU 205": "OE1" <-> "OE2" Residue "V GLU 103": "OE1" <-> "OE2" Residue "V GLU 128": "OE1" <-> "OE2" Residue "V GLU 213": "OE1" <-> "OE2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W GLU 102": "OE1" <-> "OE2" Residue "W GLU 168": "OE1" <-> "OE2" Residue "W GLU 178": "OE1" <-> "OE2" Residue "W GLU 208": "OE1" <-> "OE2" Residue "X GLU 133": "OE1" <-> "OE2" Residue "X GLU 195": "OE1" <-> "OE2" Residue "Y GLU 87": "OE1" <-> "OE2" Residue "Y GLU 115": "OE1" <-> "OE2" Residue "Y GLU 155": "OE1" <-> "OE2" Residue "Y GLU 156": "OE1" <-> "OE2" Residue "Y GLU 167": "OE1" <-> "OE2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z GLU 142": "OE1" <-> "OE2" Residue "Z GLU 145": "OE1" <-> "OE2" Residue "Z GLU 147": "OE1" <-> "OE2" Residue "Z GLU 183": "OE1" <-> "OE2" Residue "Z GLU 257": "OE1" <-> "OE2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z GLU 277": "OE1" <-> "OE2" Residue "Z GLU 279": "OE1" <-> "OE2" Residue "a TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 154": "OE1" <-> "OE2" Residue "b GLU 74": "OE1" <-> "OE2" Residue "b GLU 107": "OE1" <-> "OE2" Residue "b GLU 119": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 24.78, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.87 Conformation dependent library (CDL) restraints added in 9.3 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: 5.94 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: 20.09 Time building geometry restraints manager: 20.25 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: 98.70 - 105.78: 698 105.78 - 112.85: 25951 112.85 - 119.93: 16079 119.93 - 127.00: 22322 127.00 - 134.08: 394 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 2.440 nonbonded pdb=" O GLY D 154 " pdb=" NH2 ARG E 86 " model vdw 2.195 2.520 nonbonded pdb=" O GLY V 190 " pdb=" OH TYR V 212 " model vdw 2.196 2.440 nonbonded pdb=" O GLY H 190 " pdb=" OH TYR H 212 " model vdw 2.197 2.440 nonbonded pdb=" O ARG Z 82 " pdb=" OH TYR Z 219 " model vdw 2.197 2.440 ... (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 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: 2.680 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: 12.410 Check model and map are aligned: 0.910 Set scattering table: 0.490 Process input model: 125.120 Find NCS groups from input model: 4.590 Set up NCS constraints: 0.470 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:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.010 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 60 poor density : 691 time to evaluate : 5.524 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: 1.7398 time to fit residues: 1566.5606 Evaluate side-chains 711 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 667 time to evaluate : 5.490 ------------------------------------------------------------------------------- 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: 2.9990 chunk 454 optimal weight: 6.9990 chunk 252 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 306 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 470 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 chunk 350 optimal weight: 7.9990 chunk 544 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 237 GLN H 81 HIS H 88 GLN I 223 ASN J 174 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 172 ASN M 173 GLN M 185 ASN O 37 GLN ** 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 172 ASN a 173 GLN a 185 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 48396 Z= 0.483 Angle : 0.699 10.987 65444 Z= 0.379 Chirality : 0.051 0.244 7392 Planarity : 0.006 0.060 8412 Dihedral : 6.491 57.276 6701 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.51 % Allowed : 14.16 % Favored : 82.33 % 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: 1.06 (0.10), residues: 5994 helix: 1.49 (0.10), residues: 2220 sheet: 0.53 (0.12), residues: 1520 loop : 0.18 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP V 184 HIS 0.013 0.002 HIS A 209 PHE 0.028 0.003 PHE Y 142 TYR 0.022 0.003 TYR Q 20 ARG 0.011 0.001 ARG P 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 848 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 668 time to evaluate : 7.664 Fit side-chains revert: symmetry clash REVERT: A 120 ARG cc_start: 0.8173 (tpp80) cc_final: 0.7819 (tpt90) REVERT: B 181 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7910 (p0) REVERT: B 237 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8371 (ttmt) REVERT: C 177 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: D 41 CYS cc_start: 0.6449 (OUTLIER) cc_final: 0.6181 (p) REVERT: D 55 GLN cc_start: 0.8960 (mt0) cc_final: 0.8752 (mm-40) REVERT: D 102 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8121 (t70) REVERT: D 177 LYS cc_start: 0.7195 (mttm) cc_final: 0.6702 (mttp) REVERT: E 52 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.6058 (mptm) REVERT: E 197 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7166 (mt-10) REVERT: F 30 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7383 (mmmt) REVERT: F 86 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8335 (t0) REVERT: G 101 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6792 (tppt) REVERT: G 152 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: G 195 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: G 205 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: H 126 LYS cc_start: 0.5931 (OUTLIER) cc_final: 0.5161 (ptmm) REVERT: K 5 LEU cc_start: 0.8924 (mm) cc_final: 0.8708 (mt) REVERT: K 7 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8732 (tp) REVERT: K 23 ARG cc_start: 0.6770 (ttt-90) cc_final: 0.6476 (ttt180) REVERT: L 164 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7570 (pt0) REVERT: L 274 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7836 (ttmt) REVERT: N 102 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8072 (mmpt) REVERT: O 120 ARG cc_start: 0.8151 (tpp80) cc_final: 0.7740 (tpt90) REVERT: P 237 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8352 (ttmt) REVERT: Q 231 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7780 (mtmt) REVERT: R 55 GLN cc_start: 0.8954 (mt0) cc_final: 0.8751 (mm-40) REVERT: R 102 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8130 (t70) REVERT: S 52 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.6069 (mptm) REVERT: S 197 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7020 (mm-30) REVERT: S 211 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6511 (tttm) REVERT: S 229 LYS cc_start: 0.8012 (mmpt) cc_final: 0.7342 (mppt) REVERT: U 152 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7992 (mm-30) REVERT: U 195 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8519 (mm-40) REVERT: V 126 LYS cc_start: 0.5968 (OUTLIER) cc_final: 0.5185 (ptmm) REVERT: W 72 CYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7437 (p) REVERT: W 164 MET cc_start: 0.9162 (tpp) cc_final: 0.8952 (tpp) REVERT: Y 7 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8703 (tp) REVERT: Z 92 ASP cc_start: 0.8665 (p0) cc_final: 0.8457 (p0) REVERT: Z 274 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7794 (ttmt) REVERT: a 136 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6496 (pm20) REVERT: b 102 