Starting phenix.real_space_refine on Tue Mar 26 00:54:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6f_29765/03_2024/8g6f_29765_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6f_29765/03_2024/8g6f_29765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6f_29765/03_2024/8g6f_29765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6f_29765/03_2024/8g6f_29765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6f_29765/03_2024/8g6f_29765_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6f_29765/03_2024/8g6f_29765_updated.pdb" } resolution = 2.58 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= 0.013 sd= 0.118 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 286 5.16 5 C 33002 2.51 5 N 8627 2.21 5 O 10479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "K PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 235": "OD1" <-> "OD2" Residue "T PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 206": "OE1" <-> "OE2" Residue "a TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 52394 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2006 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 4, 'TRANS': 248} Chain: "B" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1817 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "C" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1946 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 5, 'TRANS': 237} Chain: "D" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1870 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 7, 'TRANS': 228} Chain: "E" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1829 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Chain: "F" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1897 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "G" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2025 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 5, 'TRANS': 241} Chain: "H" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1950 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 1, 'TRANS': 239} Chain breaks: 2 Chain: "I" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1693 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 209} Chain: "J" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1661 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1613 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "L" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1662 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 1, 'TRANS': 209} Chain: "M" Number of atoms: 1725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 215, 1713 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 5, 'TRANS': 209} Conformer: "B" Number of residues, atoms: 215, 1713 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 5, 'TRANS': 209} bond proxies already assigned to first conformer: 1732 Chain: "N" Number of atoms: 2105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 2094 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 256, 2094 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 1 bond proxies already assigned to first conformer: 2128 Chain: "O" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2006 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 4, 'TRANS': 248} Chain: "P" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1817 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "Q" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1946 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 5, 'TRANS': 237} Chain: "R" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1870 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 7, 'TRANS': 228} Chain: "S" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1829 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Chain: "T" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1897 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "U" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2025 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 5, 'TRANS': 241} Chain: "V" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1950 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 1, 'TRANS': 239} Chain breaks: 2 Chain: "W" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1693 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 209} Chain: "X" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1662 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 1 Chain: "Y" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1613 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "Z" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1662 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 1, 'TRANS': 209} Chain: "a" Number of atoms: 1725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 215, 1713 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 5, 'TRANS': 209} Conformer: "B" Number of residues, atoms: 215, 1713 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 5, 'TRANS': 209} bond proxies already assigned to first conformer: 1732 Chain: "b" Number of atoms: 2105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 2094 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 256, 2094 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 1 bond proxies already assigned to first conformer: 2128 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'7F1': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'7F1': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'7F1': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'7F1': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "F" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "L" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "N" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "O" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "P" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "Q" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "S" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "T" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "U" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "X" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "Y" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "a" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ATYR M 158 " occ=0.49 ... (22 atoms not shown) pdb=" OH BTYR M 158 " occ=0.51 residue: pdb=" N AARG N 211 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG N 211 " occ=0.52 residue: pdb=" N ATYR a 158 " occ=0.49 ... (22 atoms not shown) pdb=" OH BTYR a 158 " occ=0.51 residue: pdb=" N AARG b 211 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG b 211 " occ=0.52 Time building chain proxies: 29.27, per 1000 atoms: 0.56 Number of scatterers: 52394 At special positions: 0 Unit cell: (182.988, 186.3, 138.276, 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 286 16.00 O 10479 8.00 N 8627 7.00 C 33002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.51 Conformation dependent library (CDL) restraints added in 10.6 seconds 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12152 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 70 sheets defined 35.7% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.95 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 removed outlier: 3.657A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 111 Processing helix chain 'A' and resid 117 through 133 removed outlier: 3.837A pdb=" N VAL A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 Processing helix chain 'A' and resid 201 through 220 Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'B' and resid 20 through 31 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 80 through 101 Processing helix chain 'B' and resid 107 through 122 removed outlier: 3.696A pdb=" N PHE B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 177 removed outlier: 3.652A pdb=" N ARG B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 198 Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 19 through 30 Processing helix chain 'C' and resid 80 through 101 Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 185 through 200 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 229 through 242 Processing helix chain 'D' and resid 17 through 27 Processing helix chain 'D' and resid 77 through 98 Processing helix chain 'D' and resid 104 through 120 Processing helix chain 'D' and resid 165 through 175 Processing helix chain 'D' and resid 182 through 194 Processing helix chain 'D' and resid 219 through 236 Processing helix chain 'E' and resid 22 through 32 removed outlier: 3.954A pdb=" N LYS E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 82 through 103 Processing helix chain 'E' and resid 109 through 120 Processing helix chain 'E' and resid 122 through 124 No H-bonds generated for 'chain 'E' and resid 122 through 124' Processing helix chain 'E' and resid 176 through 186 Processing helix chain 'E' and resid 193 through 207 Processing helix chain 'E' and resid 234 through 243 Processing helix chain 'F' and resid 20 through 27 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 78 through 99 Processing helix chain 'F' and resid 105 through 120 removed outlier: 3.853A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR F 120 " --> pdb=" O TYR F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 178 removed outlier: 5.664A pdb=" N HIS F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 197 Processing helix chain 'F' and resid 225 through 240 Processing helix chain 'G' and resid 22 through 32 Processing helix chain 'G' and resid 53 through 55 No H-bonds generated for 'chain 'G' and resid 53 through 55' Processing helix chain 'G' and resid 84 through 105 Processing helix chain 'G' and resid 111 through 126 removed outlier: 4.038A pdb=" N TYR G 125 " --> pdb=" O TYR G 121 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 181 removed outlier: 3.683A pdb=" N LYS G 181 " --> pdb=" O THR G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 186 No H-bonds generated for 'chain 'G' and resid 184 through 186' Processing helix chain 'G' and resid 189 through 203 removed outlier: 4.282A pdb=" N GLU G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 250 Proline residue: G 239 - end of helix Processing helix chain 'H' and resid 49 through 70 Processing helix chain 'H' and resid 94 through 98 Processing helix chain 'H' and resid 129 through 142 Processing helix chain 'H' and resid 185 through 196 removed outlier: 5.146A pdb=" N SER H 191 " --> pdb=" O TYR H 188 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU H 193 " --> pdb=" O GLN H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 220 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 90 Processing helix chain 'I' and resid 131 through 141 Processing helix chain 'I' and resid 148 through 165 Processing helix chain 'J' and resid 