Starting phenix.real_space_refine on Tue Jan 14 17:31:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ud9_42148/01_2025/8ud9_42148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ud9_42148/01_2025/8ud9_42148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ud9_42148/01_2025/8ud9_42148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ud9_42148/01_2025/8ud9_42148.map" model { file = "/net/cci-nas-00/data/ceres_data/8ud9_42148/01_2025/8ud9_42148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ud9_42148/01_2025/8ud9_42148.cif" } resolution = 2.04 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= 0.008 sd= 0.128 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 300 5.16 5 C 30870 2.51 5 N 8364 2.21 5 O 10421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 49955 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1903 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain: "B" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1813 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain: "C" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1941 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain breaks: 1 Chain: "D" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1923 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 6, 'TRANS': 236} Chain: "E" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1799 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "F" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1864 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "G" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1890 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 5, 'TRANS': 235} Chain: "H" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1509 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1676 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain: "J" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "K" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1578 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "L" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1559 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "M" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1643 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "N" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "O" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1903 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain: "P" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1813 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain: "Q" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1941 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain breaks: 1 Chain: "R" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1923 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 6, 'TRANS': 236} Chain: "S" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1799 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "T" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1864 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "U" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1890 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 5, 'TRANS': 235} Chain: "V" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1509 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1676 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain: "X" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "Y" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1575 Classifications: {'peptide': 197} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Chain: "Z" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1559 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "a" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1643 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "b" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YRE': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YRE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "M" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "N" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "S" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "U" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "V" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "W" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "X" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "Z" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "a" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "b" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Time building chain proxies: 22.72, per 1000 atoms: 0.45 Number of scatterers: 49955 At special positions: 0 Unit cell: (139.932, 179.676, 144.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 300 16.00 O 10421 8.00 N 8364 7.00 C 30870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.35 Conformation dependent library (CDL) restraints added in 4.7 seconds 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11544 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 72 sheets defined 40.5% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.18 Creating SS restraints... Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.915A pdb=" N ASN A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 83 through 106 Processing helix chain 'A' and resid 110 through 128 Processing helix chain 'A' and resid 171 through 186 Processing helix chain 'A' and resid 190 through 207 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 231 through 244 Processing helix chain 'B' and resid 19 through 31 Processing helix chain 'B' and resid 79 through 102 Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 166 through 178 Processing helix chain 'B' and resid 183 through 198 removed outlier: 3.972A pdb=" N SER B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'C' and resid 18 through 30 removed outlier: 3.737A pdb=" N HIS C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 102 Processing helix chain 'C' and resid 106 through 124 removed outlier: 3.596A pdb=" N ILE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 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 251 Processing helix chain 'D' and resid 16 through 29 removed outlier: 3.517A pdb=" N GLY D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 4.094A pdb=" N ARG D 60 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 99 Processing helix chain 'D' and resid 103 through 119 Processing helix chain 'D' and resid 164 through 176 Processing helix chain 'D' and resid 183 through 197 Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 221 through 244 Processing helix chain 'E' and resid 21 through 32 Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 81 through 104 removed outlier: 3.624A pdb=" N ALA E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 173 through 185 Processing helix chain 'E' and resid 190 through 206 Processing helix chain 'E' and resid 230 through 240 removed outlier: 3.760A pdb=" N ASP E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 32 removed outlier: 3.798A pdb=" N GLY F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 100 Processing helix chain 'F' and resid 104 through 118 Processing helix chain 'F' and resid 119 through 122 Processing helix chain 'F' and resid 164 through 176 removed outlier: 4.232A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 183 through 199 removed outlier: 3.711A pdb=" N THR F 198 " --> pdb=" O ALA F 194 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU F 199 " --> pdb=" O LEU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 235 removed outlier: 4.453A pdb=" N GLY F 235 " --> pdb=" O PRO F 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 123 removed outlier: 3.867A pdb=" N TYR G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 178 Processing helix chain 'G' and resid 179 through 180 No H-bonds generated for 'chain 'G' and resid 179 through 180' Processing helix chain 'G' and resid 181 through 185 Processing helix chain 'G' and resid 186 through 202 removed outlier: 4.000A pdb=" N LYS G 192 " --> pdb=" O ARG G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 229 through 246 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 Processing helix chain 'H' and resid 129 through 134 removed outlier: 3.746A pdb=" N SER H 133 " --> pdb=" O SER H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 143 Processing helix chain 'H' and resid 148 through 167 Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 147 through 166 Processing helix chain 'J' and resid 56 through 79 Processing helix chain 'J' and resid 83 through 98 removed outlier: 3.894A pdb=" N LYS J 98 " --> pdb=" O LEU J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 