Starting phenix.real_space_refine on Mon Nov 18 00:55:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0t_17337/11_2024/8p0t_17337.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0t_17337/11_2024/8p0t_17337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0t_17337/11_2024/8p0t_17337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0t_17337/11_2024/8p0t_17337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0t_17337/11_2024/8p0t_17337.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0t_17337/11_2024/8p0t_17337.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.063 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 256 5.16 5 C 30200 2.51 5 N 8200 2.21 5 O 9122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 47778 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1843 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 8, 'TRANS': 230} Chain: "B" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1770 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain: "C" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1819 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 1 Chain: "D" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1806 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1754 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 1 Chain: "F" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1709 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 1 Chain: "G" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1836 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain: "H" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1536 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 5, 'TRANS': 198} Chain: "I" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "J" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1599 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "K" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1502 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "L" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1578 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain: "M" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1656 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 203} Chain: "N" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1594 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Classifications: {'peptide': 1} Chain: "L" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Classifications: {'peptide': 1} Restraints were copied for chains: V, Z, W, P, U, T, R, O, a, S, Q, b, Y, X Time building chain proxies: 25.82, per 1000 atoms: 0.54 Number of scatterers: 47778 At special positions: 0 Unit cell: (178.5, 177.1, 130.2, 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 256 16.00 O 9122 8.00 N 8200 7.00 C 30200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 72 " distance=2.03 Simple disulfide: pdb=" SG CYS J 11 " - pdb=" SG CYS J 143 " distance=2.03 Simple disulfide: pdb=" SG CYS J 167 " - pdb=" SG CYS J 171 " distance=2.06 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.89 Conformation dependent library (CDL) restraints added in 6.0 seconds 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11336 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 70 sheets defined 39.6% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.19 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.607A pdb=" N TYR A 8 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 30 Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 79 through 102 Processing helix chain 'A' and resid 106 through 124 Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 185 through 202 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 226 through 239 Processing helix chain 'B' and resid 17 through 29 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 77 through 100 Processing helix chain 'B' and resid 104 through 122 Processing helix chain 'B' and resid 164 through 176 Processing helix chain 'B' and resid 181 through 196 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 221 through 231 Processing helix chain 'C' and resid 18 through 30 Processing helix chain 'C' and resid 78 through 101 Processing helix chain 'C' and resid 105 through 123 Processing helix chain 'C' and resid 166 through 178 Processing helix chain 'C' and resid 183 through 198 Processing helix chain 'C' and resid 228 through 238 Processing helix chain 'D' and resid 17 through 30 Processing helix chain 'D' and resid 77 through 99 Processing helix chain 'D' and resid 104 through 122 Processing helix chain 'D' and resid 166 through 178 Processing helix chain 'D' and resid 183 through 197 Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'E' and