3 through 8 removed outlier: 4.247A pdb=" N ASN J 8 " --> pdb=" O ILE J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 80 Processing helix chain 'J' and resid 86 through 100 removed outlier: 3.837A pdb=" N ASN J 100 " --> pdb=" O ILE J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 166 Processing helix chain 'J' and resid 173 through 190 removed outlier: 3.899A pdb=" N ARG J 190 " --> pdb=" O SER J 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 72 Processing helix chain 'K' and resid 78 through 93 Processing helix chain 'K' and resid 136 through 146 removed outlier: 5.147A pdb=" N ALA K 141 " --> pdb=" O TYR K 137 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 169 Processing helix chain 'L' and resid 49 through 70 Processing helix chain 'L' and resid 76 through 90 removed outlier: 3.705A pdb=" N TYR L 90 " --> pdb=" O ILE L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 142 removed outlier: 3.524A pdb=" N ALA L 142 " --> pdb=" O ILE L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 166 Processing helix chain 'L' and resid 193 through 200 removed outlier: 3.584A pdb=" N TYR L 198 " --> pdb=" O PHE L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 107 Processing helix chain 'M' and resid 113 through 127 removed outlier: 4.058A pdb=" N ARG M 127 " --> pdb=" O ILE M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 181 Proline residue: M 175 - end of helix Processing helix chain 'M' and resid 195 through 212 removed outlier: 3.698A pdb=" N ARG M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 78 Processing helix chain 'N' and resid 82 through 84 No H-bonds generated for 'chain 'N' and resid 82 through 84' Processing helix chain 'N' and resid 88 through 104 Processing helix chain 'N' and resid 156 through 158 No H-bonds generated for 'chain 'N' and resid 156 through 158' Processing helix chain 'N' and resid 179 through 192 removed outlier: 5.733A pdb=" N ALA N 185 " --> pdb=" O ARG N 182 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU N 186 " --> pdb=" O TYR N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 216 Processing helix chain 'N' and resid 255 through 257 No H-bonds generated for 'chain 'N' and resid 255 through 257' Processing helix chain 'O' and resid 23 through 35 removed outlier: 3.680A pdb=" N THR O 35 " --> pdb=" O ALA O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 111 Processing helix chain 'O' and resid 117 through 133 removed outlier: 3.872A pdb=" N VAL O 130 " --> pdb=" O ASP O 126 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR O 131 " --> pdb=" O LYS O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 194 Processing helix chain 'O' and resid 201 through 220 Processing helix chain 'O' and resid 226 through 228 No H-bonds generated for 'chain 'O' and resid 226 through 228' Processing helix chain 'O' and resid 246 through 258 Processing helix chain 'P' and resid 20 through 31 Processing helix chain 'P' and resid 80 through 101 Processing helix chain 'P' and resid 107 through 122 removed outlier: 3.701A pdb=" N PHE P 121 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR P 122 " --> pdb=" O VAL P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 177 removed outlier: 3.636A pdb=" N ARG P 177 " --> pdb=" O PHE P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 198 Processing helix chain 'P' and resid 224 through 231 Processing helix chain 'Q' and resid 3 through 5 No H-bonds generated for 'chain 'Q' and resid 3 through 5' Processing helix chain 'Q' and resid 19 through 30 Processing helix chain 'Q' and resid 80 through 101 Processing helix chain 'Q' and resid 107 through 123 Processing helix chain 'Q' and resid 168 through 178 Processing helix chain 'Q' and resid 185 through 200 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 229 through 242 Processing helix chain 'R' and resid 17 through 28 Processing helix chain 'R' and resid 77 through 98 Processing helix chain 'R' and resid 104 through 120 Processing helix chain 'R' and resid 165 through 175 Processing helix chain 'R' and resid 182 through 194 Processing helix chain 'R' and resid 201 through 203 No H-bonds generated for 'chain 'R' and resid 201 through 203' Processing helix chain 'R' and resid 219 through 236 Processing helix chain 'S' and resid 22 through 32 removed outlier: 3.929A pdb=" N LYS S 32 " --> pdb=" O LEU S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 63 No H-bonds generated for 'chain 'S' and resid 61 through 63' Processing helix chain 'S' and resid 82 through 103 Processing helix chain 'S' and resid 109 through 120 Processing helix chain 'S' and resid 122 through 124 No H-bonds generated for 'chain 'S' and resid 122 through 124' Processing helix chain 'S' and resid 176 through 186 Processing helix chain 'S' and resid 193 through 207 Processing helix chain 'S' and resid 234 through 243 Processing helix chain 'T' and resid 20 through 27 Processing helix chain 'T' and resid 29 through 31 No H-bonds generated for 'chain 'T' and resid 29 through 31' Processing helix chain 'T' and resid 78 through 99 Processing helix chain 'T' and resid 105 through 120 removed outlier: 3.853A pdb=" N ASN T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR T 120 " --> pdb=" O TYR T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 165 through 178 removed outlier: 5.673A pdb=" N HIS T 176 " --> pdb=" O GLU T 172 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU T 177 " --> pdb=" O LYS T 173 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE T 178 " --> pdb=" O ASN T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 197 Processing helix chain 'T' and resid 225 through 240 Processing helix chain 'U' and resid 22 through 32 Processing helix chain 'U' and resid 53 through 55 No H-bonds generated for 'chain 'U' and resid 53 through 55' Processing helix chain 'U' and resid 84 through 105 Processing helix chain 'U' and resid 111 through 126 removed outlier: 4.058A pdb=" N TYR U 125 " --> pdb=" O TYR U 121 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR U 126 " --> pdb=" O ILE U 122 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 181 removed outlier: 3.721A pdb=" N LYS U 181 " --> pdb=" O THR U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 184 through 186 No H-bonds generated for 'chain 'U' and resid 184 through 186' Processing helix chain 'U' and resid 189 through 203 removed outlier: 4.263A pdb=" N GLU U 194 " --> pdb=" O ARG U 190 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP U 195 " --> pdb=" O ASP U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 234 through 250 Proline residue: U 239 - end of helix Processing helix chain 'V' and resid 49 through 69 Processing helix chain 'V' and resid 94 through 98 Processing helix chain 'V' and resid 129 through 142 Processing helix chain 'V' and resid 185 through 196 removed outlier: 5.184A pdb=" N SER V 191 " --> pdb=" O TYR V 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 203 through 220 Processing helix chain 'W' and resid 49 through 70 Processing helix chain 'W' and resid 76 through 90 Processing helix chain 'W' and resid 131 through 141 Processing helix chain 'W' and resid 148 through 165 Processing helix chain 'X' and resid 3 through 8 removed outlier: 4.289A pdb=" N ASN X 8 " --> pdb=" O ILE X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 80 Processing helix chain 'X' and resid 86 through 100 removed outlier: 3.844A pdb=" N ASN X 100 " --> pdb=" O ILE X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 156 through 166 Processing helix chain 'X' and resid 173 through 190 removed outlier: 3.893A pdb=" N ARG X 190 " --> pdb=" O SER X 186 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 72 Processing helix chain 'Y' and resid 78 through 93 Processing helix chain 'Y' and resid 136 through 146 removed outlier: 5.150A pdb=" N ALA Y 141 " --> pdb=" O TYR Y 137 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 169 Processing helix chain 'Z' and resid 49 through 70 Processing helix chain 'Z' and resid 76 through 90 removed outlier: 3.702A pdb=" N TYR Z 90 " --> pdb=" O ILE Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 142 removed outlier: 3.521A pdb=" N ALA Z 142 " --> pdb=" O ILE Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 149 through 166 Processing helix chain 'Z' and resid 193 through 200 Processing helix chain 'a' and resid 86 through 107 Processing helix chain 'a' and resid 113 through 127 removed outlier: 3.981A pdb=" N ARG a 127 " --> pdb=" O ILE a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 181 Proline residue: a 175 - end of helix Processing helix chain 'a' and resid 195 through 212 removed outlier: 3.692A pdb=" N ARG a 212 " --> pdb=" O SER a 208 " (cutoff:3.500A) Processing helix chain 'b' and resid 58 through 78 Processing helix chain 'b' and resid 82 through 84 No H-bonds generated for 'chain 'b' and resid 82 through 84' Processing helix chain 'b' and resid 88 through 105 Processing helix chain 'b' and resid 156 through 158 No H-bonds generated for 'chain 'b' and resid 156 through 158' Processing helix chain 'b' and resid 179 through 182 Processing helix chain 'b' and resid 184 through 192 Processing helix chain 'b' and resid 199 through 216 Processing helix chain 'b' and resid 255 through 257 No H-bonds generated for 'chain 'b' and resid 255 through 257' Processing sheet with id= A, first strand: chain 'A' and resid 171 through 174 Processing sheet with id= B, first strand: chain 'A' and resid 75 through 77 Processing sheet with id= C, first strand: chain 'B' and resid 160 through 163 Processing sheet with id= D, first strand: chain 'B' and resid 155 through 157 removed outlier: 6.587A pdb=" N ILE B 74 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLN B 67 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 161 through 164 Processing sheet with id= F, first strand: chain 'C' and resid 156 through 158 removed outlier: 6.479A pdb=" N CYS C 74 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LYS C 67 " --> pdb=" O CYS C 74 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL C 76 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 158 through 162 removed outlier: 5.472A pdb=" N CYS D 31 " --> pdb=" O GLU D 46 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 62 through 64 removed outlier: 4.216A pdb=" N ILE D 144 " --> pdb=" O TRP D 156 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 169 through 172 Processing sheet with id= J, first strand: chain 'E' and resid 164 through 166 removed outlier: 6.594A pdb=" N CYS E 76 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N SER E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N MET E 78 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU E 67 " --> pdb=" O MET E 78 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 157 through 160 Processing sheet with