154 Processing helix chain 'J' and resid 159 through 176 Processing helix chain 'K' and resid 51 through 72 Processing helix chain 'K' and resid 76 through 93 removed outlier: 4.182A pdb=" N ARG K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 147 removed outlier: 3.998A pdb=" N PHE K 137 " --> pdb=" O GLY K 133 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU K 138 " --> pdb=" O TYR K 134 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 89 removed outlier: 3.711A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 removed outlier: 3.541A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 167 Processing helix chain 'L' and resid 192 through 200 Processing helix chain 'M' and resid 57 through 80 Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.845A pdb=" N ARG M 99 " --> pdb=" O ILE M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 153 Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 167 through 186 removed outlier: 3.699A pdb=" N ARG M 185 " --> pdb=" O SER M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 78 removed outlier: 3.643A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 102 Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 146 through 157 Processing helix chain 'N' and resid 161 through 180 Processing helix chain 'N' and resid 209 through 213 Processing helix chain 'O' and resid 22 through 33 removed outlier: 3.915A pdb=" N ASN O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 36 No H-bonds generated for 'chain 'O' and resid 34 through 36' Processing helix chain 'O' and resid 62 through 66 Processing helix chain 'O' and resid 83 through 106 Processing helix chain 'O' and resid 110 through 128 Processing helix chain 'O' and resid 171 through 185 Processing helix chain 'O' and resid 190 through 207 Processing helix chain 'O' and resid 211 through 213 No H-bonds generated for 'chain 'O' and resid 211 through 213' Processing helix chain 'O' and resid 231 through 245 Processing helix chain 'P' and resid 19 through 31 Processing helix chain 'P' and resid 79 through 102 Processing helix chain 'P' and resid 106 through 121 Processing helix chain 'P' and resid 166 through 178 Processing helix chain 'P' and resid 183 through 198 removed outlier: 3.973A pdb=" N SER P 198 " --> pdb=" O THR P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 234 Processing helix chain 'Q' and resid 18 through 30 removed outlier: 3.736A pdb=" N HIS Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 102 Processing helix chain 'Q' and resid 106 through 124 removed outlier: 3.597A pdb=" N ILE Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 179 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 251 Processing helix chain 'R' and resid 16 through 29 removed outlier: 3.516A pdb=" N GLY R 29 " --> pdb=" O ALA R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 60 removed outlier: 4.094A pdb=" N ARG R 60 " --> pdb=" O ARG R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 99 Processing helix chain 'R' and resid 103 through 119 Processing helix chain 'R' and resid 164 through 176 Processing helix chain 'R' and resid 183 through 197 Processing helix chain 'R' and resid 221 through 244 Processing helix chain 'S' and resid 21 through 32 Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 81 through 104 removed outlier: 3.623A pdb=" N ALA S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS S 86 " --> pdb=" O ILE S 82 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 118 Processing helix chain 'S' and resid 173 through 185 Processing helix chain 'S' and resid 190 through 206 Processing helix chain 'S' and resid 230 through 240 removed outlier: 3.771A pdb=" N ASP S 240 " --> pdb=" O GLU S 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 32 removed outlier: 3.799A pdb=" N GLY T 32 " --> pdb=" O ALA T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 100 Processing helix chain 'T' and resid 104 through 118 Processing helix chain 'T' and resid 119 through 122 Processing helix chain 'T' and resid 164 through 176 removed outlier: 4.230A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 177 through 179 No H-bonds generated for 'chain 'T' and resid 177 through 179' Processing helix chain 'T' and resid 183 through 198 removed outlier: 3.755A pdb=" N THR T 198 " --> pdb=" O ALA T 194 " (cutoff:3.500A) Processing helix chain 'T' and resid 229 through 235 removed outlier: 4.562A pdb=" N GLY T 235 " --> pdb=" O PRO T 231 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 33 Processing helix chain 'U' and resid 81 through 104 Processing helix chain 'U' and resid 108 through 123 removed outlier: 3.870A pdb=" N TYR U 123 " --> pdb=" O TYR U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 178 Processing helix chain 'U' and resid 179 through 180 No H-bonds generated for 'chain 'U' and resid 179 through 180' Processing helix chain 'U' and resid 181 through 185 Processing helix chain 'U' and resid 186 through 202 removed outlier: 3.996A pdb=" N LYS U 192 " --> pdb=" O ARG U 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 220 through 222 No H-bonds generated for 'chain 'U' and resid 220 through 222' Processing helix chain 'U' and resid 229 through 246 Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 Processing helix chain 'V' and resid 129 through 134 removed outlier: 3.745A pdb=" N SER V 133 " --> pdb=" O SER V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 143 Processing helix chain 'V' and resid 148 through 167 Processing helix chain 'V' and resid 190 through 194 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 Processing helix chain 'W' and resid 130 through 142 Processing helix chain 'W' and resid 147 through 166 Processing helix chain 'X' and resid 56 through 79 Processing helix chain 'X' and resid 83 through 98 removed outlier: 3.894A pdb=" N LYS X 98 " --> pdb=" O LEU X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 154 Processing helix chain 'X' and resid 159 through 176 Processing helix chain 'Y' and resid 51 through 72 Processing helix chain 'Y' and resid 76 through 93 removed outlier: 4.180A pdb=" N ARG Y 93 " --> pdb=" O ALA Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 147 removed outlier: 3.987A pdb=" N PHE Y 137 " --> pdb=" O GLY Y 133 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU Y 138 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 171 Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 89 removed outlier: 3.710A pdb=" N GLN Z 89 " --> pdb=" O ASN Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 3.541A pdb=" N VAL Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 167 Processing helix chain 'Z' and resid 192 through 200 Processing helix chain 'a' and resid 57 through 80 Processing helix chain 'a' and resid 84 through 99 removed outlier: 3.846A pdb=" N ARG a 99 " --> pdb=" O ILE a 95 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 153 Proline residue: a 147 - end of helix Processing helix chain 'a' and resid 167 through 186 removed outlier: 3.699A pdb=" N ARG a 185 " --> pdb=" O SER a 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 78 removed outlier: 3.643A pdb=" N LEU b 77 " --> pdb=" O ASP b 73 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY b 78 " --> pdb=" O GLU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 102 Processing helix chain 'b' and resid 141 through 146 Processing helix chain 'b' and resid 146 through 157 Processing helix chain 'b' and resid 161 through 180 Processing helix chain 'b' and resid 209 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 169 removed outlier: 5.954A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 73 removed outlier: 6.339A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL A 151 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 163 Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 69 removed outlier: 6.281A pdb=" N ILE B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.660A pdb=" N GLY C 42 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 65 through 69 removed outlier: 6.323A pdb=" N MET C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AA8, first strand: chain 'D' and resid 62 through 64 Processing sheet with id=AA9, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.293A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AB3, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.391A pdb=" N ILE F 70 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE F 144 " --> pdb=" O CYS F 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 163 through 166 Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.262A pdb=" N VAL G 74 " --> pdb=" O VAL G 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 