resid 21 through 33 Processing helix chain 'E' and resid 81 through 104 Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.694A pdb=" N LEU E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 185 removed outlier: 4.110A pdb=" N ASP E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 207 Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'F' and resid 19 through 31 Processing helix chain 'F' and resid 77 through 100 Processing helix chain 'F' and resid 104 through 122 Processing helix chain 'F' and resid 164 through 175 removed outlier: 3.806A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 182 Proline residue: F 180 - end of helix Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 225 through 233 removed outlier: 4.274A pdb=" N LYS F 230 " --> pdb=" O PRO F 226 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N TYR F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP F 233 " --> pdb=" O GLN F 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.549A pdb=" N ASP G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.668A pdb=" N GLN G 119 " --> pdb=" O GLU G 115 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS G 124 " --> pdb=" O PHE G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 176 removed outlier: 3.586A pdb=" N LYS G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 182 removed outlier: 5.802A pdb=" N LYS G 180 " --> pdb=" O THR G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 199 Proline residue: G 189 - end of helix Processing helix chain 'H' and resid 48 through 67 Processing helix chain 'H' and resid 76 through 92 Processing helix chain 'H' and resid 130 through 144 removed outlier: 3.709A pdb=" N THR H 134 " --> pdb=" O GLY H 130 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE H 136 " --> pdb=" O GLY H 132 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA H 138 " --> pdb=" O THR H 134 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR H 139 " --> pdb=" O TYR H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 168 Processing helix chain 'H' and resid 198 through 202 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 removed outlier: 3.540A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 166 Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'J' and resid 57 through 80 Processing helix chain 'J' and resid 84 through 99 removed outlier: 3.776A pdb=" N LYS J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 155 Processing helix chain 'J' and resid 160 through 177 removed outlier: 3.902A pdb=" N ALA J 175 " --> pdb=" O CYS J 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 71 removed outlier: 3.543A pdb=" N GLN K 55 " --> pdb=" O GLY K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 95 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.646A pdb=" N MET K 137 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N SER K 138 " --> pdb=" O TYR K 134 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 168 Processing helix chain 'L' and resid 48 through 70 Processing helix chain 'L' and resid 75 through 90 removed outlier: 3.635A pdb=" N TYR L 90 " --> pdb=" O GLU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 removed outlier: 3.638A pdb=" N THR L 141 " --> pdb=" O GLY L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 167 Processing helix chain 'L' and resid 192 through 196 Processing helix chain 'M' and resid 68 through 91 Processing helix chain 'M' and resid 95 through 110 removed outlier: 3.617A pdb=" N LYS M 110 " --> pdb=" O THR M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 165 Proline residue: M 158 - end of helix Processing helix chain 'M' and resid 178 through 197 Processing helix chain 'N' and resid 56 through 77 Processing helix chain 'N' and resid 83 through 101 Processing helix chain 'N' and resid 140 through 145 removed outlier: 3.549A pdb=" N TYR N 144 " --> pdb=" O GLY N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 157 through 176 Processing helix chain 'N' and resid 204 through 208 removed outlier: 3.821A pdb=" N VAL N 207 " --> pdb=" O ASN N 204 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL N 208 " --> pdb=" O TRP N 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 204 through 208' Processing helix chain 'O' and resid 4 through 9 removed outlier: 3.607A pdb=" N TYR O 8 " --> pdb=" O GLY O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 30 Processing helix chain 'O' and resid 58 through 62 Processing helix chain 'O' and resid 79 through 102 Processing helix chain 'O' and resid 106 through 124 Processing helix chain 'O' and resid 168 through 180 Processing helix chain 'O' and resid 185 through 202 Processing helix chain 'O' and resid 206 through 208 No H-bonds