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8105 (mmpt) REVERT: b 191 LYS cc_start: 0.8608 (mtpp) cc_final: 0.8402 (mtpt) outliers start: 180 outliers final: 74 residues processed: 786 average time/residue: 1.7882 time to fit residues: 1719.1536 Evaluate side-chains 758 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 654 time to evaluate : 5.301 ------------------------------------------------------------------------------- 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 181 ASP Chi-restraints excluded: chain B residue 195 THR 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 21 GLU 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 62 ASP 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 F residue 173 GLU 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 126 LYS 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 164 GLN Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 274 LYS 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 62 ASP 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 140 SER Chi-restraints excluded: chain T residue 173 GLU 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 126 LYS 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 200 ASP Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 222 ASP 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 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: 0.5980 chunk 169 optimal weight: 1.9990 chunk 453 optimal weight: 4.9990 chunk 371 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 chunk 545 optimal weight: 3.9990 chunk 589 optimal weight: 7.9990 chunk 486 optimal weight: 2.9990 chunk 541 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 437 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 ASN D 122 GLN E 154 GLN G 237 GLN H 88 GLN I 115 HIS I 223 ASN J 174 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 185 ASN O 37 GLN O 39 ASN Q 156 ASN R 122 GLN ** 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 223 ASN ** Y 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 164 GLN a 75 ASN a 100 ASN a 172 ASN a 173 GLN a 178 ASN a 185 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.0989 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= 0.220 Angle : 0.534 7.589 65444 Z= 0.292 Chirality : 0.044 0.165 7392 Planarity : 0.004 0.050 8412 Dihedral : 5.792 60.889 6682 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.24 % Allowed : 14.90 % Favored : 81.86 % 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: 1.37 (0.10), residues: 5994 helix: 1.99 (0.10), residues: 2226 sheet: 0.55 (0.13), residues: 1516 loop : 0.18 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 184 HIS 0.009 0.001 HIS O 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 fitting. rotamer outliers: 166 poor density : 693 time to evaluate : 5.719 Fit side-chains revert: symmetry clash REVERT: A 120 ARG cc_start: 0.8130 (tpp80) cc_final: 0.7692 (tpt90) REVERT: C 60 ASP cc_start: 0.6649 (OUTLIER) cc_final: 0.6433 (m-30) REVERT: C 231 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7659 (mppt) REVERT: D 41 CYS cc_start: 0.6306 (OUTLIER) cc_final: 0.6044 (p) REVERT: D 55 GLN cc_start: 0.8937 (mt0) cc_final: 0.8727 (mm-40) REVERT: D 177 LYS cc_start: 0.7069 (mttm) cc_final: 0.6712 (mtmp) REVERT: E 32 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7811 (mttm) REVERT: E 52 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.5997 (mptm) REVERT: E 53 ARG cc_start: 0.7690 (ttp-170) cc_final: 0.7240 (ttm170) REVERT: E 197 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7208 (mt-10) REVERT: F 9 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6833 (m-30) REVERT: F 30 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7383 (mmmt) REVERT: F 61 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7459 (tptp) REVERT: F 106 GLU cc_start: 0.8061 (mp0) cc_final: 0.7824 (mp0) REVERT: G 195 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: G 205 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: K 7 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8651 (tp) REVERT: L 172 MET cc_start: 0.4858 (OUTLIER) cc_final: 0.3808 (ppp) REVERT: N 102 LYS cc_start: 0.8507 (mtmt) cc_final: 0.8054 (mmpt) REVERT: O 120 ARG cc_start: 0.8107 (tpp80) cc_final: 0.7721 (tpt90) REVERT: P 4 ARG cc_start: 0.7315 (mpt180) cc_final: 0.5993 (pmt170) REVERT: P 181 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7760 (p0) REVERT: R 55 GLN cc_start: 0.8931 (mt0) cc_final: 0.8727 (mm-40) REVERT: R 122 GLN cc_start: 0.7851 (pt0) cc_final: 0.7648 (tt0) REVERT: R 193 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7554 (ttpp) REVERT: S 52 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.6030 (mptm) REVERT: S 197 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7251 (mm-30) REVERT: S 229 LYS cc_start: 0.8002 (mmpt) cc_final: 0.7563 (ptpp) REVERT: T 9 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6838 (m-30) REVERT: T 61 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7439 (tptp) REVERT: T 106 GLU cc_start: 0.7972 (mp0) cc_final: 0.7699 (mp0) REVERT: U 195 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8383 (mm-40) REVERT: W 164 MET cc_start: 0.9128 (tpp) cc_final: 0.8848 (tpp) REVERT: Y 7 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8655 (tp) REVERT: Z 179 TYR cc_start: 0.7967 (t80) cc_final: 0.7717 (t80) REVERT: a 136 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6656 (mt-10) REVERT: b 102 LYS cc_start: 0.8507 (mtmt) cc_final: 0.8097 (mmpt) REVERT: b 140 LYS cc_start: 0.7183 (mtpm) cc_final: 0.6876 (mtpt) outliers start: 166 outliers final: 58 residues processed: 806 average time/residue: 1.7188 time to fit residues: 1692.5409 Evaluate side-chains 752 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 675 time to evaluate : 5.535 ------------------------------------------------------------------------------- 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 B residue 122 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 60 ASP 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 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 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 92 CYS Chi-restraints excluded: chain F residue 173 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 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 2 ASP Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 200 ASP Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 129 THR 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 P residue 122 THR Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 81 THR 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 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 173 GLU Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain U residue 206 ASP 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 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 222 ASP Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain b residue 38 ILE 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: 0.9980 chunk 283 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 260 optimal weight: 6.9990 chunk 366 optimal weight: 5.9990 chunk 547 optimal weight: 1.9990 