125 through 128 Processing sheet with id=AB7, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.832A pdb=" N THR H 20 " --> pdb=" O ALA H 27 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.446A pdb=" N ILE H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 124 through 127 removed outlier: 6.797A pdb=" N ILE I 173 " --> pdb=" O TYR I 189 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU I 175 " --> pdb=" O ARG I 187 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG I 187 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL I 177 " --> pdb=" O PHE I 185 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE I 185 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N SER I 179 " --> pdb=" O LEU I 183 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU I 183 " --> pdb=" O SER I 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.657A pdb=" N ALA I 20 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.431A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA I 97 " --> pdb=" O ALA I 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 211 through 218 removed outlier: 4.628A pdb=" N VAL J 185 " --> pdb=" O LEU J 200 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ALA J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.802A pdb=" N PHE J 28 " --> pdb=" O VAL J 35 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 42 through 46 removed outlier: 6.119A pdb=" N LEU J 49 " --> pdb=" O MET J 45 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AC7, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AC8, first strand: chain 'K' and resid 21 through 23 removed outlier: 6.499A pdb=" N ALA K 21 " --> pdb=" O MET K 28 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.239A pdb=" N ILE K 42 " --> pdb=" O MET K 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 125 through 128 removed outlier: 6.351A pdb=" N HIS L 178 " --> pdb=" O ARG L 186 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ARG L 186 " --> pdb=" O HIS L 178 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG L 180 " --> pdb=" O TRP L 184 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TRP L 184 " --> pdb=" O ARG L 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.560A pdb=" N ALA L 20 " --> pdb=" O ALA L 27 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.492A pdb=" N LEU L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 135 through 139 removed outlier: 5.131A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 29 through 31 removed outlier: 6.430A pdb=" N GLU M 31 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE M 35 " --> pdb=" O GLU M 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 43 through 47 removed outlier: 6.319A pdb=" N THR M 50 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN M 108 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL M 121 " --> pdb=" O ASP M 133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 33 through 36 removed outlier: 6.677A pdb=" N GLY N 28 " --> pdb=" O ARG N 35 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 33 through 36 removed outlier: 6.677A pdb=" N GLY N 28 " --> pdb=" O ARG N 35 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 136 through 138 removed outlier: 6.068A pdb=" N PHE N 187 " --> pdb=" O PRO N 202 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 165 through 169 removed outlier: 5.962A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 69 through 73 removed outlier: 6.338A pdb=" N ILE O 76 " --> pdb=" O ILE O 72 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL O 151 " --> pdb=" O PHE O 163 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 160 through 163 Processing sheet with id=AE4, first strand: chain 'P' and resid 66 through 69 removed outlier: 6.282A pdb=" N ILE P 72 " --> pdb=" O ILE P 68 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 161 through 164 removed outlier: 3.666A pdb=" N GLY Q 42 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 65 through 69 removed outlier: 6.325A pdb=" N MET Q 72 " --> pdb=" O LEU Q 68 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 158 through 161 Processing sheet with id=AE8, first strand: chain 'R' and resid 62 through 64 Processing sheet with id=AE9, first strand: chain 'S' and resid 167 through 170 Processing sheet with id=AF1, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.293A pdb=" N ILE S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU S 153 " --> pdb=" O CYS S 165 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 158 through 161 Processing sheet with id=AF3, first strand: chain 'T' and resid 63 through 67 removed outlier: 6.391A pdb=" N ILE T 70 " --> pdb=" O VAL T 66 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE T 144 " --> pdb=" O CYS T 156 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 163 through 166 Processing sheet with id=AF5, first strand: chain 'U' and resid 67 through 71 removed outlier: 6.262A pdb=" N VAL U 74 " --> pdb=" O VAL U 70 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 125 through 128 Processing sheet with id=AF7, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.833A pdb=" N THR V 20 " --> pdb=" O ALA V 27 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.446A pdb=" N ILE V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 124 through 127 removed outlier: 6.800A pdb=" N ILE W 173 " --> pdb=" O TYR W 189 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU W 175 " --> pdb=" O ARG W 187 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG W 187 " --> pdb=" O LEU W 175 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL W 177 " --> pdb=" O PHE W 185 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N PHE W 185 " --> pdb=" O VAL W 177 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N SER W 179 " --> pdb=" O LEU W 183 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU W 183 " --> pdb=" O SER W 179 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 20 through 22 removed outlier: 6.652A pdb=" N ALA W 20 " --> pdb=" O ALA W 27 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.432A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 211 through 218 removed outlier: 4.627A pdb=" N VAL X 185 " --> pdb=" O LEU X 200 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ALA X 10 " --> pdb=" O ASP X 25 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 28 through 30 removed outlier: 6.801A pdb=" N PHE X 28 " --> pdb=" O VAL X 35 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 42 through 46 removed outlier: 6.117A pdb=" N LEU X 49 " --> pdb=" O MET X 45 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 131 through 132 Processing sheet with id=AG7, first strand: chain 'Y' and resid 131 through 132 Processing sheet with id=AG8, first strand: chain 'Y' and resid 21 through 23 removed outlier: 6.500A pdb=" N ALA Y 21 " --> pdb=" O MET Y 28 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 35 through 37 Processing sheet with id=AH1, first strand: chain 'Z' and resid 125 through 128 removed outlier: 6.350A pdb=" N HIS Z 178 " --> pdb=" O ARG Z 186 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ARG Z 186 " --> pdb=" O HIS Z 178 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG Z 180 " --> pdb=" O TRP Z 184 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TRP Z 184 " --> pdb=" O ARG Z 180 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 20 through 22 removed outlier: 6.556A pdb=" N ALA Z 20 " --> pdb=" O ALA Z 27 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.494A pdb=" N LEU Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'a' and resid 135 through 139 removed outlier: 5.138A pdb=" N THR a 11 " --> pdb=" O ASP a 26 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'a' and resid 29 through 31 removed outlier: 6.431A pdb=" N GLU a 31 " --> pdb=" O ILE a 35 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE a 35 " --> pdb=" O GLU a 31 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'a' and resid 43 through 47 removed outlier: 6.323A pdb=" N THR a 50 " --> pdb=" O LEU a 46 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN a 108 " --> pdb=" O PHE a 124 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL a 121 " --> pdb=" O ASP a 133 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 33 through 36 removed outlier: 6.678A pdb=" N GLY b 28 " --> pdb=" O ARG b 35 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR b 49 " --> pdb=" O VAL b 45 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'b' and resid 33 through 36 removed outlier: 6.678A pdb=" N GLY b 28 " --> pdb=" O ARG b 35 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'b' and resid 136 through 138 removed outlier: 6.066A pdb=" N PHE b 187 " --> pdb=" O PRO b 202 " (cutoff:3.500A) 2943 hydrogen bonds defined for protein. 