id= L, first strand: chain 'F' and resid 152 through 155 removed outlier: 4.087A pdb=" N ILE F 143 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE F 70 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE F 72 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS F 65 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N MET F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE F 63 " --> pdb=" O MET F 74 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 165 through 168 Processing sheet with id= N, first strand: chain 'G' and resid 69 through 71 removed outlier: 3.720A pdb=" N ILE G 151 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 179 through 182 removed outlier: 3.561A pdb=" N GLY H 11 " --> pdb=" O TYR H 8 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE H 237 " --> pdb=" O THR H 234 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 172 through 176 removed outlier: 3.727A pdb=" N SER H 172 " --> pdb=" O ASN H 168 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU H 164 " --> pdb=" O LYS H 176 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL H 43 " --> pdb=" O ARG H 36 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ARG H 36 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ARG H 45 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE H 34 " --> pdb=" O ARG H 45 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.336A pdb=" N SER H 22 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE H 26 " --> pdb=" O SER H 22 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 124 through 128 Processing sheet with id= S, first strand: chain 'I' and resid 119 through 121 removed outlier: 6.487A pdb=" N CYS I 43 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TYR I 36 " --> pdb=" O CYS I 43 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLY I 45 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU I 34 " --> pdb=" O GLY I 45 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.106A pdb=" N GLU I 22 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N VAL I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 149 through 153 removed outlier: 5.390A pdb=" N CYS J 11 " --> pdb=" O ASP J 26 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA J 198 " --> pdb=" O LEU J 213 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 143 through 146 removed outlier: 3.793A pdb=" N LEU J 134 " --> pdb=" O THR J 146 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER J 56 " --> pdb=" O ASN J 108 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL J 53 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS J 46 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU J 55 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ILE J 44 " --> pdb=" O LEU J 55 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 29 through 31 removed outlier: 6.726A pdb=" N ALA J 31 " --> pdb=" O THR J 36 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N THR J 36 " --> pdb=" O ALA J 31 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 129 through 132 Processing sheet with id= Y, first strand: chain 'K' and resid 36 through 39 Processing sheet with id= Z, first strand: chain 'K' and resid 21 through 23 removed outlier: 6.476A pdb=" N ASN K 23 " --> pdb=" O LYS K 27 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS K 27 " --> pdb=" O ASN K 23 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 125 through 128 removed outlier: 6.797A pdb=" N HIS L 178 " --> pdb=" O LYS L 186 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS L 186 " --> pdb=" O HIS L 178 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N HIS L 180 " --> pdb=" O TYR L 184 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR L 184 " --> pdb=" O HIS L 180 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 120 through 122 removed outlier: 3.687A pdb=" N ILE L 41 " --> pdb=" O ASN L 38 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN L 38 " --> pdb=" O ILE L 41 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY L 43 " --> pdb=" O GLU L 36 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU L 36 " --> pdb=" O GLY L 43 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N MET L 45 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE L 34 " --> pdb=" O MET L 45 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.392A pdb=" N MET L 22 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE L 26 " --> pdb=" O MET L 22 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 163 through 167 removed outlier: 5.014A pdb=" N THR M 39 " --> pdb=" O ASP M 54 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 157 through 160 removed outlier: 4.220A pdb=" N LEU M 149 " --> pdb=" O GLU M 160 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE M 80 " --> pdb=" O LYS M 73 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LYS M 73 " --> pdb=" O ILE M 80 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N SER M 82 " --> pdb=" O ILE M 71 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE M 71 " --> pdb=" O SER M 82 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.221A pdb=" N LEU M 59 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 7 through 9 Processing sheet with id= AH, first strand: chain 'N' and resid 175 through 177 Processing sheet with id= AI, first strand: chain 'N' and resid 170 through 172 removed outlier: 6.531A pdb=" N MET N 52 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LYS N 45 " --> pdb=" O MET N 52 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N PHE N 54 " --> pdb=" O ILE N 43 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE N 43 " --> pdb=" O PHE N 54 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'O' and resid 171 through 174 Processing sheet with id= AK, first strand: chain 'O' and resid 75 through 77 Processing sheet with id= AL, first strand: chain 'P' and resid 160 through 163 Processing sheet with id= AM, first strand: chain 'P' and resid 155 through 157 removed outlier: 6.599A pdb=" N ILE P 74 " --> pdb=" O GLN P 67 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLN P 67 " --> pdb=" O ILE P 74 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'Q' and resid 161 through 164 Processing sheet with id= AO, first strand: chain 'Q' and resid 156 through 158 removed outlier: 6.478A pdb=" N CYS Q 74 " --> pdb=" O LYS Q 67 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LYS Q 67 " --> pdb=" O CYS Q 74 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL Q 76 " --> pdb=" O ILE Q 65 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE Q 65 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'R' and resid 158 through 161 Processing sheet with id= AQ, first strand: chain 'R' and resid 62 through 64 removed outlier: 4.189A pdb=" N ILE R 144 " --> pdb=" O TRP R 156 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'S' and resid 169 through 172 Processing sheet with id= AS, first strand: chain 'S' and resid 164 through 166 removed outlier: 6.601A pdb=" N CYS S 76 " --> pdb=" O SER S 69 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SER S 69 " --> pdb=" O CYS S 76 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N MET S 78 " --> pdb=" O LEU S 67 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU S 67 " --> pdb=" O MET S 78 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'T' and resid 157 through 160 Processing sheet with id= AU, first strand: chain 'T' and resid 152 through 155 removed outlier: 4.095A pdb=" N ILE T 143 " --> pdb=" O TYR T 155 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE T 70 " --> pdb=" O ASP T 67 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE T 72 " --> pdb=" O LYS T 65 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYS T 65 " --> pdb=" O ILE T 72 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N MET T 74 " --> pdb=" O ILE T 63 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE T 63 " --> pdb=" O MET T 74 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'U' and resid 165 through 168 Processing sheet with id= AW, first strand: chain 'U' and resid 69 through 71 removed outlier: 3.725A pdb=" N ILE U 151 " --> pdb=" O TYR U 163 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'V' and resid 179 through 182 removed outlier: 3.563A pdb=" N GLY V 11 " --> pdb=" O TYR V 8 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE V 237 " --> pdb=" O THR V 234 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'V' and resid 172 through 176 removed outlier: 3.728A pdb=" N SER V 172 " --> pdb=" O ASN V 168 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU V 164 " --> pdb=" O LYS V 176 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL V 43 " --> pdb=" O ARG V 36 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ARG V 36 " --> pdb=" O VAL V 43 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ARG V 45 " --> pdb=" O ILE V 34 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE V 34 " --> pdb=" O ARG V 45 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.337A pdb=" N SER V 22 " --> pdb=" O ILE V 26 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE V 26 " --> pdb=" O SER V 22 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'W' and resid 124 through 128 Processing sheet with id= BB, first strand: chain 'W' and resid 119 through 121 removed outlier: 6.477A pdb=" N CYS W 43 " --> pdb=" O TYR W 36 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TYR W 36 " --> pdb=" O CYS W 43 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLY W 45 " --> pdb=" O LEU W 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU W 34 " --> pdb=" O GLY W 45 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'W' and resid 20 through 22 removed outlier: 6.104A pdb=" N GLU W 22 " --> pdb=" O VAL W 26 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL W 26 " --> pdb=" O GLU W 22 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'X' and resid 149 through 153 removed outlier: 5.406A pdb=" N CYS X 11 " --> pdb=" O ASP X 26 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA X 198 " --> pdb=" O LEU X 213 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'X' and resid 143 through 146 removed outlier: 3.790A pdb=" N LEU X 134 " --> pdb=" O THR X 146 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER X 56 " --> pdb=" O ASN X 108 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL X 53 " --> pdb=" O LYS X 46 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LYS X 46 " --> pdb=" O VAL X 53 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU X 55 " --> pdb=" O ILE X 44 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE X 44 " --> pdb=" O LEU X 55 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'X' and resid 29 through 31 removed outlier: 6.711A pdb=" N ALA X 31 " --> pdb=" O THR X 36 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N THR