chunk 579 optimal weight: 6.9990 chunk 286 optimal weight: 5.9990 chunk 519 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 100 ASN M 185 ASN N 136 GLN O 37 GLN 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 172 ASN a 173 GLN a 185 ASN b 136 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 48396 Z= 0.366 Angle : 0.615 7.880 65444 Z= 0.334 Chirality : 0.048 0.203 7392 Planarity : 0.005 0.051 8412 Dihedral : 5.907 58.092 6665 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.32 % Allowed : 15.54 % Favored : 81.14 % 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: 1.22 (0.10), residues: 5994 helix: 1.84 (0.10), residues: 2222 sheet: 0.45 (0.13), residues: 1526 loop : 0.15 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP V 184 HIS 0.011 0.002 HIS A 209 PHE 0.023 0.003 PHE N 127 TYR 0.020 0.002 TYR C 20 ARG 0.009 0.001 ARG B 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 835 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 665 time to evaluate : 5.151 Fit side-chains REVERT: A 120 ARG cc_start: 0.8194 (tpp80) cc_final: 0.7738 (tpt90) REVERT: B 4 ARG cc_start: 0.7521 (mpt180) cc_final: 0.6181 (pmt170) REVERT: C 177 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7810 (mt0) REVERT: D 41 CYS cc_start: 0.6381 (OUTLIER) cc_final: 0.6114 (p) REVERT: D 55 GLN cc_start: 0.8946 (mt0) cc_final: 0.8740 (mm-40) REVERT: D 177 LYS cc_start: 0.7070 (mttm) cc_final: 0.6773 (mttp) REVERT: E 52 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.5992 (mptm) REVERT: E 197 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7235 (mt-10) REVERT: F 9 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.7055 (m-30) REVERT: F 30 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7266 (mmmt) REVERT: F 86 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8354 (t0) REVERT: G 195 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.7841 (mp10) REVERT: G 205 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: I 164 MET cc_start: 0.9089 (tpp) cc_final: 0.8863 (tpp) REVERT: K 7 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8679 (tp) REVERT: L 172 MET cc_start: 0.4998 (OUTLIER) cc_final: 0.3913 (ppp) REVERT: L 274 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7740 (ttmt) REVERT: N 102 LYS cc_start: 0.8532 (mtmt) cc_final: 0.8075 (mmpt) REVERT: N 191 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8364 (mtpp) REVERT: O 120 ARG cc_start: 0.8087 (tpp80) cc_final: 0.7717 (tpt90) REVERT: P 178 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7980 (mmt180) REVERT: P 181 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7912 (p0) REVERT: Q 231 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7775 (mtmt) REVERT: R 41 CYS cc_start: 0.6327 (OUTLIER) cc_final: 0.5975 (p) REVERT: R 55 GLN cc_start: 0.8941 (mt0) cc_final: 0.8740 (mm-40) REVERT: R 122 GLN cc_start: 0.7956 (pt0) cc_final: 0.7740 (tt0) REVERT: R 193 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7593 (ttpp) REVERT: S 52 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.6018 (mptm) REVERT: S 197 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.6994 (mm-30) REVERT: S 229 LYS cc_start: 0.8050 (mmpt) cc_final: 0.7630 (ptpp) REVERT: T 9 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.7052 (m-30) REVERT: T 86 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8369 (t0) REVERT: T 106 GLU cc_start: 0.7985 (mp0) cc_final: 0.7701 (mp0) REVERT: U 152 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8079 (mm-30) REVERT: U 195 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8335 (mm-40) REVERT: W 164 MET cc_start: 0.9213 (tpp) cc_final: 0.8964 (tpp) REVERT: Y 7 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8680 (tp) REVERT: Z 172 MET cc_start: 0.5129 (OUTLIER) cc_final: 0.4150 (ppp) REVERT: Z 274 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7781 (ttmt) REVERT: a 136 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6664 (mt-10) REVERT: a 154 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: b 102 LYS cc_start: 0.8549 (mtmt) cc_final: 0.8128 (mmpt) outliers start: 170 outliers final: 81 residues processed: 773 average time/residue: 1.7222 time to fit residues: 1624.9071 Evaluate side-chains 765 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 656 time to evaluate : 5.461 ------------------------------------------------------------------------------- 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 195 THR 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 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 D residue 187 THR 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 173 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 206 ASP 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 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 28 LEU Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 200 ASP Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 274 LYS Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 191 LYS 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 178 ARG Chi-restraints excluded: chain P residue 181 ASP 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 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 21 GLU 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 62 ASP Chi-restraints excluded: chain S residue 76 CYS 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 T residue 173 GLU 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 U residue 206 ASP 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 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 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 Y residue 28 LEU Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 200 ASP Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain Z residue 274 LYS Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 38 ILE 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: 0.7980 chunk 329 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 431 optimal weight: 0.9990 chunk 239 optimal weight: 5.9990 chunk 494 optimal weight: 0.6980 chunk 400 optimal weight: 0.0010 chunk 0 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 520 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 ASN G 237 GLN H 88 GLN I 86 GLN I 223 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 185 ASN O 37 GLN Q 156 ASN ** S 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 237 GLN V 88 GLN W 115 HIS W 170 HIS W 223 ASN ** Y 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 164 GLN a 100 ASN a 172 ASN a 173 GLN a 185 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 48396 Z= 0.149 Angle : 0.484 6.708 65444 Z= 0.264 Chirality : 0.042 0.158 7392 Planarity : 0.004 0.051 8412 Dihedral : 5.248 59.797 6665 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.75 % Allowed : 16.28 % 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: 1.58 (0.11), residues: 5994 helix: 2.34 (0.11), residues: 2236 sheet: 0.54 (0.13), residues: 1504 loop : 0.17 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 199 HIS 0.006 0.001 HIS O 209 PHE 0.020 0.001 PHE T 179 TYR 0.017 0.001 TYR X 70 ARG 0.004 0.000 ARG B 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 