8418 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.64 Time building geometry restraints manager: 10.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10600 1.33 - 1.45: 10784 1.45 - 1.57: 27837 1.57 - 1.69: 2 1.69 - 1.81: 490 Bond restraints: 49713 Sorted by residual: bond pdb=" C39 YRE L 301 " pdb=" N38 YRE L 301 " ideal model delta sigma weight residual 1.454 1.519 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C37 YRE L 301 " pdb=" N38 YRE L 301 " ideal model delta sigma weight residual 1.444 1.504 -0.060 2.00e-02 2.50e+03 8.85e+00 bond pdb=" C43 YRE L 301 " pdb=" N38 YRE L 301 " ideal model delta sigma weight residual 1.446 1.505 -0.059 2.00e-02 2.50e+03 8.66e+00 bond pdb=" C05 YRE Z 301 " pdb=" N06 YRE Z 301 " ideal model delta sigma weight residual 1.337 1.387 -0.050 2.00e-02 2.50e+03 6.23e+00 bond pdb=" C05 YRE L 301 " pdb=" N06 YRE L 301 " ideal model delta sigma weight residual 1.337 1.386 -0.049 2.00e-02 2.50e+03 6.06e+00 ... (remaining 49708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 66056 1.73 - 3.47: 964 3.47 - 5.20: 110 5.20 - 6.94: 6 6.94 - 8.67: 6 Bond angle restraints: 67142 Sorted by residual: angle pdb=" C GLY M 190 " pdb=" N ASP M 191 " pdb=" CA ASP M 191 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 angle pdb=" C GLY a 190 " pdb=" N ASP a 191 " pdb=" CA ASP a 191 " ideal model delta sigma weight residual 121.54 129.13 -7.59 1.91e+00 2.74e-01 1.58e+01 angle pdb=" C ILE F 118 " pdb=" CA ILE F 118 " pdb=" CB ILE F 118 " ideal model delta sigma weight residual 113.70 110.56 3.14 9.50e-01 1.11e+00 1.09e+01 angle pdb=" C ILE T 118 " pdb=" CA ILE T 118 " pdb=" CB ILE T 118 " ideal model delta sigma weight residual 113.70 110.58 3.12 9.50e-01 1.11e+00 1.08e+01 angle pdb=" C40 YRE L 301 " pdb=" C39 YRE L 301 " pdb=" N38 YRE L 301 " ideal model delta sigma weight residual 109.73 118.40 -8.67 3.00e+00 1.11e-01 8.36e+00 ... (remaining 67137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.05: 28064 25.05 - 50.09: 1586 50.09 - 75.14: 335 75.14 - 100.19: 93 100.19 - 125.23: 4 Dihedral angle restraints: 30082 sinusoidal: 12006 harmonic: 18076 Sorted by residual: dihedral pdb=" CA GLY J 101 " pdb=" C GLY J 101 " pdb=" N PRO J 102 " pdb=" CA PRO J 102 " ideal model delta harmonic sigma weight residual 180.00 -155.34 -24.66 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLY X 101 " pdb=" C GLY X 101 " pdb=" N PRO X 102 " pdb=" CA PRO X 102 " ideal model delta harmonic sigma weight residual -180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA LEU K 102 " pdb=" C LEU K 102 " pdb=" N LEU K 103 " pdb=" CA LEU K 103 " ideal model delta harmonic sigma weight residual 180.00 156.75 23.25 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 30079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 6577 0.064 - 0.127: 895 0.127 - 0.191: 43 0.191 - 0.255: 1 0.255 - 0.319: 2 Chirality restraints: 7518 Sorted by residual: chirality pdb=" C16 YRE L 301 " pdb=" C15 YRE L 301 " pdb=" C17 YRE L 301 " pdb=" N29 YRE L 301 " both_signs ideal model delta sigma weight residual False 2.13 2.45 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C16 YRE Z 301 " pdb=" C15 YRE Z 301 " pdb=" C17 YRE Z 301 " pdb=" N29 YRE Z 301 " both_signs ideal model delta sigma weight residual False 2.13 2.45 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C13 YRE L 301 " pdb=" C02 YRE L 301 " pdb=" C36 YRE L 301 " pdb=" N14 YRE L 301 " both_signs ideal model delta sigma weight residual False 2.60 2.80 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 7515 not shown) Planarity restraints: 8653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 148 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO F 149 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 149 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 149 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS T 148 " 0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO T 149 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO T 149 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO T 149 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG W 203 " 0.124 9.50e-02 1.11e+02 5.56e-02 2.14e+00 pdb=" NE ARG W 203 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG W 203 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG W 203 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG W 203 " 0.002 2.00e-02 2.50e+03 ... (remaining 8650 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 8990 2.77 - 3.30: 48709 3.30 - 3.83: 92255 3.83 - 4.37: 111191 4.37 - 4.90: 183842 Nonbonded interactions: 444987 Sorted by model distance: nonbonded pdb=" NZ LYS O 54 " pdb=" OE2 GLU O 216 " model vdw 2.235 3.120 nonbonded pdb=" NZ LYS A 54 " pdb=" OE2 GLU A 216 " model vdw 2.259 3.120 nonbonded pdb=" O HOH T 329 " pdb=" O HOH T 336 " model vdw 2.269 3.040 nonbonded pdb=" ND2 ASN D 221 " pdb=" OE2 GLU D 224 " model vdw 2.270 3.120 nonbonded pdb=" ND2 ASN R 221 " pdb=" OE2 GLU R 224 " model vdw 2.272 3.120 ... (remaining 444982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = (chain 'K' and (resid 1 through 5 or (resid 6 and (name N or name CA or name C ) \ ) or (resid 7 and (name N or name CA or name C or name CB or name CG1 or name CG \ 2 or name CD1)) or resid 8 through 40 or (resid 41 and (name N or name CA or nam \ e C or name CB or name CG or name CD or name CE or name NZ )) or resid 42 throug \ h 197)) selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 0.030 Extract box with map and model: 1.590 Check model and map are aligned: 0.290 Set scattering table: 0.340 Process input model: 88.830 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.320 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: 0.020 Load rotamer database and sin/cos tables:9.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 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 0.065 49713 Z= 0.242 Angle : 0.562 8.675 67142 Z= 0.316 Chirality : 0.043 0.319 7518 Planarity : 0.004 0.056 8653 Dihedral : 16.936 125.234 18538 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.15 % Allowed : 13.94 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.10), residues: 6204 helix: 2.00 (0.10), residues: 2358 sheet: 0.65 (0.13), residues: 1505 loop : -0.15 (0.12), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 100 HIS 0.005 0.001 HIS N 89 PHE 0.018 0.002 PHE X 69 TYR 0.016 0.002 TYR K 117 ARG 0.009 0.001 ARG I 203 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 831 time to evaluate : 4.516 Fit side-chains REVERT: A 232 GLU cc_start: 0.7456 (mp0) cc_final: 0.7202 (mp0) REVERT: B 166 ASN cc_start: 0.8370 (t0) cc_final: 0.8030 (t0) REVERT: C 174 MET cc_start: 0.7672 (mtp) cc_final: 0.7457 (mtp) REVERT: C 238 LYS cc_start: 0.7756 (ttmm) cc_final: 0.6960 (mtpp) REVERT: E 86 LYS cc_start: 0.8059 (mttp) cc_final: 0.7522 (mtmp) REVERT: G 186 THR cc_start: 0.8235 (p) cc_final: 0.7964 (m) REVERT: H 84 LYS cc_start: 0.9054 (tmmm) cc_final: 0.8680 (tttp) REVERT: N 156 LYS cc_start: 0.7459 (ptpt) cc_final: 0.7248 (tmmt) REVERT: O 232 GLU cc_start: 0.7402 (mp0) cc_final: 0.7134 (mp0) REVERT: P 55 ILE cc_start: 0.8610 (tt) cc_final: 0.8316 (pt) REVERT: P 166 ASN cc_start: 0.8371 (t0) cc_final: 0.8023 (t0) REVERT: Q 174 MET cc_start: 0.7692 (mtp) cc_final: 0.7480 (mtp) REVERT: S 86 LYS cc_start: 0.8148 (mttp) cc_final: 0.7593 (mtmp) REVERT: U 186 THR cc_start: 0.8214 (p) cc_final: 0.7948 (m) REVERT: V 84 LYS cc_start: 0.9035 (tmmm) cc_final: 0.8583 (tttp) outliers start: 8 outliers final: 8 residues processed: 839 average time/residue: 1.6361 time to fit residues: 1645.8398 Evaluate side-chains 736 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 728 time to evaluate : 4.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 114 ASP Chi-restraints excluded: chain Z residue 102 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 520 optimal weight: 9.9990 chunk 466 optimal weight: 9.9990 chunk 259 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 314 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 chunk 482 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 293 optimal weight: 9.9990 chunk 359 optimal weight: 10.0000 chunk 559 optimal weight: 9.9990 overall best weight: 6.