generated for 'chain 'O' and resid 206 through 208' Processing helix chain 'O' and resid 226 through 239 Processing helix chain 'P' and resid 17 through 29 Processing helix chain 'P' and resid 56 through 60 Processing helix chain 'P' and resid 77 through 100 Processing helix chain 'P' and resid 104 through 122 Processing helix chain 'P' and resid 164 through 176 Processing helix chain 'P' and resid 181 through 196 Processing helix chain 'P' and resid 202 through 204 No H-bonds generated for 'chain 'P' and resid 202 through 204' Processing helix chain 'P' and resid 221 through 231 Processing helix chain 'Q' and resid 18 through 30 Processing helix chain 'Q' and resid 78 through 101 Processing helix chain 'Q' and resid 105 through 123 Processing helix chain 'Q' and resid 166 through 178 Processing helix chain 'Q' and resid 183 through 198 Processing helix chain 'Q' and resid 228 through 238 Processing helix chain 'R' and resid 17 through 30 Processing helix chain 'R' and resid 77 through 99 Processing helix chain 'R' and resid 104 through 122 Processing helix chain 'R' and resid 166 through 178 Processing helix chain 'R' and resid 183 through 197 Processing helix chain 'R' and resid 221 through 233 Processing helix chain 'S' and resid 21 through 33 Processing helix chain 'S' and resid 81 through 104 Processing helix chain 'S' and resid 108 through 119 removed outlier: 3.693A pdb=" N LEU S 119 " --> pdb=" O SER S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 185 removed outlier: 4.110A pdb=" N ASP S 185 " --> pdb=" O ALA S 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 207 Processing helix chain 'S' and resid 233 through 244 Processing helix chain 'T' and resid 19 through 31 Processing helix chain 'T' and resid 77 through 100 Processing helix chain 'T' and resid 104 through 122 Processing helix chain 'T' and resid 164 through 175 removed outlier: 3.806A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 182 Proline residue: T 180 - end of helix Processing helix chain 'T' and resid 183 through 195 Processing helix chain 'T' and resid 225 through 233 removed outlier: 4.274A pdb=" N LYS T 230 " --> pdb=" O PRO T 226 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N TYR T 231 " --> pdb=" O GLU T 227 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP T 233 " --> pdb=" O GLN T 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 34 removed outlier: 3.549A pdb=" N ASP U 34 " --> pdb=" O ALA U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 104 Processing helix chain 'U' and resid 108 through 126 removed outlier: 3.668A pdb=" N GLN U 119 " --> pdb=" O GLU U 115 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS U 124 " --> pdb=" O PHE U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 166 through 176 removed outlier: 3.585A pdb=" N LYS U 176 " --> pdb=" O ALA U 172 " (cutoff:3.500A) Processing helix chain 'U' and resid 177 through 182 removed outlier: 5.802A pdb=" N LYS U 180 " --> pdb=" O THR U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 199 Proline residue: U 189 - end of helix Processing helix chain 'V' and resid 48 through 67 Processing helix chain 'V' and resid 76 through 92 Processing helix chain 'V' and resid 130 through 144 removed outlier: 3.710A pdb=" N THR V 134 " --> pdb=" O GLY V 130 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR V 135 " --> pdb=" O SER V 131 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE V 136 " --> pdb=" O GLY V 132 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA V 138 " --> pdb=" O THR V 134 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR V 139 " --> pdb=" O TYR V 135 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 168 Processing helix chain 'V' and resid 198 through 202 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 removed outlier: 3.539A pdb=" N VAL W 137 " --> pdb=" O ALA W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 166 Processing helix chain 'W' and resid 201 through 205 Processing helix chain 'X' and resid 57 through 80 Processing helix chain 'X' and resid 84 through 99 removed outlier: 3.776A pdb=" N LYS X 99 " --> pdb=" O THR X 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 155 Processing helix chain 'X' and resid 160 through 177 removed outlier: 3.903A pdb=" N ALA X 175 " --> pdb=" O CYS X 171 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 71 removed outlier: 3.543A pdb=" N GLN Y 55 " --> pdb=" O GLY Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 95 Processing helix chain 'Y' and resid 132 through 144 removed outlier: 3.645A pdb=" N MET Y 137 " --> pdb=" O GLN Y 133 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N SER Y 138 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL Y 139 " --> pdb=" O PHE Y 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 149 through 168 Processing helix chain 'Z' and resid 48 through 70 Processing helix chain 'Z' and resid 75 through 90 removed outlier: 3.634A pdb=" N TYR Z 90 " --> pdb=" O GLU Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 3.638A pdb=" N THR Z 141 " --> pdb=" O GLY Z 137 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 167 Processing helix chain 'Z' and resid 192 through 196 Processing helix chain 'a' and resid 68 through 91 Processing helix chain 'a' and resid 95 through 110 removed outlier: 3.617A pdb=" N LYS a 110 " --> pdb=" O THR a 106 " (cutoff:3.500A) Processing helix chain 'a' and resid 152 through 165 Proline residue: a 158 - end of helix Processing helix chain 'a' and resid 178 through 197 Processing helix chain 'b' and resid 56 through 77 Processing helix chain 'b' and resid 83 through 101 Processing helix chain 'b' and resid 140 through 145 removed outlier: 3.549A pdb=" N TYR b 144 " --> pdb=" O GLY b 140 " (cutoff:3.500A) Processing helix chain 'b' and resid 157 through 176 Processing helix chain 'b' and resid 204 through 208 removed outlier: 3.821A pdb=" N VAL b 207 " --> pdb=" O ASN b 204 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL b 208 " --> pdb=" O TRP b 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 204 through 208' Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 166 removed outlier: 4.851A pdb=" N THR A 34 " --> pdb=" O GLN A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 67 Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 160 removed outlier: 3.683A pdb=" N GLY B 41 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE B 208 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 65 removed outlier: 4.017A pdb=" N LEU B 144 " --> pdb=" O TRP B 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 160 through 163 removed outlier: 3.731A pdb=" N GLY C 42 " --> pdb=" O PHE C 39 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE C 211 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 65 through 68 removed outlier: 5.185A pdb=" N LYS C 66 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR C 73 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 160 through 163 Processing sheet with id=AA8, first strand: chain 'D' and resid 64 through 67 removed outlier: 6.066A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 169 through 172 Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 68 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: 6.401A pdb=" N ILE F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU F 144 " --> pdb=" O TYR F 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 160 through 163 Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 69 Processing sheet with id=AB6, first strand: chain 'H' and resid 126 through 129 Processing sheet with id=AB7, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.923A pdb=" N THR H 20 " --> pdb=" O PRO H 27 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.306A pdb=" N ILE H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL H 112 " --> pdb=" O LYS H 124 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 124 through 127 removed outlier: 3.532A pdb=" N GLY I 11 " --> pdb=" O PHE I 8 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU I 175 " --> pdb=" O ASP I 197 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP I 197 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL I 177 " --> pdb=" O TYR I 195 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N TYR I 195 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LYS I 179 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR I 193 " --> pdb=" O LYS I 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.444A pdb=" N ALA I 20 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE I 25 " --> pdb=" O ALA I 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.159A pdb=" N LEU I 34 " --> pdb=" O GLY I 45 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLY I 45 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N TYR I 36 " --> pdb=" O VAL I 43 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL I 43 " --> pdb=" O TYR I 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 221 through 228 removed outlier: 3.783A pdb=" N LYS J 195 " --> pdb=" O THR J 192 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N CYS J 11 " --> pdb=" O ASP J 26 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 29 through 31 removed outlier: 6.544A pdb=" N LEU J 29 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 43 through 47 removed outlier: 6.295A pdb=" N ILE J 50 " --> pdb=" O ILE J 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 