860 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 719 time to evaluate : 5.628 Fit side-chains REVERT: A 120 ARG cc_start: 0.8087 (tpp80) cc_final: 0.7693 (tpt90) REVERT: B 4 ARG cc_start: 0.7209 (mpt180) cc_final: 0.6006 (pmt170) REVERT: D 41 CYS cc_start: 0.5965 (OUTLIER) cc_final: 0.5698 (p) REVERT: D 55 GLN cc_start: 0.8936 (mt0) cc_final: 0.8720 (mm-40) REVERT: D 177 LYS cc_start: 0.6891 (mttm) cc_final: 0.6615 (mttp) REVERT: E 32 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7765 (mttm) REVERT: E 53 ARG cc_start: 0.7651 (ttp-170) cc_final: 0.7411 (ttm170) REVERT: E 115 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.8015 (t) REVERT: E 188 HIS cc_start: 0.7511 (p90) cc_final: 0.7078 (p90) REVERT: E 197 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: F 30 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7366 (mmmt) REVERT: F 41 ASN cc_start: 0.8466 (m-40) cc_final: 0.8266 (t0) REVERT: F 61 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7439 (tptp) REVERT: F 106 GLU cc_start: 0.8045 (mp0) cc_final: 0.7825 (mp0) REVERT: F 148 GLN cc_start: 0.8571 (mm110) cc_final: 0.8362 (mm-40) REVERT: G 195 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7849 (mp10) REVERT: H 103 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: I 164 MET cc_start: 0.9057 (tpp) cc_final: 0.8790 (tpp) REVERT: K 49 GLU cc_start: 0.7299 (tp30) cc_final: 0.6872 (mm-30) REVERT: K 169 GLU cc_start: 0.6549 (mt-10) cc_final: 0.6221 (pt0) REVERT: K 174 MET cc_start: 0.7284 (ptt) cc_final: 0.6894 (ppp) REVERT: N 90 ASP cc_start: 0.8423 (t70) cc_final: 0.8188 (t70) REVERT: N 102 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8038 (mmpt) REVERT: N 140 LYS cc_start: 0.7165 (mtpm) cc_final: 0.6874 (mtpt) REVERT: O 120 ARG cc_start: 0.8054 (tpp80) cc_final: 0.7678 (tpt90) REVERT: P 4 ARG cc_start: 0.7228 (mpt180) cc_final: 0.6073 (pmt170) REVERT: P 181 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7737 (p0) REVERT: Q 175 LEU cc_start: 0.8505 (mm) cc_final: 0.8133 (mt) REVERT: R 55 GLN cc_start: 0.8929 (mt0) cc_final: 0.8722 (mm-40) REVERT: S 89 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8302 (mt) REVERT: S 197 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7197 (mm-30) REVERT: S 229 LYS cc_start: 0.8018 (mmpt) cc_final: 0.7590 (ptpp) REVERT: T 9 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6797 (m-30) REVERT: T 61 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7447 (tptp) REVERT: T 93 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7750 (t0) REVERT: T 148 GLN cc_start: 0.8598 (mm110) cc_final: 0.8396 (mm-40) REVERT: U 195 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8472 (mm-40) REVERT: W 164 MET cc_start: 0.9141 (tpp) cc_final: 0.8835 (tpp) REVERT: a 136 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6679 (mt-10) REVERT: b 90 ASP cc_start: 0.8407 (t70) cc_final: 0.8177 (t70) REVERT: b 102 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8081 (mmpt) REVERT: b 140 LYS cc_start: 0.7147 (mtpm) cc_final: 0.6863 (mtpt) outliers start: 141 outliers final: 57 residues processed: 821 average time/residue: 1.6890 time to fit residues: 1700.2098 Evaluate side-chains 732 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 661 time to evaluate : 5.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 225 VAL 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 F residue 173 GLU Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain G residue 134 VAL 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 206 ASP Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 103 GLU 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 L residue 212 TYR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 129 THR 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 208 THR Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 195 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 225 VAL Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain S residue 9 ASP 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 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 U residue 206 ASP 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 200 ASP Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 136 GLU 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: 0.0050 chunk 522 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 340 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 580 optimal weight: 0.8980 chunk 481 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 chunk 304 optimal weight: 5.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN C 156 ASN D 122 GLN G 237 GLN H 88 GLN I 86 GLN I 115 HIS ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 185 ASN N 136 GLN O 37 GLN O 39 ASN P 123 GLN Q 156 ASN R 122 GLN 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 114 GLN a 172 ASN a 173 GLN a 185 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 48396 Z= 0.265 Angle : 0.551 8.459 65444 Z= 0.298 Chirality : 0.045 0.166 7392 Planarity : 0.004 0.048 8412 Dihedral : 5.378 57.507 6654 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.12 % Allowed : 16.56 % Favored : 80.32 % 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: 2.25 (0.10), residues: 2230 sheet: 0.47 (0.13), residues: 1544 loop : 0.21 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP Z 100 HIS 0.010 0.001 HIS A 209 PHE 0.022 0.002 PHE Y 142 TYR 0.020 0.002 TYR M 151 ARG 0.005 0.000 ARG P 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 814 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 654 time to evaluate : 5.582 Fit side-chains REVERT: A 120 ARG cc_start: 0.8174 (tpp80) cc_final: 0.7757 (tpt90) REVERT: B 4 ARG cc_start: 0.7262 (mpt180) cc_final: 0.6030 (pmt170) REVERT: C 231 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7666 (mppt) REVERT: D 41 CYS cc_start: 0.6161 (OUTLIER) cc_final: 0.5900 (p) REVERT: D 55 GLN cc_start: 0.8946 (mt0) cc_final: 0.8731 (mm-40) REVERT: D 177 LYS cc_start: 0.6916 (mttm) cc_final: 0.6612 (mttp) REVERT: E 115 SER cc_start: 0.8308 (OUTLIER) cc_final: 0.8001 (m) REVERT: E 188 HIS cc_start: 0.7530 (p90) cc_final: 0.7103 (p90) REVERT: E 197 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: F 30 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7367 (mmmt) REVERT: F 41 ASN cc_start: 0.8506 (m-40) cc_final: 0.8300 (t0) REVERT: F 61 LYS cc_start: 0.8148 (ttmm) cc_final: 0.7441 (tptp) REVERT: F 86 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8326 (t0) REVERT: G 195 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7846 (mp10) REVERT: G 205 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: K 7 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8695 (tp) REVERT: K 174 MET cc_start: 0.7362 (ptt) cc_final: 0.6981 (ppp) REVERT: L 92 ASP cc_start: 0.8647 (p0) cc_final: 0.8436 (p0) REVERT: L 172 MET cc_start: 0.4784 (OUTLIER) cc_final: 0.3897 (ppp) REVERT: L 258 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: O 120 ARG cc_start: 0.8069 (tpp80) cc_final: 0.7687 (tpt90) REVERT: P 4 ARG cc_start: 0.7296 (mpt180) cc_final: 0.6083 (pmt170) REVERT: P 181 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7780 (p0) REVERT: Q 231 