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 224 ASN B 52 GLN B 96 GLN D 85 ASN D 175 ASN E 13 ASN E 155 HIS E 225 ASN F 59 HIS F 86 ASN F 166 GLN F 175 HIS F 183 ASN G 64 ASN G 98 ASN G 144 ASN G 225 HIS K 65 GLN L 162 GLN M 159 GLN N 157 GLN O 172 GLN O 224 ASN P 96 GLN R 85 ASN S 155 HIS S 225 ASN T 59 HIS T 166 GLN T 175 HIS T 183 ASN U 64 ASN U 98 ASN U 144 ASN U 225 HIS Y 65 GLN Z 162 GLN a 159 GLN b 157 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.104409 restraints weight = 45641.805| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.09 r_work: 0.3146 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 49713 Z= 0.417 Angle : 0.691 10.300 67142 Z= 0.385 Chirality : 0.049 0.183 7518 Planarity : 0.006 0.072 8653 Dihedral : 6.944 130.854 7016 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.13 % Allowed : 13.73 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.10), residues: 6204 helix: 1.90 (0.10), residues: 2362 sheet: 0.63 (0.12), residues: 1543 loop : 0.02 (0.13), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP b 209 HIS 0.007 0.002 HIS G 225 PHE 0.024 0.003 PHE C 61 TYR 0.020 0.003 TYR I 90 ARG 0.008 0.001 ARG b 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 721 time to evaluate : 4.742 Fit side-chains REVERT: A 232 GLU cc_start: 0.7705 (mp0) cc_final: 0.7350 (mp0) REVERT: B 166 ASN cc_start: 0.8418 (t0) cc_final: 0.8089 (t0) REVERT: C 174 MET cc_start: 0.7702 (mtp) cc_final: 0.7480 (mtt) REVERT: C 238 LYS cc_start: 0.7711 (ttmm) cc_final: 0.7008 (mtpm) REVERT: E 86 LYS cc_start: 0.8165 (mttp) cc_final: 0.7593 (mtmp) REVERT: G 186 THR cc_start: 0.8004 (p) cc_final: 0.7789 (m) REVERT: H 84 LYS cc_start: 0.9157 (tmmm) cc_final: 0.8760 (tttp) REVERT: O 209 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6940 (p0) REVERT: P 55 ILE cc_start: 0.8620 (tt) cc_final: 0.8294 (pt) REVERT: P 143 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8002 (ttt180) REVERT: P 166 ASN cc_start: 0.8424 (t0) cc_final: 0.8100 (t0) REVERT: P 203 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7622 (ttm) REVERT: Q 174 MET cc_start: 0.7705 (mtp) cc_final: 0.7486 (mtt) REVERT: S 86 LYS cc_start: 0.8176 (mttp) cc_final: 0.7602 (mtmp) REVERT: T 49 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8333 (tm) REVERT: U 148 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8368 (mt0) REVERT: U 186 THR cc_start: 0.8007 (p) cc_final: 0.7785 (m) REVERT: V 84 LYS cc_start: 0.9129 (tmmm) cc_final: 0.8736 (tttp) REVERT: a 99 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8607 (mmt90) outliers start: 111 outliers final: 58 residues processed: 810 average time/residue: 1.5464 time to fit residues: 1517.9010 Evaluate side-chains 771 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 707 time to evaluate : 4.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 209 ASP Chi-restraints excluded: chain P residue 18 LYS Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 173 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 167 SER Chi-restraints excluded: chain T residue 176 MET Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 148 GLN Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain V residue 72 GLU Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 99 ARG Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 85 optimal weight: 6.9990 chunk 317 optimal weight: 2.9990 chunk 489 optimal weight: 2.9990 chunk 324 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 342 optimal weight: 7.9990 chunk 309 optimal weight: 9.9990 chunk 493 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 362 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 52 GLN B 96 GLN D 85 ASN E 225 ASN F 86 ASN F 166 GLN F 183 ASN G 98 ASN G 144 ASN K 65 GLN L 151 GLN M 131 GLN M 159 GLN N 157 GLN O 224 ASN P 96 GLN P 189 HIS R 85 ASN S 225 ASN T 166 GLN T 183 ASN U 98 ASN U 144 ASN Y 65 GLN Z 151 GLN a 131 GLN a 159 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.131766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.104981 restraints weight = 45945.455| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.11 r_work: 0.3152 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 49713 Z= 0.327 Angle : 0.632 9.990 67142 Z= 0.353 Chirality : 0.047 0.167 7518 Planarity : 0.005 0.061 8653 Dihedral : 6.810 131.368 7012 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.15 % Allowed : 13.99 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.38 (0.10), residues: 6204 helix: 2.01 (0.10), residues: 2372 sheet: 0.72 (0.13), residues: 1529 loop : -0.03 (0.13), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP S 100 HIS 0.005 0.001 HIS Y 99 PHE 0.023 0.002 PHE C 61 TYR 0.019 0.002 TYR b 124 ARG 0.007 0.001 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 734 time to evaluate : 4.536 Fit side-chains REVERT: A 232 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: B 166 ASN cc_start: 0.8354 (t0) cc_final: 0.8028 (t0) REVERT: C 231 LYS cc_start: 0.7967 (mmmt) cc_final: 0.7680 (tptp) REVERT: C 238 LYS cc_start: 0.7682 (ttmm) cc_final: 0.7316 (mtpm) REVERT: E 86 LYS cc_start: 0.8141 (mttp) cc_final: 0.7584 (mtmp) REVERT: G 244 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6521 (mm) REVERT: H 84 LYS cc_start: 0.9115 (tmmm) cc_final: 0.8740 (tttp) REVERT: H 196 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8013 (mttp) REVERT: K 110 HIS cc_start: 0.7522 (m90) cc_final: 0.7275 (m-70) REVERT: M 99 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8644 (mmt90) REVERT: P 55 ILE cc_start: 0.8654 (tt) cc_final: 0.8321 (pt) REVERT: P 143 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7870 (ttp-170) REVERT: P 166 ASN cc_start: 0.8370 (t0) cc_final: 0.8044 (t0) REVERT: Q 174 MET cc_start: 0.7670 (mtp) cc_final: 0.7455 (mtt) REVERT: Q 231 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7688 (tptp) REVERT: S 86 LYS cc_start: 0.8153 (mttp) cc_final: 0.7596 (mtmp) REVERT: T 49 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8305 (tm) REVERT: U 148 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8399 (mt0) REVERT: U 244 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6536 (mm) REVERT: V 84 LYS cc_start: 0.9104 (tmmm) cc_final: 0.8733 (tttp) REVERT: V 196 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8058 (mttp) REVERT: Y 110 HIS cc_start: 0.7495 (m90) cc_final: 0.7250 (m-70) REVERT: a 99 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8623 (mmt90) outliers start: 112 outliers final: 61 residues processed: 817 average time/residue: 1.5504 time to fit residues: 1535.9067 Evaluate side-chains 778 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 707 time to evaluate : 4.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 99 ARG Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 173 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 239 ASN Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 167 SER Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 148 GLN Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 99 ARG Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 119 optimal weight: 6.9990 chunk 308 optimal weight: 20.0000 chunk 515 optimal weight: 10.0000 chunk 513 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 467 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 258 optimal weight: 6.9990 chunk 584 optimal weight: 0.9980 chunk 348 optimal weight: 0.9980 chunk 614 optimal weight: 6.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 52 GLN B 96 GLN B 189 HIS C 146 GLN D 85 ASN D 175 ASN E 225 ASN F 86 ASN F 166 GLN F 183 ASN F 185 ASN G 64 ASN G 98 ASN G 144 ASN K 24 ASN K 65 GLN L 151 GLN M 131 GLN M 159 GLN N 157 GLN O 92 GLN O 224 ASN P 52 GLN P 96 GLN P 189 HIS Q 146 GLN R 85 ASN S 225 ASN T 166 GLN T 183 ASN T 185 ASN U 64 ASN U 98 ASN U 144 ASN Y 65 GLN Z 151 GLN a 131 GLN a 159 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.134456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.108139 restraints weight = 46049.344| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.05 r_work: 0.3206 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 49713 Z= 0.177 Angle : 0.530 8.805 67142 Z= 0.295 Chirality : 0.043 0.148 7518 Planarity : 0.004 0.047 8653 Dihedral : 6.388 134.480 7012 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.06 % Allowed : 14.07 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.72 (0.10), residues: 6204 helix: 2.42 (0.10), residues: 2380 sheet: 0.83 (0.13), residues: 1517 loop : 0.06 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Z 55 HIS 0.004 0.001 HIS N 89 PHE 0.018 0.001 PHE W 36 TYR 0.016 0.001 TYR N 124 ARG 0.008 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 733 time to evaluate : 4.445 Fit side-chains REVERT: A 232 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: B 143 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7757 (ttt180) REVERT: B 166 ASN cc_start: 0.8237 (t0) cc_final: 0.7947 (t0) REVERT: C 174 MET cc_start: 0.7892 (mtt) cc_final: 