X 36 " --> pdb=" O ALA X 31 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'Y' and resid 129 through 132 Processing sheet with id= BH, first strand: chain 'Y' and resid 36 through 39 Processing sheet with id= BI, first strand: chain 'Y' and resid 21 through 23 removed outlier: 6.494A pdb=" N ASN Y 23 " --> pdb=" O LYS Y 27 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LYS Y 27 " --> pdb=" O ASN Y 23 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'Z' and resid 125 through 128 removed outlier: 6.789A pdb=" N HIS Z 178 " --> pdb=" O LYS Z 186 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS Z 186 " --> pdb=" O HIS Z 178 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N HIS Z 180 " --> pdb=" O TYR Z 184 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR Z 184 " --> pdb=" O HIS Z 180 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'Z' and resid 120 through 122 removed outlier: 3.732A pdb=" N ILE Z 41 " --> pdb=" O ASN Z 38 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN Z 38 " --> pdb=" O ILE Z 41 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY Z 43 " --> pdb=" O GLU Z 36 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLU Z 36 " --> pdb=" O GLY Z 43 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N MET Z 45 " --> pdb=" O ILE Z 34 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE Z 34 " --> pdb=" O MET Z 45 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'Z' and resid 20 through 22 removed outlier: 6.383A pdb=" N MET Z 22 " --> pdb=" O ILE Z 26 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE Z 26 " --> pdb=" O MET Z 22 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'a' and resid 163 through 167 removed outlier: 4.985A pdb=" N THR a 39 " --> pdb=" O ASP a 54 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'a' and resid 157 through 160 removed outlier: 4.224A pdb=" N LEU a 149 " --> pdb=" O GLU a 160 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE a 80 " --> pdb=" O LYS a 73 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LYS a 73 " --> pdb=" O ILE a 80 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER a 82 " --> pdb=" O ILE a 71 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE a 71 " --> pdb=" O SER a 82 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'a' and resid 57 through 59 removed outlier: 6.184A pdb=" N LEU a 59 " --> pdb=" O ILE a 63 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'b' and resid 7 through 9 Processing sheet with id= BQ, first strand: chain 'b' and resid 175 through 177 Processing sheet with id= BR, first strand: chain 'b' and resid 170 through 172 removed outlier: 6.523A pdb=" N MET b 52 " --> pdb=" O LYS b 45 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS b 45 " --> pdb=" O MET b 52 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N PHE b 54 " --> pdb=" O ILE b 43 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE b 43 " --> pdb=" O PHE b 54 " (cutoff:3.500A) 2632 hydrogen bonds defined for protein. 7535 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: 23.43 Time building geometry restraints manager: 21.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16657 1.34 - 1.45: 7669 1.45 - 1.57: 28027 1.57 - 1.69: 0 1.69 - 1.81: 410 Bond restraints: 52763 Sorted by residual: bond pdb=" N GLU S 159 " pdb=" CA GLU S 159 " ideal model delta sigma weight residual 1.453 1.485 -0.032 8.30e-03 1.45e+04 1.46e+01 bond pdb=" C03 7F1 I 301 " pdb=" S01 7F1 I 301 " ideal model delta sigma weight residual 1.760 1.696 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C03 7F1 W 301 " pdb=" S01 7F1 W 301 " ideal model delta sigma weight residual 1.760 1.697 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C03 7F1 L 301 " pdb=" S01 7F1 L 301 " ideal model delta sigma weight residual 1.760 1.702 0.058 2.00e-02 2.50e+03 8.41e+00 bond pdb=" C03 7F1 Z 301 " pdb=" S01 7F1 Z 301 " ideal model delta sigma weight residual 1.760 1.704 0.056 2.00e-02 2.50e+03 7.95e+00 ... (remaining 52758 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.53: 801 106.53 - 113.51: 29102 113.51 - 120.49: 20747 120.49 - 127.48: 20280 127.48 - 134.46: 335 Bond angle restraints: 71265 Sorted by residual: angle pdb=" N SER a 154 " pdb=" CA SER a 154 " pdb=" CB SER a 154 " ideal model delta sigma weight residual 114.17 109.83 4.34 1.14e+00 7.69e-01 1.45e+01 angle pdb=" N SER M 154 " pdb=" CA SER M 154 " pdb=" CB SER M 154 " ideal model delta sigma weight residual 114.17 109.92 4.25 1.14e+00 7.69e-01 1.39e+01 angle pdb=" C PHE a 135 " pdb=" N ASN a 136 " pdb=" CA ASN a 136 " ideal model delta sigma weight residual 122.94 117.39 5.55 1.50e+00 4.44e-01 1.37e+01 angle pdb=" C PHE M 135 " pdb=" N ASN M 136 " pdb=" CA ASN M 136 " ideal model delta sigma weight residual 122.94 117.40 5.54 1.50e+00 4.44e-01 1.37e+01 angle pdb=" N ASN M 136 " pdb=" CA ASN M 136 " pdb=" C ASN M 136 " ideal model delta sigma weight residual 109.40 115.42 -6.02 1.63e+00 3.76e-01 1.36e+01 ... (remaining 71260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 27832 17.95 - 35.90: 3074 35.90 - 53.85: 645 53.85 - 71.80: 137 71.80 - 89.74: 74 Dihedral angle restraints: 31762 sinusoidal: 12760 harmonic: 19002 Sorted by residual: dihedral pdb=" CA TYR X 137 " pdb=" C TYR X 137 " pdb=" N ASP X 138 " pdb=" CA ASP X 138 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TYR J 137 " pdb=" C TYR J 137 " pdb=" N ASP J 138 " pdb=" CA ASP J 138 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP b 191 " pdb=" C ASP b 191 " pdb=" N HIS b 192 " pdb=" CA HIS b 192 " ideal model delta harmonic sigma weight residual 180.00 -160.46 -19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 31759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 5209 0.035 - 0.070: 1937 0.070 - 0.105: 539 0.105 - 0.140: 248 0.140 - 0.175: 17 Chirality restraints: 7950 Sorted by residual: chirality pdb=" CA GLU O 230 " pdb=" N GLU O 230 " pdb=" C GLU O 230 " pdb=" CB GLU O 230 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA GLU A 230 " pdb=" N GLU A 230 " pdb=" C GLU A 230 " pdb=" CB GLU A 230 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA VAL Z 14 " pdb=" N VAL Z 14 " pdb=" C VAL Z 14 " pdb=" CB VAL Z 14 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 7947 not shown) Planarity restraints: 9078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 7F1 L 301 " -0.120 2.00e-02 2.50e+03 2.60e-01 6.77e+02 pdb=" C02 7F1 L 301 " 0.370 2.00e-02 2.50e+03 pdb=" C03 7F1 L 301 " -0.334 2.00e-02 2.50e+03 pdb=" S01 7F1 L 301 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7F1 Z 301 " -0.118 2.00e-02 2.50e+03 2.59e-01 6.71e+02 pdb=" C02 7F1 Z 301 " 0.367 2.00e-02 2.50e+03 pdb=" C03 7F1 Z 301 " -0.335 2.00e-02 2.50e+03 pdb=" S01 7F1 Z 301 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7F1 W 301 " 0.119 2.00e-02 2.50e+03 2.57e-01 6.60e+02 pdb=" C02 7F1 W 301 " -0.366 2.00e-02 2.50e+03 pdb=" C03 7F1 W 301 " 0.330 2.00e-02 2.50e+03 pdb=" S01 7F1 W 301 " -0.083 2.00e-02 2.50e+03 ... (remaining 9075 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4684 2.74 - 3.28: 50872 3.28 - 3.82: 92659 3.82 - 4.36: 119493 4.36 - 4.90: 197974 Nonbonded interactions: 465682 Sorted by model distance: nonbonded pdb=" O ASP a 153 " pdb=" OG SER a 154 " model vdw 2.197 2.440 nonbonded pdb=" OG SER J 94 " pdb=" O GLY J 141 " model vdw 2.208 2.440 nonbonded pdb=" O LYS b 28 " pdb=" O HOH b 301 " model vdw 2.208 2.440 nonbonded pdb=" OD1 ASP b 84 " pdb=" O HOH b 302 " model vdw 2.212 2.440 nonbonded pdb=" OG SER X 94 " pdb=" O GLY X 141 " model vdw 2.213 2.440 ... (remaining 465677 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' and ((resid 2 and (name CA or name C or name O )) or resid 3 through \ 218)) } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = (chain 'M' and (resid 26 through 157 or resid 159 through 240)) selection = (chain 'a' and (resid 26 through 157 or resid 159 through 240)) } ncs_group { reference = (chain 'N' and (resid 2 through 210 or resid 212 through 265)) selection = (chain 'b' and (resid 2 through 210 or resid 212 through 265)) } 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=0.48 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 11.960 Check model and map are aligned: 0.840 Set scattering table: 0.550 Process input model: 141.540 Find NCS groups from input model: 5.250 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 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 : 0.004 0.064 52763 Z= 0.291 Angle : 0.508 6.536 71265 Z= 0.287 Chirality : 0.043 0.175 7950 Planarity : 0.007 0.260 9078 Dihedral : 16.097 89.745 19610 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.51 % Allowed : 15.58 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.59 (0.10), residues: 6402 helix: 2.48 (0.10), residues: 2407 sheet: 0.70 (0.13), residues: 1542 loop : -0.11 (0.12), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 117 HIS 0.008 0.001 HIS V 61 PHE 0.033 0.002 PHE C 73 TYR 0.026 0.001 TYR a 64 ARG 0.002 0.000 ARG S 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 472 time to evaluate : 4.996 Fit side-chains revert: symmetry clash REVERT: A 179 GLN cc_start: 0.7546 (mp10) cc_final: 0.7241 (tt0) REVERT: C 3 ARG cc_start: 0.7867 (ptp90) cc_final: 0.7628 (ptt90) REVERT: C 8 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.8066 (mtm-85) REVERT: E 239 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7731 (ttp80) REVERT: J 105 TYR cc_start: 0.8900 (m-80) cc_final: 0.8667 (m-80) REVERT: M 239 GLN cc_start: 0.7919 (mt0) cc_final: 0.7652 (mt0) REVERT: O 19 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7932 (p0) REVERT: O 197 GLN cc_start: 0.6057 (pm20) cc_final: 0.5735 (pm20) REVERT: S 227 GLN cc_start: 0.8110 (mt0) cc_final: 0.7857 (mt0) REVERT: T 122 LYS cc_start: 0.8859 (mmtp) cc_final: 0.8420 (mmtt) REVERT: X 105 TYR cc_start: 0.8932 (m-80) cc_final: 0.8675 (m-80) REVERT: a 75 THR cc_start: 0.9119 (m) cc_final: 0.8849 (p) outliers start: 29 outliers final: 12 residues processed: 494 average time/residue: 1.9593 time to fit residues: 1178.4165 Evaluate side-chains 441 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 428 time to evaluate : 6.