126 through 129 removed outlier: 4.148A pdb=" N VAL K 177 " --> pdb=" O ILE K 188 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 21 through 23 removed outlier: 6.628A pdb=" N VAL K 21 " --> pdb=" O MET K 28 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'L' and resid 125 through 128 removed outlier: 6.224A pdb=" N VAL L 174 " --> pdb=" O LYS L 189 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS L 189 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL L 176 " --> pdb=" O ILE L 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.573A pdb=" N GLY L 22 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE L 26 " --> pdb=" O GLY L 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.541A pdb=" N MET L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE L 111 " --> pdb=" O GLY L 123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 146 through 150 removed outlier: 5.148A pdb=" N THR M 22 " --> pdb=" O ASP M 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 40 through 42 removed outlier: 6.715A pdb=" N LEU M 40 " --> pdb=" O ASP M 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 54 through 56 removed outlier: 3.815A pdb=" N ILE M 119 " --> pdb=" O TYR M 135 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU M 132 " --> pdb=" O LEU M 144 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 32 through 35 removed outlier: 5.487A pdb=" N PHE N 33 " --> pdb=" O TYR N 29 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR N 29 " --> pdb=" O PHE N 33 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 32 through 35 removed outlier: 5.487A pdb=" N PHE N 33 " --> pdb=" O TYR N 29 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR N 29 " --> pdb=" O PHE N 33 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 136 through 139 removed outlier: 4.921A pdb=" N PHE N 185 " --> pdb=" O ALA N 197 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ALA N 197 " --> pdb=" O PHE N 185 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR N 187 " --> pdb=" O HIS N 195 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N HIS N 195 " --> pdb=" O THR N 187 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR N 189 " --> pdb=" O ILE N 193 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE N 193 " --> pdb=" O THR N 189 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 162 through 166 removed outlier: 4.850A pdb=" N THR O 34 " --> pdb=" O GLN O 49 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 65 through 67 Processing sheet with id=AE2, first strand: chain 'P' and resid 158 through 160 removed outlier: 3.683A pdb=" N GLY P 41 " --> pdb=" O ALA P 38 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE P 208 " --> pdb=" O LEU P 220 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 64 through 65 removed outlier: 4.017A pdb=" N LEU P 144 " --> pdb=" O TRP P 156 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 160 through 163 removed outlier: 3.731A pdb=" N GLY Q 42 " --> pdb=" O PHE Q 39 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE Q 211 " --> pdb=" O LEU Q 227 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 65 through 68 removed outlier: 5.185A pdb=" N LYS Q 66 " --> pdb=" O THR Q 73 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR Q 73 " --> pdb=" O LYS Q 66 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 160 through 163 Processing sheet with id=AE7, first strand: chain 'R' and resid 64 through 67 removed outlier: 6.066A pdb=" N VAL R 70 " --> pdb=" O LEU R 66 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 169 through 172 Processing sheet with id=AE9, first strand: chain 'S' and resid 67 through 68 Processing sheet with id=AF1, first strand: chain 'T' and resid 158 through 161 Processing sheet with id=AF2, first strand: chain 'T' and resid 63 through 67 removed outlier: 6.400A pdb=" N ILE T 70 " --> pdb=" O ILE T 66 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU T 144 " --> pdb=" O TYR T 156 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 160 through 163 Processing sheet with id=AF4, first strand: chain 'U' and resid 67 through 69 Processing sheet with id=AF5, first strand: chain 'V' and resid 126 through 129 Processing sheet with id=AF6, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.922A pdb=" N THR V 20 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.305A pdb=" N ILE V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL V 112 " --> pdb=" O LYS V 124 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 124 through 127 removed outlier: 3.532A pdb=" N GLY W 11 " --> pdb=" O PHE W 8 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU W 175 " --> pdb=" O ASP W 197 