0.7681 (mtp) REVERT: C 231 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7832 (tptp) REVERT: C 238 LYS cc_start: 0.7810 (ttmm) cc_final: 0.7374 (mtpm) REVERT: E 86 LYS cc_start: 0.8125 (mttp) cc_final: 0.7611 (mtmp) REVERT: G 168 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8241 (pttt) REVERT: H 84 LYS cc_start: 0.9067 (tmmm) cc_final: 0.8719 (tttp) REVERT: H 196 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.8007 (mttp) REVERT: K 109 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6931 (pm20) REVERT: K 110 HIS cc_start: 0.7499 (m90) cc_final: 0.7276 (m-70) REVERT: N 156 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7183 (tmmt) REVERT: P 55 ILE cc_start: 0.8635 (tt) cc_final: 0.8341 (pt) REVERT: P 143 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7810 (ttt180) REVERT: P 166 ASN cc_start: 0.8249 (t0) cc_final: 0.7960 (t0) REVERT: Q 212 GLU cc_start: 0.8039 (pt0) cc_final: 0.7630 (pt0) REVERT: Q 231 LYS cc_start: 0.8024 (mmmt) cc_final: 0.7797 (tptp) REVERT: S 86 LYS cc_start: 0.8134 (mttp) cc_final: 0.7619 (mtmp) REVERT: T 49 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8304 (tm) REVERT: U 168 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8231 (pttt) REVERT: U 244 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6470 (mm) REVERT: V 84 LYS cc_start: 0.9065 (tmmm) cc_final: 0.8714 (tttp) REVERT: V 196 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8023 (mttp) REVERT: Y 109 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6938 (pm20) REVERT: Y 110 HIS cc_start: 0.7485 (m90) cc_final: 0.7257 (m-70) REVERT: a 99 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8516 (mmt90) outliers start: 107 outliers final: 50 residues processed: 816 average time/residue: 1.5280 time to fit residues: 1513.8885 Evaluate side-chains 780 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 717 time to evaluate : 4.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 54 CYS Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 173 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain a residue 54 CYS Chi-restraints excluded: chain a residue 99 ARG Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 443 optimal weight: 0.9990 chunk 270 optimal weight: 0.0970 chunk 221 optimal weight: 5.9990 chunk 288 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 531 optimal weight: 0.9980 chunk 507 optimal weight: 0.9980 chunk 195 optimal weight: 0.6980 chunk 328 optimal weight: 9.9990 chunk 296 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 52 GLN B 96 GLN E 186 HIS E 225 ASN F 86 ASN F 166 GLN F 183 ASN G 98 ASN G 144 ASN K 65 GLN L 151 GLN M 131 GLN M 159 GLN O 224 ASN P 96 GLN S 225 ASN T 166 GLN T 183 ASN U 98 ASN U 144 ASN Y 65 GLN Z 151 GLN a 131 GLN a 159 GLN b 157 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.109651 restraints weight = 46434.576| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.04 r_work: 0.3213 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 49713 Z= 0.130 Angle : 0.480 7.771 67142 Z= 0.266 Chirality : 0.041 0.135 7518 Planarity : 0.004 0.046 8653 Dihedral : 5.955 135.873 7012 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.85 % Allowed : 14.67 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.95 (0.11), residues: 6204 helix: 2.66 (0.10), residues: 2382 sheet: 0.94 (0.13), residues: 1511 loop : 0.13 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 55 HIS 0.003 0.001 HIS b 89 PHE 0.018 0.001 PHE W 36 TYR 0.013 0.001 TYR N 124 ARG 0.008 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 744 time to evaluate : 4.482 Fit side-chains REVERT: A 185 LYS cc_start: 0.6389 (OUTLIER) cc_final: 0.6086 (ttpp) REVERT: A 232 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: B 166 ASN cc_start: 0.8153 (t0) cc_final: 0.7878 (t0) REVERT: C 174 MET cc_start: 0.7899 (mtt) cc_final: 0.7636 (mtp) REVERT: C 238 LYS cc_start: 0.7885 (ttmm) cc_final: 0.7477 (mtpm) REVERT: E 86 LYS cc_start: 0.8107 (mttp) cc_final: 0.7616 (mtmp) REVERT: G 168 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8120 (pttt) REVERT: H 84 LYS cc_start: 0.8968 (tmmm) cc_final: 0.8634 (tttp) REVERT: H 196 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7963 (mttp) REVERT: I 93 TYR cc_start: 0.8267 (m-80) cc_final: 0.8034 (m-80) REVERT: K 110 HIS cc_start: 0.7443 (m90) cc_final: 0.7235 (m-70) REVERT: N 156 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.7103 (ttmt) REVERT: P 55 ILE cc_start: 0.8608 (tt) cc_final: 0.8329 (pt) REVERT: P 166 ASN cc_start: 0.8143 (t0) cc_final: 0.7868 (t0) REVERT: R 163 ARG cc_start: 0.8296 (ptt180) cc_final: 0.8066 (ptt180) REVERT: S 86 LYS cc_start: 0.8113 (mttp) cc_final: 0.7615 (mtmp) REVERT: T 49 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8278 (tm) REVERT: U 168 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8116 (pttt) REVERT: U 244 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6434 (mm) REVERT: V 84 LYS cc_start: 0.9030 (tmmm) cc_final: 0.8636 (tttp) REVERT: V 196 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7959 (mttp) REVERT: W 93 TYR cc_start: 0.8253 (m-80) cc_final: 0.8022 (m-80) REVERT: Y 110 HIS cc_start: 0.7441 (m90) cc_final: 0.7229 (m-70) REVERT: a 99 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8488 (mmt90) REVERT: b 156 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.7042 (tmmt) outliers start: 96 outliers final: 44 residues processed: 816 average time/residue: 1.5125 time to fit residues: 1500.1529 Evaluate side-chains 772 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 717 time to evaluate : 4.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 132 HIS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 54 CYS Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 150 ASP Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 238 GLU Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 114 ASP Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Y residue 18 ASP Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain a residue 54 CYS Chi-restraints excluded: chain a residue 99 ARG Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 156 LYS Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 159 optimal weight: 6.9990 chunk 422 optimal weight: 9.9990 chunk 394 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 330 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 464 optimal weight: 8.9990 chunk 193 optimal weight: 9.9990 chunk 376 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 601 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 52 GLN B 96 GLN B 189 HIS D 175 ASN E 225 ASN F 68 ASN F 86 ASN F 166 GLN F 185 ASN G 64 ASN G 144 ASN K 65 GLN M 131 GLN M 159 GLN O 224 ASN P 96 GLN R 175 ASN S 225 ASN T 68 ASN T 166 GLN T 185 ASN U 64 ASN U 144 ASN Y 65 GLN a 131 GLN a 159 GLN b 157 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102499 restraints weight = 45501.181| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.06 r_work: 0.3113 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 49713 Z= 0.394 Angle : 0.666 10.415 67142 Z= 0.370 Chirality : 0.048 0.155 7518 Planarity : 0.006 0.075 8653 Dihedral : 6.698 129.014 7009 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.96 % Allowed : 14.63 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.53 (0.10), residues: 6204 helix: 2.18 (0.10), residues: 2363 sheet: 0.72 (0.12), residues: 1551 loop : 0.06 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP b 209 HIS 0.007 0.002 HIS b 89 PHE 0.025 0.003 PHE J 69 TYR 0.021 0.003 TYR I 90 ARG 0.008 0.001 ARG J 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 708 time to evaluate : 4.495 Fit side-chains REVERT: A 232 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: B 143 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7891 (ttp-170) REVERT: B 166 ASN cc_start: 0.8304 (t0) cc_final: 0.7985 (t0) REVERT: C 174 MET cc_start: 0.7974 (mtt) cc_final: 0.7714 (mtt) REVERT: C 231 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7720 (tptp) REVERT: D 163 ARG cc_start: 0.8407 (ptt180) cc_final: 0.8136 (ptt180) REVERT: E 86 LYS cc_start: 0.8154 (mttp) cc_final: 0.7608 (mtmp) REVERT: F 83 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8843 (mp) REVERT: G 168 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8350 (pttt) REVERT: G 244 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6533 (mm) REVERT: H 196 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8027 (mttp) REVERT: K 110 HIS cc_start: 0.7536 (m90) cc_final: 0.7304 (m-70) REVERT: P 55 ILE cc_start: 0.8644 (tt) cc_final: 0.8349 (pt) REVERT: P 143 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7909 (ttt180) REVERT: P 166 ASN cc_start: 0.8297 (t0) cc_final: 0.7976 (t0) REVERT: Q 231 LYS cc_start: 0.8017 (mmmt) cc_final: 0.7695 (tptp) REVERT: S 86 LYS cc_start: 0.8157 (mttp) cc_final: 0.7605 (mtmp) REVERT: T 49 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8286 (tm) REVERT: T 83 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8840 (mp) REVERT: U 168 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8349 (pttt) REVERT: U 244 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6571 (mm) REVERT: V 84 LYS cc_start: 0.9101 (tmmm) cc_final: 0.8740 (tttp) REVERT: V 196 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8047 (mttp) outliers start: 102 outliers final: 54 residues processed: 787 average time/residue: 1.5003 time to fit residues: 1439.5304 Evaluate side-chains 769 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 703 time to evaluate : 4.