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain Z residue 84 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 535 optimal weight: 8.9990 chunk 480 optimal weight: 6.9990 chunk 266 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 324 optimal weight: 9.9990 chunk 256 optimal weight: 2.9990 chunk 496 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 chunk 369 optimal weight: 0.9990 chunk 575 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN B 100 GLN F 4 ASN F 165 HIS F 221 GLN H 109 ASN H 245 ASN K 23 ASN M 136 ASN N 135 ASN P 71 HIS R 177 GLN T 165 HIS V 109 ASN V 245 ASN b 19 HIS b 135 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.0530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 52763 Z= 0.335 Angle : 0.543 11.739 71265 Z= 0.295 Chirality : 0.045 0.348 7950 Planarity : 0.004 0.049 9078 Dihedral : 6.501 88.540 7235 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.04 % Allowed : 15.24 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.59 (0.10), residues: 6402 helix: 2.39 (0.10), residues: 2389 sheet: 0.77 (0.13), residues: 1554 loop : -0.04 (0.12), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 117 HIS 0.008 0.001 HIS V 61 PHE 0.032 0.002 PHE Q 73 TYR 0.027 0.002 TYR a 64 ARG 0.008 0.000 ARG P 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 433 time to evaluate : 6.079 Fit side-chains revert: symmetry clash REVERT: C 3 ARG cc_start: 0.7971 (ptp90) cc_final: 0.7615 (ptt90) REVERT: C 8 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.8179 (mtm110) REVERT: D 67 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7807 (pm20) REVERT: D 205 GLU cc_start: 0.7999 (tt0) cc_final: 0.7770 (tt0) REVERT: E 206 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: E 239 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7739 (ttp80) REVERT: F 179 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: F 222 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7919 (mm-30) REVERT: H 41 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8781 (tt) REVERT: H 72 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8757 (mttt) REVERT: I 216 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7771 (mppt) REVERT: M 239 GLN cc_start: 0.7911 (mt0) cc_final: 0.7691 (mt0) REVERT: O 19 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7955 (p0) REVERT: O 197 GLN cc_start: 0.6005 (pm20) cc_final: 0.5671 (pm20) REVERT: R 89 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9132 (tt) REVERT: S 227 GLN cc_start: 0.8194 (mt0) cc_final: 0.7937 (mt0) REVERT: T 122 LYS cc_start: 0.8880 (mmtp) cc_final: 0.8463 (mmmt) REVERT: U 146 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7941 (mtmm) REVERT: V 41 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8833 (tt) REVERT: X 80 GLN cc_start: 0.8283 (tp40) cc_final: 0.7711 (mp10) REVERT: X 105 TYR cc_start: 0.8933 (m-80) cc_final: 0.8689 (m-80) REVERT: Y 111 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8232 (m-30) outliers start: 173 outliers final: 90 residues processed: 567 average time/residue: 1.7538 time to fit residues: 1234.6443 Evaluate side-chains 528 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 426 time to evaluate : 5.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 72 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 181 SER Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 54 ASN Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 181 ASN Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 38 SER Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 231 GLN Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 74 MET Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 197 SER Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain U residue 146 LYS Chi-restraints excluded: chain U residue 203 SER Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 135 THR Chi-restraints excluded: chain X residue 144 CYS Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 165 SER Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 64 ASN Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 111 ASP Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 161 LYS Chi-restraints excluded: chain Z residue 102 SER Chi-restraints excluded: chain Z residue 107 THR Chi-restraints excluded: chain Z residue 192 ASP Chi-restraints excluded: chain b residue 200 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 319 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 479 optimal weight: 4.9990 chunk 392 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 576 optimal weight: 10.0000 chunk 623 optimal weight: 4.9990 chunk 513 optimal weight: 1.9990 chunk 571 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 462 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN B 100 GLN F 165 HIS F 221 GLN H 245 ASN M 136 ASN M 151 ASN N 135 ASN O 59 GLN T 165 HIS V 245 ASN b 135 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.0648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 52763 Z= 0.334 Angle : 0.535 12.265 71265 Z= 0.291 Chirality : 0.045 0.298 7950 Planarity : 0.004 0.050 9078 Dihedral : 6.420 89.824 7230 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.20 % Allowed : 15.67 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.54 (0.10), residues: 6402 helix: 2.29 (0.10), residues: 2383 sheet: 0.80 (0.13), residues: 1558 loop : -0.03 (0.12), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 117 HIS 0.008 0.001 HIS V 61 PHE 0.031 0.002 PHE Q 73 TYR 0.020 0.002 TYR a 64 ARG 0.008 0.000 ARG P 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 433 time to evaluate : 6.165 Fit side-chains REVERT: B 214 TYR cc_start: 0.6277 (OUTLIER) cc_final: 0.5589 (p90) REVERT: C 3 ARG cc_start: 0.7961 (ptp90) cc_final: 0.7580 (ptt90) REVERT: C 8 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8163 (mtm110) REVERT: D 67 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: D 205 GLU cc_start: 0.7982 (tt0) cc_final: 0.7765 (tt0) REVERT: E 206 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: E 239 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7746 (ttp80) REVERT: F 179 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: F 222 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: H 41 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8816 (tt) REVERT: H 72 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8790 (mttt) REVERT: H 123 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8211 (t0) REVERT: J 173 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7817 (pt0) REVERT: K 111 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8215 (m-30) REVERT: M 239 GLN cc_start: 0.7936 (mt0) cc_final: 0.7698 (mt0) REVERT: O 19 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.8010 (p0) REVERT: O 197 GLN cc_start: 0.6064 (pm20) cc_final: 0.5718 (pm20) REVERT: R 89 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9136 (tt) REVERT: S 227 GLN cc_start: 0.8234 (mt0) cc_final: 0.7949 (mt0) REVERT: T 122 LYS cc_start: 0.8887 (mmtp) cc_final: 0.8473 (mmmt) REVERT: U 146 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7929 (mtmm) REVERT: V 41 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8840 (tt) REVERT: X 80 GLN cc_start: 0.8348 (tp40) cc_final: 0.7712 (mp10) outliers start: 182 outliers final: 109 residues processed: 579 average time/residue: 1.7462 time to fit residues: 1253.3544 Evaluate side-chains 543 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 420 time to evaluate : 5.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 72 LYS Chi-restraints excluded: chain H residue 123 ASN Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 173 GLU Chi-restraints excluded: chain J residue 181 SER Chi-restraints excluded: chain K residue 64 ASN Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 54 ASN Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 208 ILE Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 177 GLN Chi-restraints excluded: chain Q residue 181 ASN Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 231 GLN Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 197 SER Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain U residue 146 LYS Chi-restraints excluded: chain U residue 203 SER Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 135 THR Chi-restraints excluded: chain X residue 144 CYS Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 165 SER Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 64 ASN Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 161 LYS Chi-restraints excluded: chain Z residue 102 SER Chi-restraints excluded: chain Z residue 107 THR Chi-restraints excluded: chain Z residue 192 ASP Chi-restraints excluded: chain b residue 52 MET Chi-restraints excluded: chain b residue 197 MET Chi-restraints excluded: chain b residue 200 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 569 optimal weight: 9.9990 chunk 433 optimal weight: 3.9990 chunk 299 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 275 optimal weight: 7.9990 chunk 387 optimal weight: 4.9990 chunk 578 optimal weight: 9.9990 chunk 612 optimal weight: 6.9990 chunk 302 optimal weight: 0.7980 chunk 548 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN B 100 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS H 245 ASN M 194 ASN N 135 ASN T 165 HIS T 218 HIS V 245 ASN b 135 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 52763 Z= 0.231 Angle : 0.488 10.187 71265 Z= 0.268 Chirality : 0.043 0.245 7950 Planarity : 0.003 0.050 9078 Dihedral : 6.256 89.510 7228 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.14 % Allowed : 16.23 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.66 (0.10), residues: 6402 helix: 2.43 (0.10), residues: 2375 sheet: 0.85 (0.13), residues: 1558 loop : -0.01 (0.12), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 117 HIS 0.006 0.001 HIS V 61 PHE 0.025 0.001 PHE C 73 TYR 0.016 0.001 TYR Z 198 ARG 0.009 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 435 time to evaluate : 5.798 Fit side-chains REVERT: A 179 GLN cc_start: 0.7491 (mp10) cc_final: 0.7141 (tt0) REVERT: C 3 ARG cc_start: 0.7987 (ptp90) cc_final: 0.7553 (ptt90) REVERT: D 67 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: D 181 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6852 (mm-30) REVERT: D 205 GLU cc_start: 0.7969 (tt0) cc_final: 0.7750 (tt0) REVERT: E 20 ARG cc_start: 0.8083 (mtt90) cc_final: 0.7847 (mtp85) REVERT: F 3 ARG cc_start: 0.7112 (tpp80) cc_final: 0.6642 (tpp-160) REVERT: F 179 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: F 222 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: H 41 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8799 (tt) REVERT: H 72 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8774 (mttt) REVERT: H 123 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8246 (t0) REVERT: J 173 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7767 (pt0) REVERT: K 2 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8057 (m-30) REVERT: M 239 GLN cc_start: 0.7904 (mt0) cc_final: 0.7660 (mt0) REVERT: O 197 GLN cc_start: 0.6019 (pm20) cc_final: 0.5675 (pm20) REVERT: R 67 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: R 89 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9117 (tt) REVERT: S 227 GLN cc_start: 0.8273 (mt0) cc_final: 0.7934 (mt0) REVERT: T 122 LYS cc_start: 0.8877 (mmtp) cc_final: 0.8431 (mmmt) REVERT: U 204 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7133 (t70) REVERT: V 13 MET cc_start: 0.9313 (mtt) cc_final: 0.9086 (mtt) REVERT: V 41 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8826 (tt) REVERT: V 123 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8262 (t0) REVERT: Y 111 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8176 (m-30) outliers start: 179 outliers final: 100 residues processed: 582 average time/residue: 1.6451 time to fit residues: 1193.2572 Evaluate side-chains 543 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 428 time to evaluate : 5.