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7769 (mtmt) REVERT: R 55 GLN cc_start: 0.8942 (mt0) cc_final: 0.8735 (mm-40) REVERT: S 197 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.6933 (mm-30) REVERT: S 229 LYS cc_start: 0.8043 (mmpt) cc_final: 0.7604 (ptpp) REVERT: T 9 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6814 (m-30) REVERT: T 61 LYS cc_start: 0.8133 (ttmm) cc_final: 0.7451 (tptp) REVERT: T 86 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8345 (t0) REVERT: U 195 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8552 (mm-40) REVERT: W 164 MET cc_start: 0.9179 (tpp) cc_final: 0.8963 (tpp) REVERT: X 177 ASP cc_start: 0.8643 (m-30) cc_final: 0.8419 (m-30) REVERT: Y 7 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8679 (tp) REVERT: Z 258 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7553 (m-30) REVERT: a 136 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6648 (mt-10) REVERT: b 102 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8127 (mmpt) REVERT: b 140 LYS cc_start: 0.7141 (mtpm) cc_final: 0.6833 (mtpt) outliers start: 160 outliers final: 81 residues processed: 763 average time/residue: 1.7084 time to fit residues: 1592.8209 Evaluate side-chains 757 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 657 time to evaluate : 5.327 ------------------------------------------------------------------------------- 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 92 VAL Chi-restraints excluded: chain B residue 195 THR 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 216 ILE 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 76 CYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 154 GLN 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 F residue 92 CYS Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 200 SER 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 206 ASP Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 56 VAL 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 K residue 28 LEU Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 200 ASP Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 258 ASP Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 129 THR 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 O residue 179 THR Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 195 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 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 187 THR Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 76 CYS Chi-restraints excluded: chain S residue 154 GLN 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 T residue 173 GLU Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain U residue 206 ASP 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 Y residue 28 LEU Chi-restraints excluded: chain Z residue 200 ASP Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain Z residue 258 ASP Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 208 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 559 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 330 optimal weight: 1.9990 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: 0.9980 chunk 361 optimal weight: 1.9990 chunk 352 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 ASN ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 GLN H 88 GLN H 125 ASN I 115 HIS ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 185 ASN N 136 GLN O 37 GLN Q 156 ASN 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 Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 48396 Z= 0.306 Angle : 0.581 9.970 65444 Z= 0.314 Chirality : 0.046 0.179 7392 Planarity : 0.005 0.052 8412 Dihedral : 5.527 54.738 6654 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.24 % Allowed : 16.42 % Favored : 80.34 % 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: 1.39 (0.11), residues: 5994 helix: 2.11 (0.10), residues: 2224 sheet: 0.46 (0.13), residues: 1540 loop : 0.16 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Z 100 HIS 0.011 0.001 HIS O 209 PHE 0.025 0.002 PHE Y 142 TYR 0.020 0.002 TYR M 151 ARG 0.005 0.000 ARG R 166 *********************** 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 832 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 666 time to evaluate : 5.646 Fit side-chains REVERT: A 120 ARG cc_start: 0.8202 (tpp80) cc_final: 0.7793 (tpt90) REVERT: C 231 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7657 (mppt) REVERT: D 39 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7164 (mtmm) REVERT: D 41 CYS cc_start: 0.6339 (OUTLIER) cc_final: 0.6081 (p) REVERT: D 55 GLN cc_start: 0.8948 (mt0) cc_final: 0.8735 (mm-40) REVERT: D 142 ASP cc_start: 0.7330 (t0) cc_final: 0.6443 (m-30) REVERT: D 177 LYS cc_start: 0.6927 (mttm) cc_final: 0.6620 (mttp) REVERT: E 32 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7806 (mttm) REVERT: E 115 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.7985 (m) REVERT: E 197 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7369 (mt-10) REVERT: F 30 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7195 (mmmt) REVERT: F 61 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7448 (tptp) REVERT: F 86 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8329 (t0) REVERT: G 195 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: G 205 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: K 7 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8692 (tp) REVERT: K 174 MET cc_start: 0.7335 (ptt) cc_final: 0.6903 (ppp) REVERT: L 172 MET cc_start: 0.4843 (OUTLIER) cc_final: 0.4606 (ppp) REVERT: L 258 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: M 87 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7878 (mmm-85) REVERT: N 102 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8128 (mmpt) REVERT: O 120 ARG cc_start: 0.8089 (tpp80) cc_final: 0.7710 (tpt90) REVERT: P 181 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7796 (p0) REVERT: Q 231 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7778 (mtmt) REVERT: R 55 GLN cc_start: 0.8944 (mt0) cc_final: 0.8734 (mm-40) REVERT: R 142 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6918 (t0) REVERT: S 197 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7248 (mm-30) REVERT: S 229 LYS cc_start: 0.8062 (mmpt) cc_final: 0.7619 (ptpp) REVERT: T 9 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6828 (m-30) REVERT: T 61 LYS cc_start: 0.8136 (ttmm) cc_final: 0.7453 (tptp) REVERT: T 86 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8358 (t0) REVERT: U 195 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8613 (mm-40) REVERT: W 164 MET cc_start: 0.9186 (tpp) cc_final: 0.8972 (tpp) REVERT: X 177 ASP cc_start: 0.8628 (m-30) cc_final: 0.8371 (m-30) REVERT: Y 7 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8672 (tp) REVERT: Y 174 MET cc_start: 0.7105 (ptt) cc_final: 0.5734 (ppp) REVERT: Z 172 MET cc_start: 0.4984 (OUTLIER) cc_final: 0.4778 (ppp) REVERT: Z 179 TYR cc_start: 0.8095 (t80) cc_final: 0.7814 (t80) REVERT: a 87 ARG cc_start: 0.8150 (mtp180) cc_final: 0.7889 (mmm-85) REVERT: a 136 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6647 (mt-10) REVERT: b 102 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8126 (mmpt) REVERT: b 140 LYS cc_start: 0.7097 (mtpm) cc_final: 0.6794 (mtpt) outliers start: 166 outliers final: 93 residues processed: 779 average time/residue: 1.7339 time to fit residues: 1648.2904 Evaluate side-chains 778 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 662 time to evaluate : 5.760 ------------------------------------------------------------------------------- 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 235 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 195 THR 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 216 ILE 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 39 LYS 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 76 CYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 154 GLN 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 F residue 92 CYS Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 200 SER 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 206 ASP 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 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 28 LEU Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 200 ASP Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 258 ASP Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 129 THR 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 235 THR Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 195 THR 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 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 142 ASP Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 76 CYS Chi-restraints excluded: chain S residue 154 GLN 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 T residue 173 GLU Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain U residue 206 ASP 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 Y residue 28 LEU Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 200 ASP Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 102 LYS Chi-restraints excluded: chain b residue 173 SER Chi-restraints excluded: chain b residue 208 GLU 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: 0.9990 chunk 174 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 367 optimal weight: 5.9990 chunk 393 optimal weight: 7.9990 chunk 285 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 454 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 ASN G 170 GLN H 88 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 185 ASN O 37 GLN Q 156 ASN U 170 GLN V 88 GLN V 125 ASN 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1385 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= 0.188 Angle : 0.512 9.043 65444 Z= 0.278 Chirality : 0.043 0.173 7392 Planarity : 0.004 0.054 8412 Dihedral : 5.183 52.480 6654 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.65 % Allowed : 17.20 % Favored : 80.15 % 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: 1.57 (0.11), residues: 5994 helix: 2.35 (0.11), residues: 2232 sheet: 0.53 (0.13), residues: 1504 loop : 0.15 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 100 HIS 0.007 0.001 HIS O 209 PHE 0.021 0.002 PHE K 142 TYR 0.017 0.001 TYR X 70 ARG 0.004 0.000 ARG B 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 818 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 682 time to evaluate : 5.346 Fit side-chains REVERT: A 120 ARG cc_start: 0.8149 (tpp80) cc_final: 0.7749 (tpt90) REVERT: B 4 ARG cc_start: 0.7184 (mpt180) cc_final: 0.5964 (pmt170) REVERT: C 175 LEU cc_start: 0.8469 (mm) cc_final: 0.8182 (mt) REVERT: C 231 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7641 (mppt) REVERT: D 41 CYS cc_start: 0.5997 (OUTLIER) cc_final: 0.5732 (p) REVERT: D 55 GLN cc_start: 0.8943 (mt0) cc_final: 0.8735 (mm-40) REVERT: D 142 ASP cc_start: 0.7268 (t0) cc_final: 0.6386 (m-30) REVERT: D 177 LYS cc_start: 0.6905 (mttm) cc_final: 0.6602 (mttp) REVERT: E 32 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7786 (mttm) REVERT: E 115 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.8005 (m) REVERT: E 188 HIS cc_start: 0.7548 (p90) cc_final: 0.7135 (p90) REVERT: E 197 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: F 30 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7269 (mmmt) REVERT: F 31 GLN cc_start: 0.7676 (mp10) cc_final: 0.7369 (mm110) REVERT: F 61 LYS cc_start: 0.8131 (ttmm) cc_final: 0.7441 (tptp) REVERT: F 106 GLU cc_start: 0.8052 (mp0) cc_final: 0.7832 (mp0) REVERT: G 191 GLU cc_start: 0.7310 (tp30) cc_final: 0.7092 (tp30) REVERT: G 195 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: G 205 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: K 49 GLU cc_start: 0.7260 (tp30) cc_final: 0.6837 (mm-30) REVERT: K 174 MET cc_start: 0.7278 (ptt) cc_final: 0.6949 (ppp) REVERT: L 258 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: M 87 ARG cc_start: 0.8106 (mtp180) cc_final: 0.7865 (mmm-85) REVERT: N 102 LYS cc_start: 0.8464 (mtmt) cc_final: 0.8124 (mmpt) REVERT: N 140 LYS cc_start: 0.7200 (mtpm) cc_final: 0.6913 (mtpt) REVERT: O 120 ARG cc_start: 0.8100 (tpp80) cc_final: 0.7711 (tpt90) REVERT: P 4 ARG cc_start: 0.7248 (mpt180) cc_final: 0.6059 (pmt170) REVERT: P 181 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7764 (p0) REVERT: Q 231 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7762 (mtmt) REVERT: R 142 ASP cc_start: 0.7203 (OUTLIER) cc_final: 0.6988 (t0) REVERT: S 197 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: S 229 LYS cc_start: 0.7995 (mmpt) cc_final: 0.7424 (mtmm) REVERT: T 9 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6798 (m-30) REVERT: T 61 LYS cc_start: 0.8115 (ttmm) cc_final: 0.7447 (tptp) REVERT: T 93 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7739 (t0) REVERT: U 195 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8567 (mm-40) REVERT: W 164 MET cc_start: 0.9185 (tpp) cc_final: 0.8943 (tpp) REVERT: X 177 ASP cc_start: 0.8598 (m-30) cc_final: 0.8355 (m-30) REVERT: Y 7 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8643 (tp) REVERT: Z 258 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: a 87 ARG cc_start: 0.8131 (mtp180) cc_final: 0.7888 (mmm-85) REVERT: a 154 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: b 102 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8105 (mmpt) REVERT: b 140 LYS cc_start: 0.7131 (mtpm) cc_final: 0.6826 (mtpt) outliers start: 136 outliers final: 81 residues processed: 778 average time/residue: 1.6862 time to fit residues: 1607.5422 Evaluate side-chains 770 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 670 time to evaluate : 6.172 ------------------------------------------------------------------------------- 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 B residue 122 THR Chi-restraints excluded: chain B residue 195 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 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 76 CYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 154 GLN 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 F residue 173 GLU Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain G residue 134 VAL 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 206 ASP Chi-restraints excluded: chain G residue 210 LYS 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 