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 104 LYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 114 ASP Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 156 LYS Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 525 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 433 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 520 optimal weight: 3.9990 chunk 286 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 357 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 52 GLN B 96 GLN B 189 HIS D 175 ASN E 225 ASN F 86 ASN F 166 GLN F 185 ASN G 98 ASN G 144 ASN K 65 GLN M 159 GLN O 224 ASN P 96 GLN P 189 HIS R 175 ASN S 225 ASN T 90 GLN T 166 GLN T 185 ASN U 98 ASN U 144 ASN Y 65 GLN a 131 GLN a 159 GLN b 157 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.131381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104032 restraints weight = 45555.205| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.06 r_work: 0.3124 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 49713 Z= 0.266 Angle : 0.589 9.552 67142 Z= 0.328 Chirality : 0.045 0.147 7518 Planarity : 0.005 0.051 8653 Dihedral : 6.538 131.358 7009 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.65 % Allowed : 15.15 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.10), residues: 6204 helix: 2.25 (0.10), residues: 2364 sheet: 0.75 (0.12), residues: 1529 loop : 0.05 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 100 HIS 0.006 0.001 HIS N 89 PHE 0.020 0.002 PHE X 69 TYR 0.018 0.002 TYR N 124 ARG 0.008 0.001 ARG Q 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 725 time to evaluate : 4.537 Fit side-chains REVERT: A 232 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: B 166 ASN cc_start: 0.8272 (t0) cc_final: 0.7946 (t0) REVERT: C 174 MET cc_start: 0.7937 (mtt) cc_final: 0.7632 (mtt) REVERT: C 231 LYS cc_start: 0.8041 (mmmt) cc_final: 0.7796 (tptp) REVERT: D 163 ARG cc_start: 0.8365 (ptt180) cc_final: 0.8160 (ptt180) REVERT: E 86 LYS cc_start: 0.8124 (mttp) cc_final: 0.7562 (mtmp) REVERT: F 83 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8810 (mp) REVERT: G 168 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8305 (pttt) REVERT: H 196 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7998 (mttp) REVERT: I 54 MET cc_start: 0.8623 (mmt) cc_final: 0.8410 (mmp) REVERT: I 93 TYR cc_start: 0.8296 (m-80) cc_final: 0.7990 (m-80) REVERT: K 110 HIS cc_start: 0.7489 (m90) cc_final: 0.7237 (m-70) REVERT: P 55 ILE cc_start: 0.8630 (tt) cc_final: 0.8348 (pt) REVERT: P 166 ASN cc_start: 0.8262 (t0) cc_final: 0.7934 (t0) REVERT: Q 231 LYS cc_start: 0.8051 (mmmt) cc_final: 0.7772 (tptp) REVERT: R 163 ARG cc_start: 0.8379 (ptt180) cc_final: 0.8142 (ptt180) REVERT: S 86 LYS cc_start: 0.8136 (mttp) cc_final: 0.7568 (mtmp) REVERT: T 49 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8287 (tm) REVERT: T 83 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8808 (mp) REVERT: U 168 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8304 (pttt) REVERT: U 244 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6561 (mm) REVERT: V 84 LYS cc_start: 0.9084 (tmmm) cc_final: 0.8727 (tttp) REVERT: V 196 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8003 (mttp) outliers start: 86 outliers final: 55 residues processed: 790 average time/residue: 1.5440 time to fit residues: 1488.6409 Evaluate side-chains 773 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 709 time to evaluate : 4.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 150 ASP Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 100 ASP Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 238 GLU Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 114 ASP Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 213 optimal weight: 0.5980 chunk 274 optimal weight: 5.9990 chunk 501 optimal weight: 5.9990 chunk 354 optimal weight: 0.7980 chunk 172 optimal weight: 7.9990 chunk 388 optimal weight: 7.9990 chunk 378 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 52 GLN B 96 GLN B 189 HIS D 175 ASN E 225 ASN F 86 ASN F 166 GLN F 183 ASN F 185 ASN G 98 ASN G 144 ASN K 65 GLN M 159 GLN O 224 ASN P 96 GLN P 189 HIS R 175 ASN S 186 HIS S 225 ASN T 90 GLN T 166 GLN T 183 ASN T 185 ASN U 98 ASN U 144 ASN Y 65 GLN a 159 GLN b 157 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.132293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105053 restraints weight = 45797.941| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.06 r_work: 0.3145 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 49713 Z= 0.210 Angle : 0.555 9.182 67142 Z= 0.308 Chirality : 0.043 0.148 7518 Planarity : 0.004 0.049 8653 Dihedral : 6.387 132.795 7009 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.60 % Allowed : 15.32 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.68 (0.10), residues: 6204 helix: 2.37 (0.10), residues: 2374 sheet: 0.82 (0.13), residues: 1513 loop : 0.05 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 189 HIS 0.005 0.001 HIS N 89 PHE 0.019 0.002 PHE I 36 TYR 0.017 0.002 TYR N 124 ARG 0.008 0.001 ARG J 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 718 time to evaluate : 5.080 Fit side-chains REVERT: A 232 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: B 143 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7739 (ttt180) REVERT: B 166 ASN cc_start: 0.8247 (t0) cc_final: 0.7958 (t0) REVERT: C 174 MET cc_start: 0.7956 (mtt) cc_final: 0.7686 (mtt) REVERT: C 231 LYS cc_start: 0.8017 (mmmt) cc_final: 0.7774 (tptp) REVERT: C 238 LYS cc_start: 0.7905 (ttmm) cc_final: 0.7447 (mtpm) REVERT: D 163 ARG cc_start: 0.8363 (ptt180) cc_final: 0.8159 (ptt180) REVERT: E 86 LYS cc_start: 0.8119 (mttp) cc_final: 0.7606 (mtmp) REVERT: G 168 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8289 (pttt) REVERT: G 244 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6493 (mm) REVERT: H 84 LYS cc_start: 0.9078 (tmmm) cc_final: 0.8725 (tttp) REVERT: H 196 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7984 (mttp) REVERT: I 54 MET cc_start: 0.8623 (mmt) cc_final: 0.8415 (mmp) REVERT: K 109 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: K 110 HIS cc_start: 0.7470 (m90) cc_final: 0.7246 (m-70) REVERT: P 55 ILE cc_start: 0.8631 (tt) cc_final: 0.8357 (pt) REVERT: P 143 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7736 (ttt180) REVERT: P 166 ASN cc_start: 0.8241 (t0) cc_final: 0.7950 (t0) REVERT: Q 174 MET cc_start: 0.7895 (mtp) cc_final: 0.7690 (mtp) REVERT: Q 231 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7762 (tptp) REVERT: R 163 ARG cc_start: 0.8368 (ptt180) cc_final: 0.8110 (ptt-90) REVERT: S 86 LYS cc_start: 0.8134 (mttp) cc_final: 0.7621 (mtmp) REVERT: T 49 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8288 (tm) REVERT: U 168 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8283 (pttt) REVERT: U 244 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6525 (mm) REVERT: V 196 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7995 (mttp) outliers start: 83 outliers final: 53 residues processed: 777 average time/residue: 1.5357 time to fit residues: 1449.4685 Evaluate side-chains 774 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 710 time to evaluate : 4.