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 72 LYS Chi-restraints excluded: chain H residue 123 ASN Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 173 GLU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 64 ASN Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 156 GLU Chi-restraints excluded: chain O residue 176 ASN Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 54 ASN Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 181 ASN Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 67 GLU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 197 SER Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 203 SER Chi-restraints excluded: chain U residue 204 ASP Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 123 ASN Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 135 THR Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 165 SER Chi-restraints excluded: chain Y residue 64 ASN Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 111 ASP Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 161 LYS Chi-restraints excluded: chain Z residue 102 SER Chi-restraints excluded: chain Z residue 192 ASP Chi-restraints excluded: chain b residue 52 MET Chi-restraints excluded: chain b residue 197 MET Chi-restraints excluded: chain b residue 200 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 510 optimal weight: 6.9990 chunk 347 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 456 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 522 optimal weight: 5.9990 chunk 423 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 312 optimal weight: 1.9990 chunk 550 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN B 100 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 ASN M 192 ASN N 19 HIS N 135 ASN O 21 ASN O 77 ASN S 195 GLN T 165 HIS ** U 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 245 ASN X 80 GLN b 135 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 52763 Z= 0.334 Angle : 0.535 12.168 71265 Z= 0.291 Chirality : 0.045 0.287 7950 Planarity : 0.004 0.050 9078 Dihedral : 6.275 89.727 7221 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.46 % Allowed : 16.07 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.10), residues: 6402 helix: 2.28 (0.10), residues: 2377 sheet: 0.86 (0.13), residues: 1554 loop : -0.02 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 117 HIS 0.008 0.001 HIS V 61 PHE 0.032 0.002 PHE Q 73 TYR 0.020 0.002 TYR Z 198 ARG 0.008 0.000 ARG P 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 422 time to evaluate : 5.885 Fit side-chains REVERT: B 177 ARG cc_start: 0.8235 (ptp90) cc_final: 0.8020 (ptp90) REVERT: C 3 ARG cc_start: 0.7996 (ptp90) cc_final: 0.7640 (ptt90) REVERT: D 67 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: D 181 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6888 (mm-30) REVERT: D 205 GLU cc_start: 0.7982 (tt0) cc_final: 0.7756 (tt0) REVERT: E 206 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: F 179 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7546 (tm-30) REVERT: F 222 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7928 (mm-30) REVERT: G 146 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7874 (mtmm) REVERT: H 41 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8811 (tt) REVERT: H 72 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8789 (mttt) REVERT: H 123 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8187 (t0) REVERT: J 173 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7816 (pt0) REVERT: K 2 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8065 (m-30) REVERT: K 4 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8963 (mt) REVERT: K 111 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8159 (m-30) REVERT: M 239 GLN cc_start: 0.7904 (mt0) cc_final: 0.7664 (mt0) REVERT: O 197 GLN cc_start: 0.6042 (pm20) cc_final: 0.5692 (pm20) REVERT: P 177 ARG cc_start: 0.8222 (ptp90) cc_final: 0.8022 (ptp90) REVERT: R 89 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9133 (tt) REVERT: S 227 GLN cc_start: 0.8358 (mt0) cc_final: 0.7991 (mt0) REVERT: T 122 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8477 (mmmt) REVERT: U 146 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7927 (mtmm) REVERT: U 204 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7167 (t70) REVERT: V 13 MET cc_start: 0.9319 (mtt) cc_final: 0.9090 (mtt) REVERT: V 41 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8839 (tt) REVERT: V 123 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8242 (t0) REVERT: W 216 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7793 (mppt) REVERT: Y 4 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8973 (mt) REVERT: Y 111 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8184 (m-30) outliers start: 197 outliers final: 121 residues processed: 582 average time/residue: 1.6194 time to fit residues: 1171.7428 Evaluate side-chains 561 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 419 time to evaluate : 5.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 72 LYS Chi-restraints excluded: chain H residue 123 ASN Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 173 GLU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 64 ASN Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 156 GLU Chi-restraints excluded: chain O residue 176 ASN Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 54 ASN Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 208 ILE Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 181 ASN Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 139 ASN Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 231 GLN Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 105 GLU Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 197 SER Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 237 MET Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain U residue 146 LYS Chi-restraints excluded: chain U residue 204 ASP Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 123 ASN Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 216 LYS Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 135 THR Chi-restraints excluded: chain X residue 144 CYS Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 156 SER Chi-restraints excluded: chain X residue 165 SER Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 64 ASN Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 111 ASP Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 161 LYS Chi-restraints excluded: chain Z residue 102 SER Chi-restraints excluded: chain Z residue 107 THR Chi-restraints excluded: chain Z residue 174 VAL Chi-restraints excluded: chain Z residue 192 ASP Chi-restraints excluded: chain b residue 52 MET Chi-restraints excluded: chain b residue 197 MET Chi-restraints excluded: chain b residue 200 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 206 optimal weight: 3.9990 chunk 551 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 359 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 613 optimal weight: 0.9990 chunk 509 optimal weight: 5.9990 chunk 284 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 322 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN B 100 GLN F 165 HIS H 245 ASN M 192 ASN N 135 ASN O 77 ASN ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 GLN T 165 HIS V 245 ASN X 80 GLN b 135 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 52763 Z= 0.247 Angle : 0.496 10.511 71265 Z= 0.272 Chirality : 0.043 0.251 7950 Planarity : 0.003 0.051 9078 Dihedral : 6.172 89.321 7221 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.21 % Allowed : 16.61 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.65 (0.10), residues: 6402 helix: 2.38 (0.10), residues: 2373 sheet: 0.89 (0.13), residues: 1558 loop : 0.00 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Y 117 HIS 0.007 0.001 HIS V 61 PHE 0.026 0.002 PHE C 73 TYR 0.017 0.001 TYR Z 198 ARG 0.008 0.000 ARG P 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 427 time to evaluate : 6.166 Fit side-chains REVERT: B 177 ARG cc_start: 0.8194 (ptp90) cc_final: 0.7983 (ptp90) REVERT: C 3 ARG cc_start: 0.7996 (ptp90) cc_final: 0.7600 (ptt90) REVERT: D 181 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6883 (mm-30) REVERT: D 205 GLU cc_start: 0.7968 (tt0) cc_final: 0.7746 (tt0) REVERT: E 20 ARG cc_start: 0.8100 (mtt90) cc_final: 0.7857 (mtp85) REVERT: F 179 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: G 146 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7857 (mtmm) REVERT: H 41 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8800 (tt) REVERT: H 72 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8790 (mttt) REVERT: H 123 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8256 (t0) REVERT: J 173 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7805 (pt0) REVERT: K 2 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: K 4 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8939 (mt) REVERT: M 192 ASN cc_start: 0.8052 (t0) cc_final: 0.7315 (p0) REVERT: M 239 GLN cc_start: 0.7894 (mt0) cc_final: 0.7644 (mt0) REVERT: O 197 GLN cc_start: 0.6037 (pm20) cc_final: 0.5687 (pm20) REVERT: P 177 ARG cc_start: 0.8195 (ptp90) cc_final: 0.7994 (ptp90) REVERT: R 89 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9127 (tt) REVERT: S 227 GLN cc_start: 0.8350 (mt0) cc_final: 0.8037 (mt0) REVERT: T 122 LYS cc_start: 0.8913 (mmtp) cc_final: 0.8461 (mmmt) REVERT: U 146 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7924 (mtmm) REVERT: U 204 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7154 (t70) REVERT: V 13 MET cc_start: 0.9303 (mtt) cc_final: 0.9076 (mtt) REVERT: V 41 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8828 (tt) REVERT: V 123 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8268 (t0) REVERT: Y 111 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8173 (m-30) outliers start: 183 outliers final: 125 residues processed: 581 average time/residue: 1.4992 time to fit residues: 1082.0994 Evaluate side-chains 561 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 421 time to evaluate : 4.