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP W 197 " --> pdb=" O LEU W 175 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL W 177 " --> pdb=" O TYR W 195 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N TYR W 195 " --> pdb=" O VAL W 177 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LYS W 179 " --> pdb=" O THR W 193 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR W 193 " --> pdb=" O LYS W 179 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 20 through 22 removed outlier: 6.444A pdb=" N ALA W 20 " --> pdb=" O ALA W 27 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE W 25 " --> pdb=" O ALA W 22 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.160A pdb=" N LEU W 34 " --> pdb=" O GLY W 45 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY W 45 " --> pdb=" O LEU W 34 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N TYR W 36 " --> pdb=" O VAL W 43 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL W 43 " --> pdb=" O TYR W 36 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 221 through 228 removed outlier: 3.783A pdb=" N LYS X 195 " --> pdb=" O THR X 192 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N CYS X 11 " --> pdb=" O ASP X 26 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 29 through 31 removed outlier: 6.544A pdb=" N LEU X 29 " --> pdb=" O VAL X 36 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 43 through 47 removed outlier: 6.295A pdb=" N ILE X 50 " --> pdb=" O ILE X 46 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Y' and resid 126 through 129 removed outlier: 4.148A pdb=" N VAL Y 177 " --> pdb=" O ILE Y 188 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 21 through 23 removed outlier: 6.627A pdb=" N VAL Y 21 " --> pdb=" O MET Y 28 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 35 through 37 Processing sheet with id=AG8, first strand: chain 'Z' and resid 125 through 128 removed outlier: 6.224A pdb=" N VAL Z 174 " --> pdb=" O LYS Z 189 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS Z 189 " --> pdb=" O VAL Z 174 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL Z 176 " --> pdb=" O ILE Z 187 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 20 through 22 removed outlier: 6.573A pdb=" N GLY Z 22 " --> pdb=" O ILE Z 26 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE Z 26 " --> pdb=" O GLY Z 22 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.541A pdb=" N MET Z 41 " --> pdb=" O LEU Z 37 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE Z 111 " --> pdb=" O GLY Z 123 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'a' and resid 146 through 150 removed outlier: 5.147A pdb=" N THR a 22 " --> pdb=" O ASP a 37 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 40 through 42 removed outlier: 6.715A pdb=" N LEU a 40 " --> pdb=" O ASP a 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'a' and resid 54 through 56 removed outlier: 3.815A pdb=" N ILE a 119 " --> pdb=" O TYR a 135 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU a 132 " --> pdb=" O LEU a 144 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 32 through 35 removed outlier: 5.485A pdb=" N PHE b 33 " --> pdb=" O TYR b 29 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR b 29 " --> pdb=" O PHE b 33 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE b 48 " --> pdb=" O VAL b 44 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 32 through 35 removed outlier: 5.485A pdb=" N PHE b 33 " --> pdb=" O TYR b 29 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR b 29 " --> pdb=" O PHE b 33 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 136 through 139 removed outlier: 4.921A pdb=" N PHE b 185 " --> pdb=" O ALA b 197 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ALA b 197 " --> pdb=" O PHE b 185 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR b 187 " --> pdb=" O HIS b 195 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N HIS b 195 " --> pdb=" O THR b 187 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR b 189 " --> pdb=" O ILE b 193 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE b 193 " --> pdb=" O THR b 189 " (cutoff:3.500A) 2822 hydrogen bonds defined for protein. 8088 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.63 Time building geometry restraints manager: 14.