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 150 ASP Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 100 ASP Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 238 GLU Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 114 ASP Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain a residue 54 CYS Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 379 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 480 optimal weight: 7.9990 chunk 266 optimal weight: 0.4980 chunk 153 optimal weight: 5.9990 chunk 397 optimal weight: 9.9990 chunk 430 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 52 GLN B 96 GLN B 189 HIS D 175 ASN E 225 ASN F 86 ASN F 90 GLN F 166 GLN F 183 ASN F 185 ASN G 64 ASN G 98 ASN G 144 ASN K 65 GLN M 159 GLN O 224 ASN P 96 GLN P 189 HIS R 175 ASN S 225 ASN T 90 GLN T 166 GLN T 183 ASN T 185 ASN U 64 ASN U 98 ASN U 144 ASN Y 65 GLN a 159 GLN b 157 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.102919 restraints weight = 45538.175| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.06 r_work: 0.3108 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 49713 Z= 0.361 Angle : 0.656 10.304 67142 Z= 0.364 Chirality : 0.047 0.155 7518 Planarity : 0.005 0.074 8653 Dihedral : 6.728 130.893 7009 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.61 % Allowed : 15.44 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.10), residues: 6204 helix: 2.05 (0.10), residues: 2373 sheet: 0.69 (0.12), residues: 1551 loop : 0.02 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP O 189 HIS 0.006 0.002 HIS N 89 PHE 0.024 0.002 PHE J 69 TYR 0.022 0.002 TYR T 153 ARG 0.009 0.001 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 703 time to evaluate : 4.488 Fit side-chains REVERT: A 232 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: B 143 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7921 (ttt180) REVERT: B 166 ASN cc_start: 0.8283 (t0) cc_final: 0.7962 (t0) REVERT: C 174 MET cc_start: 0.7940 (mtt) cc_final: 0.7630 (mtt) REVERT: C 231 LYS cc_start: 0.8022 (mmmt) cc_final: 0.7706 (tptp) REVERT: C 238 LYS cc_start: 0.7917 (ttmm) cc_final: 0.7442 (mtpm) REVERT: D 163 ARG cc_start: 0.8397 (ptt180) cc_final: 0.8171 (ptt180) REVERT: E 86 LYS cc_start: 0.8154 (mttp) cc_final: 0.7600 (mtmp) REVERT: G 168 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8345 (pttt) REVERT: G 244 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6497 (mm) REVERT: H 196 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7981 (mttp) REVERT: I 54 MET cc_start: 0.8635 (mmt) cc_final: 0.8425 (mmp) REVERT: K 110 HIS cc_start: 0.7499 (m90) cc_final: 0.7252 (m-70) REVERT: P 55 ILE cc_start: 0.8642 (tt) cc_final: 0.8373 (pt) REVERT: P 143 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7912 (ttt180) REVERT: P 166 ASN cc_start: 0.8283 (t0) cc_final: 0.7960 (t0) REVERT: Q 174 MET cc_start: 0.7899 (mtp) cc_final: 0.7647 (mtp) REVERT: Q 231 LYS cc_start: 0.7973 (mmmt) cc_final: 0.7669 (tptp) REVERT: R 163 ARG cc_start: 0.8401 (ptt180) cc_final: 0.8189 (ptt180) REVERT: S 86 LYS cc_start: 0.8156 (mttp) cc_final: 0.7601 (mtmp) REVERT: T 49 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8294 (tm) REVERT: U 168 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8342 (pttt) REVERT: U 244 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6544 (mm) REVERT: V 196 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8047 (mttp) outliers start: 84 outliers final: 54 residues processed: 763 average time/residue: 1.5127 time to fit residues: 1405.7905 Evaluate side-chains 766 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 702 time to evaluate : 4.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 100 ASP Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 238 GLU Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 114 ASP Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain U residue 224 ARG Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 101 optimal weight: 10.0000 chunk 458 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 514 optimal weight: 10.0000 chunk 272 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 381 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 52 GLN B 96 GLN B 189 HIS D 15 HIS D 175 ASN E 225 ASN F 86 ASN F 166 GLN F 183 ASN F 185 ASN G 98 ASN G 144 ASN K 65 GLN M 159 GLN O 224 ASN P 52 GLN P 96 GLN P 189 HIS R 175 ASN S 225 ASN T 166 GLN T 183 ASN T 185 ASN U 98 ASN U 144 ASN Y 65 GLN a 159 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.130217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102736 restraints weight = 45760.302| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.06 r_work: 0.3104 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 49713 Z= 0.335 Angle : 0.644 10.038 67142 Z= 0.357 Chirality : 0.047 0.152 7518 Planarity : 0.005 0.067 8653 Dihedral : 6.714 131.138 7009 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.48 % Allowed : 15.71 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.38 (0.10), residues: 6204 helix: 2.01 (0.10), residues: 2374 sheet: 0.68 (0.12), residues: 1547 loop : -0.00 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP O 189 HIS 0.006 0.001 HIS N 89 PHE 0.023 0.002 PHE J 69 TYR 0.020 0.002 TYR K 134 ARG 0.008 0.001 ARG C 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 706 time to evaluate : 4.516 Fit side-chains REVERT: A 232 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: B 143 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7910 (ttt180) REVERT: B 166 ASN cc_start: 0.8286 (t0) cc_final: 0.7966 (t0) REVERT: C 174 MET cc_start: 0.7948 (mtt) cc_final: 0.7669 (mtt) REVERT: C 231 LYS cc_start: 0.8012 (mmmt) cc_final: 0.7766 (tptp) REVERT: C 238 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7471 (mtpm) REVERT: D 163 ARG cc_start: 0.8384 (ptt180) cc_final: 0.8157 (ptt180) REVERT: E 86 LYS cc_start: 0.8149 (mttp) cc_final: 0.7598 (mtmp) REVERT: G 168 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8319 (pttt) REVERT: G 244 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6499 (mm) REVERT: H 196 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7976 (mttp) REVERT: I 54 MET cc_start: 0.8625 (mmt) cc_final: 0.8417 (mmp) REVERT: K 109 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6891 (pm20) REVERT: K 110 HIS cc_start: 0.7520 (m90) cc_final: 0.7302 (m-70) REVERT: P 55 ILE cc_start: 0.8635 (tt) cc_final: 0.8372 (pt) REVERT: P 143 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7900 (ttt180) REVERT: P 166 ASN cc_start: 0.8286 (t0) cc_final: 0.7965 (t0) REVERT: Q 231 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7668 (tptp) REVERT: R 163 ARG cc_start: 0.8386 (ptt180) cc_final: 0.8174 (ptt180) REVERT: S 86 LYS cc_start: 0.8150 (mttp) cc_final: 0.7596 (mtmp) REVERT: T 49 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8295 (tm) REVERT: U 168 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8321 (pttt) REVERT: U 244 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6553 (mm) REVERT: V 196 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8044 (mttp) outliers start: 77 outliers final: 53 residues processed: 764 average time/residue: 1.5664 time to fit residues: 1462.4400 Evaluate side-chains 763 residues out of total 5206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 699 time to evaluate : 4.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 150 ASP Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 100 ASP Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 238 GLU Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain U residue 224 ARG Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 254 optimal weight: 6.9990 chunk 366 optimal weight: 10.0000 chunk 512 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 353 optimal weight: 0.4980 chunk 18 optimal weight: 9.9990 chunk 462 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 256 optimal weight: 4.9990 chunk 383 optimal weight: 10.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 52 GLN B 96 GLN B 189 HIS D 15 HIS D 175 ASN E 186 HIS E 225 ASN F 86 ASN F 166 GLN F 183 ASN F 185 ASN G 98 ASN G 144 ASN K 65 GLN L 151 GLN M 159 GLN O 224 ASN P 96 GLN P 189 HIS R 175 ASN S 186 HIS S 225 ASN T 166 GLN T 183 ASN T 185 ASN U 98 ASN U 144 ASN Y 24 ASN Y 65 GLN Z 151 GLN a 159 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.130246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.102857 restraints weight = 45615.080| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.06 r_work: 0.3108 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 49713 Z= 0.355 Angle : 0.657 10.142 67142 Z= 0.365 Chirality : 0.047 0.153 7518 Planarity : 0.005 0.071 8653 Dihedral : 6.755 131.123 7009 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.52 % Allowed : 15.72 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.35 (0.10), residues: 6204 helix: 1.97 (0.10), residues: 2373 sheet: 0.67 (0.12), residues: 1547 loop : -0.01 (0.13), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP O 189 HIS 0.006 0.001 HIS K 99 PHE 0.024 0.002 PHE J 69 TYR 0.023 0.002 TYR K 134 ARG 0.009 0.001 ARG Q 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40810.05 seconds wall clock time: 695 minutes 57.14 seconds (41757.14 seconds total)