78 LYS Chi-restraints excluded: chain J residue 194 ASP Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain L residue 200 ASP Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 258 ASP Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 129 THR 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 92 VAL Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 195 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 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 142 ASP Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 154 GLN 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 U residue 206 ASP 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 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 200 ASP Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain Z residue 258 ASP Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 102 LYS Chi-restraints excluded: chain b residue 173 SER Chi-restraints excluded: chain b residue 208 GLU 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: 0.9980 chunk 505 optimal weight: 3.9990 chunk 538 optimal weight: 0.7980 chunk 553 optimal weight: 8.9990 chunk 324 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 423 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 486 optimal weight: 10.0000 chunk 509 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 ASN D 122 GLN ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN H 88 GLN I 115 HIS ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 185 ASN N 136 GLN O 37 GLN Q 156 ASN ** S 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 48396 Z= 0.378 Angle : 0.625 10.410 65444 Z= 0.336 Chirality : 0.048 0.213 7392 Planarity : 0.005 0.051 8412 Dihedral : 5.617 54.199 6654 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.67 % Allowed : 17.24 % Favored : 80.09 % 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: 1.34 (0.11), residues: 5994 helix: 2.03 (0.10), residues: 2222 sheet: 0.46 (0.13), residues: 1528 loop : 0.14 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 133 HIS 0.013 0.002 HIS A 209 PHE 0.031 0.003 PHE Y 142 TYR 0.022 0.002 TYR C 20 ARG 0.005 0.001 ARG D 166 *********************** 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 799 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 662 time to evaluate : 5.448 Fit side-chains REVERT: A 120 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7737 (tpt90) REVERT: B 4 ARG cc_start: 0.7276 (mpt180) cc_final: 0.6016 (pmt170) REVERT: B 181 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7900 (p0) REVERT: C 231 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7659 (mppt) REVERT: D 39 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7173 (mtmm) REVERT: D 41 CYS cc_start: 0.6391 (OUTLIER) cc_final: 0.6094 (p) REVERT: D 55 GLN cc_start: 0.8940 (mt0) cc_final: 0.8729 (mm-40) REVERT: D 142 ASP cc_start: 0.7358 (t0) cc_final: 0.6477 (m-30) REVERT: D 177 LYS cc_start: 0.6936 (mttm) cc_final: 0.6624 (mttp) REVERT: E 115 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.8003 (m) REVERT: E 197 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: F 30 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7211 (mmmt) REVERT: F 61 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7458 (tptp) REVERT: F 86 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8343 (t0) REVERT: G 191 GLU cc_start: 0.7369 (tp30) cc_final: 0.7150 (tp30) REVERT: G 195 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: G 205 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: I 164 MET cc_start: 0.9111 (tpp) cc_final: 0.8904 (tpp) REVERT: K 7 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8691 (tp) REVERT: K 174 MET cc_start: 0.7325 (ptt) cc_final: 0.6894 (ppp) REVERT: L 258 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: N 102 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8135 (mmpt) REVERT: O 120 ARG cc_start: 0.8113 (tpp80) cc_final: 0.7673 (tpt90) REVERT: P 181 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7922 (p0) REVERT: Q 231 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7796 (mtmt) REVERT: R 142 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6981 (t0) REVERT: S 197 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: S 229 LYS cc_start: 0.8046 (mmpt) cc_final: 0.7570 (ptpp) REVERT: T 9 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.7040 (m-30) REVERT: T 61 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7461 (tptp) REVERT: T 86 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8352 (t0) REVERT: U 195 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8497 (mm-40) REVERT: Y 7 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8695 (tp) REVERT: Z 172 MET cc_start: 0.5929 (ppp) cc_final: 0.5419 (tmm) REVERT: Z 258 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: b 140 LYS cc_start: 0.7164 (mtpm) cc_final: 0.6861 (mtpt) outliers start: 137 outliers final: 85 residues processed: 754 average time/residue: 1.7430 time to fit residues: 1603.2099 Evaluate side-chains 765 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 660 time to evaluate : 5.823 ------------------------------------------------------------------------------- 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 235 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 195 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 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 39 LYS 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 76 CYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 154 GLN 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 F residue 92 CYS Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 200 SER 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 206 ASP Chi-restraints excluded: chain G residue 210 LYS 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 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 200 ASP Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 258 ASP Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 129 THR 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 235 THR Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 195 THR 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 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 142 ASP Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 154 GLN 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 T residue 173 GLU Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain U residue 206 ASP 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 200 ASP Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain Z residue 258 ASP Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 173 SER Chi-restraints excluded: chain b residue 208 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 537 optimal weight: 0.9980 chunk 353 optimal weight: 3.9990 chunk 569 optimal weight: 2.9990 chunk 347 optimal weight: 0.9980 chunk 270 optimal weight: 0.5980 chunk 396 optimal weight: 10.0000 chunk 597 optimal weight: 2.9990 chunk 550 optimal weight: 9.9990 chunk 475 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 367 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 ASN G 170 GLN H 88 