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 12371 1.33 - 1.47: 15053 1.47 - 1.61: 20868 1.61 - 1.76: 0 1.76 - 1.90: 398 Bond restraints: 48690 Sorted by residual: bond pdb=" C37 X5C W 301 " pdb=" C45 X5C W 301 " ideal model delta sigma weight residual 1.554 1.468 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C37 X5C I 301 " pdb=" C45 X5C I 301 " ideal model delta sigma weight residual 1.554 1.468 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C37 X5C L 301 " pdb=" C45 X5C L 301 " ideal model delta sigma weight residual 1.554 1.474 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C37 X5C Z 301 " pdb=" C45 X5C Z 301 " ideal model delta sigma weight residual 1.554 1.474 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C45 X5C I 301 " pdb=" C46 X5C I 301 " ideal model delta sigma weight residual 1.530 1.469 0.061 2.00e-02 2.50e+03 9.35e+00 ... (remaining 48685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.93: 65880 6.93 - 13.86: 12 13.86 - 20.79: 2 20.79 - 27.72: 0 27.72 - 34.64: 4 Bond angle restraints: 65898 Sorted by residual: angle pdb=" C45 X5C Z 301 " pdb=" C54 X5C Z 301 " pdb=" C56 X5C Z 301 " ideal model delta sigma weight residual 110.69 76.05 34.64 3.00e+00 1.11e-01 1.33e+02 angle pdb=" C45 X5C L 301 " pdb=" C54 X5C L 301 " pdb=" C56 X5C L 301 " ideal model delta sigma weight residual 110.69 76.05 34.64 3.00e+00 1.11e-01 1.33e+02 angle pdb=" C45 X5C W 301 " pdb=" C54 X5C W 301 " pdb=" C56 X5C W 301 " ideal model delta sigma weight residual 110.69 76.26 34.43 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C45 X5C I 301 " pdb=" C54 X5C I 301 " pdb=" C56 X5C I 301 " ideal model delta sigma weight residual 110.69 76.26 34.43 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C55 X5C L 301 " pdb=" C54 X5C L 301 " pdb=" C56 X5C L 301 " ideal model delta sigma weight residual 108.91 122.92 -14.01 3.00e+00 1.11e-01 2.18e+01 ... (remaining 65893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 26793 17.92 - 35.84: 1934 35.84 - 53.75: 475 53.75 - 71.67: 89 71.67 - 89.59: 26 Dihedral angle restraints: 29317 sinusoidal: 11647 harmonic: 17670 Sorted by residual: dihedral pdb=" CB CYS D 64 " pdb=" SG CYS D 64 " pdb=" SG CYS D 72 " pdb=" CB CYS D 72 " ideal model delta sinusoidal sigma weight residual -86.00 -140.96 54.96 1 1.00e+01 1.00e-02 4.09e+01 dihedral pdb=" CA ARG X 28 " pdb=" C ARG X 28 " pdb=" N LEU X 29 " pdb=" CA LEU X 29 " ideal model delta harmonic sigma weight residual 180.00 152.99 27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ARG J 28 " pdb=" C ARG J 28 " pdb=" N LEU J 29 " pdb=" CA LEU J 29 " ideal model delta harmonic sigma weight residual 180.00 153.04 26.96 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 29314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 6956 0.095 - 0.190: 456 0.190 - 0.285: 4 0.285 - 0.380: 2 0.380 - 0.475: 2 Chirality restraints: 7420 Sorted by residual: chirality pdb=" C37 X5C L 301 " pdb=" C38 X5C L 301 " pdb=" C45 X5C L 301 " pdb=" N36 X5C L 301 " both_signs ideal model delta sigma weight residual False -2.47 -2.00 -0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C37 X5C Z 301 " pdb=" C38 X5C Z 301 " pdb=" C45 X5C Z 301 " pdb=" N36 X5C Z 301 " both_signs ideal model delta sigma weight residual False -2.47 -2.00 -0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C37 X5C I 301 " pdb=" C38 X5C I 301 " pdb=" C45 X5C I 301 " pdb=" N36 X5C I 301 " both_signs ideal model delta sigma weight residual False -2.47 -2.16 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 7417 not shown) Planarity restraints: 8514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 X5C L 301 " 0.018 2.00e-02 2.50e+03 5.29e-02 3.50e+01 pdb=" C37 X5C L 301 " -0.064 2.00e-02 2.50e+03 pdb=" CA1 X5C L 301 " -0.049 2.00e-02 2.50e+03 pdb=" N36 X5C L 301 " 0.084 2.00e-02 2.50e+03 pdb=" O1 X5C L 301 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 X5C Z 301 " -0.018 2.00e-02 2.50e+03 5.29e-02 3.50e+01 pdb=" C37 X5C Z 301 " 0.064 2.00e-02 2.50e+03 pdb=" CA1 X5C Z 301 " 0.049 2.00e-02 2.50e+03 pdb=" N36 X5C Z 301 " -0.084 2.00e-02 2.50e+03 pdb=" O1 X5C Z 301 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 X5C I 301 " 0.007 2.00e-02 2.50e+03 3.16e-02 1.24e+01 pdb=" C37 X5C I 301 " -0.038 2.00e-02 2.50e+03 pdb=" CA1 X5C I 301 " -0.028 2.00e-02 2.50e+03 pdb=" N36 X5C I 301 " 0.052 2.00e-02 2.50e+03 pdb=" O1 X5C I 301 " 0.008 2.00e-02 2.50e+03 ... (remaining 8511 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 313 2.45 - 3.06: 34659 3.06 - 3.68: 84310 3.68 - 4.29: 134167 4.29 - 4.90: 215054 Nonbonded interactions: 468503 Sorted by model distance: nonbonded pdb=" O ARG I 19 " pdb=" O57 X5C I 301 " model vdw 1.840 3.040 nonbonded pdb=" O ARG W 19 " pdb=" O57 X5C W 301 " model vdw 1.841 3.040 nonbonded pdb=" O ARG Z 19 " pdb=" O57 X5C Z 301 " model vdw 1.878 3.040 nonbonded pdb=" O ARG L 19 " pdb=" O57 X5C L 301 " model vdw 1.878 3.040 nonbonded pdb=" OG1 THR R 32 " pdb=" O ARG R 165 " model vdw 1.935 3.040 ... (remaining 468498 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.790 Check model and map are aligned: 0.290 