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 72 LYS Chi-restraints excluded: chain H residue 123 ASN Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 173 GLU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 64 ASN Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 156 GLU Chi-restraints excluded: chain O residue 176 ASN Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 54 ASN Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 208 ILE Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 181 ASN Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 139 ASN Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 197 SER Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain U residue 146 LYS Chi-restraints excluded: chain U residue 204 ASP Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 123 ASN Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 135 THR Chi-restraints excluded: chain X residue 145 GLU Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 156 SER Chi-restraints excluded: chain X residue 165 SER Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 64 ASN Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 111 ASP Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 161 LYS Chi-restraints excluded: chain Z residue 102 SER Chi-restraints excluded: chain Z residue 107 THR Chi-restraints excluded: chain Z residue 174 VAL Chi-restraints excluded: chain Z residue 192 ASP Chi-restraints excluded: chain b residue 52 MET Chi-restraints excluded: chain b residue 197 MET Chi-restraints excluded: chain b residue 200 GLU Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 591 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 349 optimal weight: 2.9990 chunk 447 optimal weight: 0.3980 chunk 347 optimal weight: 6.9990 chunk 516 optimal weight: 4.9990 chunk 342 optimal weight: 0.5980 chunk 611 optimal weight: 10.0000 chunk 382 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN B 100 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS F 218 HIS H 245 ASN M 194 ASN N 135 ASN S 195 GLN T 165 HIS V 245 ASN X 80 GLN b 135 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 52763 Z= 0.190 Angle : 0.471 9.300 71265 Z= 0.259 Chirality : 0.042 0.215 7950 Planarity : 0.003 0.049 9078 Dihedral : 6.042 89.960 7221 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.04 % Allowed : 17.04 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.76 (0.10), residues: 6402 helix: 2.52 (0.10), residues: 2365 sheet: 0.95 (0.13), residues: 1544 loop : 0.04 (0.12), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 117 HIS 0.006 0.001 HIS V 61 PHE 0.023 0.001 PHE C 73 TYR 0.015 0.001 TYR Z 198 ARG 0.009 0.000 ARG P 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 434 time to evaluate : 4.732 Fit side-chains REVERT: A 179 GLN cc_start: 0.7437 (mp10) cc_final: 0.7111 (tt0) REVERT: C 3 ARG cc_start: 0.7995 (ptp90) cc_final: 0.7609 (ptt90) REVERT: D 181 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6894 (mm-30) REVERT: D 205 GLU cc_start: 0.7986 (tt0) cc_final: 0.7746 (tt0) REVERT: E 20 ARG cc_start: 0.8121 (mtt90) cc_final: 0.7885 (mtp85) REVERT: F 3 ARG cc_start: 0.7137 (tpp80) cc_final: 0.6642 (tpp-160) REVERT: F 4 ASN cc_start: 0.7994 (t0) cc_final: 0.7792 (t160) REVERT: F 179 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: G 146 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7848 (mtmm) REVERT: G 181 LYS cc_start: 0.8810 (mttp) cc_final: 0.8561 (mtpp) REVERT: G 251 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6725 (pp) REVERT: H 41 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8806 (tt) REVERT: H 72 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8783 (mttt) REVERT: H 240 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: I 216 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7652 (mppt) REVERT: J 173 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7767 (pt0) REVERT: K 4 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8947 (mt) REVERT: K 111 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8022 (m-30) REVERT: M 192 ASN cc_start: 0.8027 (t0) cc_final: 0.7273 (p0) REVERT: M 239 GLN cc_start: 0.7888 (mt0) cc_final: 0.7625 (mt0) REVERT: O 197 GLN cc_start: 0.6008 (pm20) cc_final: 0.5665 (pm20) REVERT: Q 208 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7875 (pt0) REVERT: S 227 GLN cc_start: 0.8347 (mt0) cc_final: 0.7994 (mt0) REVERT: T 122 LYS cc_start: 0.8904 (mmtp) cc_final: 0.8454 (mmmt) REVERT: U 146 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7910 (mtmm) REVERT: U 204 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7127 (t70) REVERT: V 13 MET cc_start: 0.9290 (mtt) cc_final: 0.9077 (mtm) REVERT: V 41 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8836 (tt) REVERT: W 216 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7744 (mppt) outliers start: 173 outliers final: 110 residues processed: 574 average time/residue: 1.4280 time to fit residues: 1015.3889 Evaluate side-chains 552 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 426 time to evaluate : 4.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 72 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 240 GLU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 173 GLU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 64 ASN Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 156 GLU Chi-restraints excluded: chain O residue 176 ASN Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 139 ASN Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 197 SER Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain U residue 146 LYS Chi-restraints excluded: chain U residue 204 ASP Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 216 LYS Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 135 THR Chi-restraints excluded: chain X residue 145 GLU Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 156 SER Chi-restraints excluded: chain X residue 165 SER Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 64 ASN Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 161 LYS Chi-restraints excluded: chain Z residue 102 SER Chi-restraints excluded: chain Z residue 107 THR Chi-restraints excluded: chain Z residue 192 ASP Chi-restraints excluded: chain b residue 52 MET Chi-restraints excluded: chain b residue 197 MET Chi-restraints excluded: chain b residue 200 GLU Chi-restraints excluded: chain b residue 226 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 378 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 364 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 388 optimal weight: 10.0000 chunk 416 optimal weight: 10.0000 chunk 302 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 480 optimal weight: 9.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 198 GLN B 100 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 165 HIS ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 ASN N 135 ASN O 77 ASN ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 GLN T 165 HIS ** U 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 245 ASN X 80 GLN b 135 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 52763 Z= 0.446 Angle : 0.590 13.908 71265 Z= 0.318 Chirality : 0.048 0.305 7950 Planarity : 0.004 0.050 9078 Dihedral : 6.332 89.863 7219 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.30 % Allowed : 17.09 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.47 (0.10), residues: 6402 helix: 2.14 (0.10), residues: 2365 sheet: 0.90 (0.13), residues: 1544 loop : -0.05 (0.12), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 117 HIS 0.010 0.001 HIS V 61 PHE 0.037 0.002 PHE Q 73 TYR 0.023 0.002 TYR Z 198 ARG 0.009 0.001 ARG Y 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 421 time to evaluate : 4.617 Fit side-chains REVERT: D 67 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7838 (pm20) REVERT: D 181 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6945 (mm-30) REVERT: E 20 ARG cc_start: 0.8162 (mtt90) cc_final: 0.7936 (mtp85) REVERT: F 3 ARG cc_start: 0.7188 (tpp80) cc_final: 0.6705 (tpp-160) REVERT: F 4 ASN cc_start: 0.8020 (t0) cc_final: 0.7810 (t160) REVERT: F 179 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: F 222 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8029 (mm-30) REVERT: G 146 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7897 (mtmm) REVERT: H 41 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8819 (tt) REVERT: H 72 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8794 (mttt) REVERT: H 123 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8209 (t0) REVERT: H 240 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: I 216 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7830 (mppt) REVERT: J 173 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7771 (pt0) REVERT: K 2 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: K 4 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8994 (mt) REVERT: K 111 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: M 239 GLN cc_start: 0.7932 (mt0) cc_final: 0.7722 (mt0) REVERT: O 197 GLN cc_start: 0.6068 (pm20) cc_final: 0.5721 (pm20) REVERT: R 89 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9134 (tt) REVERT: S 227 GLN cc_start: 0.8402 (mt0) cc_final: 0.8046 (mt0) REVERT: T 122 LYS cc_start: 0.8938 (mmtp) cc_final: 0.8495 (mmmt) REVERT: U 146 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7923 (mtmm) REVERT: U 204 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7220 (t70) REVERT: V 41 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8852 (tt) REVERT: V 123 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8217 (t0) REVERT: W 216 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7874 (mppt) REVERT: Y 2 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8256 (m-30) REVERT: Y 4 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8962 (mt) REVERT: Y 111 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8060 (m-30) outliers start: 188 outliers final: 124 residues processed: 576 average time/residue: 1.3991 time to fit residues: 997.6044 Evaluate side-chains 564 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 417 time to evaluate : 4.