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 185 ASN O 37 GLN Q 156 ASN ** S 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 48396 Z= 0.211 Angle : 0.538 9.704 65444 Z= 0.290 Chirality : 0.044 0.180 7392 Planarity : 0.004 0.053 8412 Dihedral : 5.302 52.539 6654 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.22 % Allowed : 17.88 % Favored : 79.89 % 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: 1.48 (0.11), residues: 5994 helix: 2.24 (0.10), residues: 2228 sheet: 0.51 (0.13), residues: 1516 loop : 0.12 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 100 HIS 0.008 0.001 HIS A 209 PHE 0.026 0.002 PHE Y 142 TYR 0.018 0.002 TYR C 20 ARG 0.004 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 785 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 671 time to evaluate : 5.817 Fit side-chains REVERT: A 120 ARG cc_start: 0.8163 (tpp80) cc_final: 0.7760 (tpt90) REVERT: B 4 ARG cc_start: 0.7200 (mpt180) cc_final: 0.5977 (pmt170) REVERT: C 175 LEU cc_start: 0.8526 (mm) cc_final: 0.8234 (mt) REVERT: C 231 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7646 (mppt) REVERT: D 41 CYS cc_start: 0.6181 (OUTLIER) cc_final: 0.5870 (p) REVERT: D 55 GLN cc_start: 0.8938 (mt0) cc_final: 0.8724 (mm-40) REVERT: D 142 ASP cc_start: 0.7335 (t0) cc_final: 0.6479 (m-30) REVERT: D 177 LYS cc_start: 0.6912 (mttm) cc_final: 0.6609 (mttp) REVERT: E 32 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7801 (mttm) REVERT: E 188 HIS cc_start: 0.7542 (p90) cc_final: 0.7138 (p90) REVERT: E 197 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: F 30 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7218 (mmmt) REVERT: F 31 GLN cc_start: 0.7745 (mp10) cc_final: 0.7432 (mm110) REVERT: F 61 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7447 (tptp) REVERT: F 106 GLU cc_start: 0.8055 (mp0) cc_final: 0.7826 (mp0) REVERT: G 191 GLU cc_start: 0.7325 (tp30) cc_final: 0.7097 (tp30) REVERT: G 195 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: G 205 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: I 164 MET cc_start: 0.9031 (tpp) cc_final: 0.8793 (tpp) REVERT: K 7 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8658 (tp) REVERT: K 49 GLU cc_start: 0.7263 (tp30) cc_final: 0.6835 (mm-30) REVERT: L 92 ASP cc_start: 0.8645 (p0) cc_final: 0.8434 (p0) REVERT: L 172 MET cc_start: 0.5646 (ppp) cc_final: 0.5198 (tmm) REVERT: L 258 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7614 (m-30) REVERT: N 102 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8146 (mmpt) REVERT: N 140 LYS cc_start: 0.7196 (mtpm) cc_final: 0.6907 (mtpt) REVERT: O 120 ARG cc_start: 0.8119 (tpp80) cc_final: 0.7737 (tpt90) REVERT: P 181 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7782 (p0) REVERT: Q 231 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7764 (mtmt) REVERT: R 142 ASP cc_start: 0.7181 (OUTLIER) cc_final: 0.6965 (t0) REVERT: S 197 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7210 (mm-30) REVERT: S 229 LYS cc_start: 0.8028 (mmpt) cc_final: 0.7453 (mtmm) REVERT: T 9 ASP cc_start: 0.7052 (OUTLIER) cc_final: 0.6806 (m-30) REVERT: T 61 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7446 (tptp) REVERT: T 86 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8330 (t0) REVERT: U 195 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8533 (mm-40) REVERT: Y 7 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8661 (tp) REVERT: Z 172 MET cc_start: 0.5898 (ppp) cc_final: 0.5426 (tmm) REVERT: Z 258 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: b 102 LYS cc_start: 0.8513 (mtmt) cc_final: 0.8128 (mmpt) REVERT: b 140 LYS cc_start: 0.7124 (mtpm) cc_final: 0.6811 (mtpt) outliers start: 114 outliers final: 81 residues processed: 749 average time/residue: 1.7985 time to fit residues: 1665.2715 Evaluate side-chains 761 residues out of total 5128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 663 time to evaluate : 5.476 ------------------------------------------------------------------------------- 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 235 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 195 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 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 76 CYS Chi-restraints excluded: chain E residue 154 GLN 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 F residue 173 GLU Chi-restraints excluded: chain F residue 200 SER 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 206 ASP Chi-restraints excluded: chain G residue 210 LYS 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 J residue 22 VAL Chi-restraints excluded: chain J residue 67 MET 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 200 ASP Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 258 ASP Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 129 THR 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 235 THR Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 195 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 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 142 ASP Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 154 GLN 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 T residue 173 GLU Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain U residue 206 ASP 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 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 200 ASP Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain Z residue 258 ASP Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 173 SER Chi-restraints excluded: chain b residue 208 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 291 optimal weight: 3.9990 chunk 378 optimal weight: 7.9990 chunk 507 optimal weight: 0.4980 chunk 145 optimal weight: 7.9990 chunk 438 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 476 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 489 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 ASN ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN H 88 GLN I 115 HIS ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 185 ASN O 37 GLN Q 156 ASN ** S 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 69 ASN a 100 ASN a 114 GLN a 185 ASN b 136 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.145525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115330 restraints weight = 48139.699| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.83 r_work: 0.3075 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1422 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= 0.414 Angle : 0.652 10.121 65444 Z= 0.350 Chirality : 0.049 0.228 7392 Planarity : 0.005 0.051 8412 Dihedral : 5.718 54.108 6654 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.46 % Allowed : 17.82 % Favored : 79.72 % 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: 1.22 (0.10), residues: 5994 helix: 1.90 (0.10), residues: 2218 sheet: 0.44 (0.13), residues: 1530 loop : 0.08 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 179 HIS 0.015 0.002 HIS O 209 PHE 0.036 0.003 PHE Y 142 TYR 0.024 0.003 TYR C 20 ARG 0.005 0.001 ARG D 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22690.28 seconds wall clock time: 400 minutes 10.26 seconds (24010.26 seconds total)