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 72 LYS Chi-restraints excluded: chain H residue 123 ASN Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 240 GLU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 173 GLU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 64 ASN Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 156 GLU Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 54 ASN Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 181 ASN Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 57 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 139 ASN Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 105 GLU Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 197 SER Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 237 MET Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain U residue 146 LYS Chi-restraints excluded: chain U residue 204 ASP Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 123 ASN Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 216 LYS Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 135 THR Chi-restraints excluded: chain X residue 144 CYS Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 156 SER Chi-restraints excluded: chain X residue 165 SER Chi-restraints excluded: chain Y residue 2 ASP Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 111 ASP Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 161 LYS Chi-restraints excluded: chain Z residue 102 SER Chi-restraints excluded: chain Z residue 107 THR Chi-restraints excluded: chain Z residue 192 ASP Chi-restraints excluded: chain b residue 52 MET Chi-restraints excluded: chain b residue 197 MET Chi-restraints excluded: chain b residue 200 GLU Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 555 optimal weight: 0.9990 chunk 585 optimal weight: 6.9990 chunk 534 optimal weight: 0.9980 chunk 569 optimal weight: 7.9990 chunk 342 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 447 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 514 optimal weight: 5.9990 chunk 538 optimal weight: 10.0000 chunk 567 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN B 100 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 165 HIS F 174 ASN M 194 ASN N 135 ASN ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 GLN T 165 HIS V 245 ASN ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 GLN Z 106 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 52763 Z= 0.135 Angle : 0.448 7.919 71265 Z= 0.249 Chirality : 0.041 0.161 7950 Planarity : 0.003 0.048 9078 Dihedral : 5.920 89.938 7219 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.88 % Allowed : 18.41 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.79 (0.11), residues: 6402 helix: 2.56 (0.10), residues: 2365 sheet: 0.96 (0.13), residues: 1568 loop : 0.03 (0.13), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Y 117 HIS 0.005 0.001 HIS Z 106 PHE 0.015 0.001 PHE C 73 TYR 0.013 0.001 TYR X 71 ARG 0.010 0.000 ARG Y 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 452 time to evaluate : 4.482 Fit side-chains REVERT: A 179 GLN cc_start: 0.7337 (mp10) cc_final: 0.6994 (tt0) REVERT: C 3 ARG cc_start: 0.7993 (ptp90) cc_final: 0.7554 (ptt90) REVERT: D 181 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: E 20 ARG cc_start: 0.8114 (mtt90) cc_final: 0.7872 (mtp85) REVERT: F 3 ARG cc_start: 0.7055 (tpp80) cc_final: 0.6627 (tpp-160) REVERT: F 222 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7998 (mm-30) REVERT: G 181 LYS cc_start: 0.8775 (mttp) cc_final: 0.8540 (mtpp) REVERT: G 250 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7535 (mmtm) REVERT: H 41 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8810 (tt) REVERT: H 72 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8770 (mttt) REVERT: J 173 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7783 (pt0) REVERT: K 111 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8031 (m-30) REVERT: K 161 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8232 (tptp) REVERT: M 192 ASN cc_start: 0.8050 (t0) cc_final: 0.7315 (p0) REVERT: M 239 GLN cc_start: 0.7853 (mt0) cc_final: 0.7581 (mt0) REVERT: O 197 GLN cc_start: 0.5971 (pm20) cc_final: 0.5640 (pm20) REVERT: S 227 GLN cc_start: 0.8356 (mt0) cc_final: 0.8028 (mt0) REVERT: T 122 LYS cc_start: 0.8873 (mmtp) cc_final: 0.8423 (mmmt) REVERT: T 179 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: T 222 GLU cc_start: 0.8045 (mp0) cc_final: 0.7838 (mp0) REVERT: U 146 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7868 (mtmm) REVERT: V 41 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8838 (tt) REVERT: W 89 LYS cc_start: 0.8749 (ttmm) cc_final: 0.8509 (tttt) REVERT: X 80 GLN cc_start: 0.8325 (tp40) cc_final: 0.7732 (mp10) REVERT: Y 111 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8041 (m-30) outliers start: 107 outliers final: 70 residues processed: 534 average time/residue: 1.4598 time to fit residues: 961.4423 Evaluate side-chains 513 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 432 time to evaluate : 3.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 72 LYS Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 173 GLU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 54 ASN Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 139 ASN Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 179 GLU Chi-restraints excluded: chain T residue 197 SER Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain U residue 146 LYS Chi-restraints excluded: chain U residue 213 GLN Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 135 THR Chi-restraints excluded: chain X residue 145 GLU Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 165 SER Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 111 ASP Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 161 LYS Chi-restraints excluded: chain Z residue 102 SER Chi-restraints excluded: chain Z residue 107 THR Chi-restraints excluded: chain Z residue 192 ASP Chi-restraints excluded: chain b residue 197 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 373 optimal weight: 6.9990 chunk 602 optimal weight: 10.0000 chunk 367 optimal weight: 0.7980 chunk 285 optimal weight: 0.9980 chunk 418 optimal weight: 10.0000 chunk 631 optimal weight: 10.0000 chunk 581 optimal weight: 1.9990 chunk 502 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 388 optimal weight: 6.9990 chunk 308 optimal weight: 6.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 198 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 165 HIS F 174 ASN H 245 ASN M 151 ASN N 135 ASN O 77 ASN ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 GLN S 195 GLN T 165 HIS V 245 ASN a 151 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 52763 Z= 0.213 Angle : 0.483 9.879 71265 Z= 0.265 Chirality : 0.043 0.225 7950 Planarity : 0.003 0.048 9078 Dihedral : 5.975 89.702 7218 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.69 % Allowed : 18.63 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.78 (0.10), residues: 6402 helix: 2.53 (0.10), residues: 2367 sheet: 0.96 (0.13), residues: 1550 loop : 0.03 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 117 HIS 0.006 0.001 HIS V 61 PHE 0.025 0.001 PHE C 73 TYR 0.016 0.001 TYR Z 198 ARG 0.009 0.000 ARG P 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12804 Ramachandran restraints generated. 6402 Oldfield, 0 Emsley, 6402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 435 time to evaluate : 4.238 Fit side-chains REVERT: A 179 GLN cc_start: 0.7415 (mp10) cc_final: 0.7056 (tt0) REVERT: C 3 ARG cc_start: 0.8004 (ptp90) cc_final: 0.7599 (ptt90) REVERT: D 181 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6890 (mm-30) REVERT: E 20 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7899 (mtp85) REVERT: F 3 ARG cc_start: 0.7098 (tpp80) cc_final: 0.6631 (tpp-160) REVERT: F 222 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: G 146 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7861 (mtmm) REVERT: G 250 LYS cc_start: 0.7809 (mmtm) cc_final: 0.7538 (mmtm) REVERT: H 41 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8787 (tt) REVERT: H 72 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8776 (mttt) REVERT: J 173 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7780 (pt0) REVERT: K 111 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8033 (m-30) REVERT: M 192 ASN cc_start: 0.8031 (t0) cc_final: 0.7270 (p0) REVERT: M 239 GLN cc_start: 0.7900 (mt0) cc_final: 0.7623 (mt0) REVERT: O 197 GLN cc_start: 0.5976 (pm20) cc_final: 0.5650 (pm20) REVERT: S 227 GLN cc_start: 0.8360 (mt0) cc_final: 0.8006 (mt0) REVERT: T 122 LYS cc_start: 0.8909 (mmtp) cc_final: 0.8460 (mmmt) REVERT: T 179 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7546 (tm-30) REVERT: U 146 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7910 (mtmm) REVERT: V 41 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8838 (tt) REVERT: X 80 GLN cc_start: 0.8352 (tp40) cc_final: 0.7756 (mp10) REVERT: Y 2 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8223 (m-30) REVERT: Y 111 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8043 (m-30) outliers start: 96 outliers final: 70 residues processed: 513 average time/residue: 1.3630 time to fit residues: 862.0864 Evaluate side-chains 512 residues out of total 5686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 430 time to evaluate : 3.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 72 LYS Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 173 GLU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 54 ASN Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 139 ASN Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 179 GLU Chi-restraints excluded: chain T residue 197 SER Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain U residue 146 LYS Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 135 THR Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 165 SER Chi-restraints excluded: chain Y residue 2 ASP Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 111 ASP Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 161 LYS Chi-restraints excluded: chain Z residue 102 SER Chi-restraints excluded: chain Z residue 107 THR Chi-restraints excluded: chain Z residue 192 ASP Chi-restraints excluded: chain b residue 197 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 399 optimal weight: 9.9990 chunk 535 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 463 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 503 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 517 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 198 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 165 HIS ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 ASN N 135 ASN O 77 ASN ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 GLN S 195 GLN T 165 HIS ** U 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 245 ASN b 135 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.077441 restraints weight = 132946.064| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.99 r_work: 0.2826 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 52763 Z= 0.407 Angle : 0.579 13.201 71265 Z= 0.313 Chirality : 0.047 0.309 7950 Planarity : 0.004 0.049 9078 Dihedral : 6.268 89.958 7218 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.98 % Allowed : 18.34 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.52 (0.10), residues: 6402 helix: 2.20 (0.10), residues: 2369 sheet: 0.92 (0.13), residues: 1550 loop : -0.04 (0.12), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP W 58 HIS 0.009 0.001 HIS V 61 PHE 0.036 0.002 PHE Q 73 TYR 0.022 0.002 TYR Z 198 ARG 0.008 0.001 ARG P 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16612.49 seconds wall clock time: 293 minutes 1.35 seconds (17581.35 seconds total)