Set scattering table: 0.380 Process input model: 106.280 Find NCS groups from input model: 4.000 Set up NCS constraints: 0.420 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:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 0.092 48690 Z= 0.277 Angle : 0.631 34.645 65898 Z= 0.317 Chirality : 0.045 0.475 7420 Planarity : 0.004 0.053 8514 Dihedral : 13.918 89.590 17972 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.21 % Allowed : 8.66 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.11), residues: 6062 helix: 1.11 (0.11), residues: 2252 sheet: -1.04 (0.13), residues: 1466 loop : 0.01 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 156 HIS 0.005 0.001 HIS M 145 PHE 0.017 0.002 PHE I 8 TYR 0.018 0.001 TYR M 115 ARG 0.004 0.001 ARG a 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1357 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 1295 time to evaluate : 5.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.7662 (ptm-80) cc_final: 0.6725 (tpt170) REVERT: A 30 GLN cc_start: 0.7368 (mt0) cc_final: 0.7077 (mt0) REVERT: A 113 MET cc_start: 0.9107 (mtp) cc_final: 0.8895 (mtt) REVERT: A 229 LYS cc_start: 0.7416 (mptt) cc_final: 0.6951 (mmtt) REVERT: B 29 LEU cc_start: 0.8234 (pp) cc_final: 0.7519 (mt) REVERT: B 163 LYS cc_start: 0.8404 (mtmt) cc_final: 0.8196 (mttp) REVERT: B 184 ASP cc_start: 0.7303 (m-30) cc_final: 0.7033 (m-30) REVERT: C 188 MET cc_start: 0.7552 (mtm) cc_final: 0.7308 (mtt) REVERT: C 223 LYS cc_start: 0.8115 (mptt) cc_final: 0.7686 (tmtt) REVERT: C 236 MET cc_start: 0.6310 (mmm) cc_final: 0.5157 (mmm) REVERT: D 216 THR cc_start: 0.8435 (p) cc_final: 0.8084 (t) REVERT: E 62 SER cc_start: 0.7784 (p) cc_final: 0.7529 (m) REVERT: E 230 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6782 (tp30) REVERT: F 26 MET cc_start: 0.7027 (mtp) cc_final: 0.6583 (mmm) REVERT: F 227 GLU cc_start: 0.6015 (mt-10) cc_final: 0.5773 (mt-10) REVERT: G 29 LYS cc_start: 0.7794 (mttp) cc_final: 0.7435 (mtpt) REVERT: G 44 ASP cc_start: 0.7372 (t70) cc_final: 0.7156 (t70) REVERT: G 51 GLU cc_start: 0.8149 (tt0) cc_final: 0.7901 (tt0) REVERT: G 52 LYS cc_start: 0.8794 (mtmm) cc_final: 0.8468 (mtmm) REVERT: G 97 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7397 (tp30) REVERT: G 118 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7353 (mt0) REVERT: G 156 TYR cc_start: 0.8511 (m-80) cc_final: 0.8287 (m-80) REVERT: G 190 GLU cc_start: 0.7329 (tp30) cc_final: 0.7107 (tp30) REVERT: I 39 ASP cc_start: 0.8338 (m-30) cc_final: 0.8107 (m-30) REVERT: I 68 MET cc_start: 0.8696 (mtm) cc_final: 0.8480 (ttm) REVERT: I 86 ARG cc_start: 0.8600 (ttm-80) cc_final: 0.8341 (ttt-90) REVERT: I 196 LYS cc_start: 0.8819 (tptm) cc_final: 0.8520 (tptp) REVERT: J 76 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8310 (mt-10) REVERT: J 170 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7108 (tmmt) REVERT: J 199 LYS cc_start: 0.8755 (mttm) cc_final: 0.8482 (mttt) REVERT: K 145 LYS cc_start: 0.8489 (mmtm) cc_final: 0.8251 (mmtp) REVERT: K 151 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7336 (mp0) REVERT: L 53 GLN cc_start: 0.8208 (pt0) cc_final: 0.7921 (pt0) REVERT: M 136 ASP cc_start: 0.8673 (p0) cc_final: 0.8469 (p0) REVERT: M 140 THR cc_start: 0.9028 (m) cc_final: 0.8825 (m) REVERT: M 142 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: M 144 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8479 (pp) REVERT: M 172 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7550 (mmt90) REVERT: N 144 TYR cc_start: 0.8285 (m-80) cc_final: 0.7920 (m-80) REVERT: N 159 ASP cc_start: 0.8088 (m-30) cc_final: 0.7846 (m-30) REVERT: N 163 LYS cc_start: 0.8390 (tmtp) cc_final: 0.8109 (tttt) REVERT: O 7 ARG cc_start: 0.7661 (ptm-80) cc_final: 0.6723 (tpt170) REVERT: O 30 GLN cc_start: 0.7372 (mt0) cc_final: 0.7083 (mt0) REVERT: O 113 MET cc_start: 0.9106 (mtp) cc_final: 0.8895 (mtt) REVERT: O 229 LYS cc_start: 0.7414 (mptt) cc_final: 0.6948 (mmtt) REVERT: P 29 LEU cc_start: 0.8232 (pp) cc_final: 0.7533 (mt) REVERT: P 163 LYS cc_start: 0.8408 (mtmt) cc_final: 0.8200 (mttp) REVERT: P 184 ASP cc_start: 0.7304 (m-30) cc_final: 0.7032 (m-30) REVERT: Q 188 MET cc_start: 0.7548 (mtm) cc_final: 0.7307 (mtt) REVERT: Q 223 LYS cc_start: 0.8117 (mptt) cc_final: 0.7687 (tmtt) REVERT: Q 236 MET cc_start: 0.6310 (mmm) cc_final: 0.5161 (mmm) REVERT: R 216 THR cc_start: 0.8437 (p) cc_final: 0.8090 (t) REVERT: S 62 SER cc_start: 0.7787 (p) cc_final: 0.7534 (m) REVERT: S 230 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6778 (tp30) REVERT: T 26 MET cc_start: 0.7029 (mtp) cc_final: 0.6584 (mmm) REVERT: T 227 GLU cc_start: 0.6015 (mt-10) cc_final: 0.5770 (mt-10) REVERT: U 29 LYS cc_start: 0.7798 (mttp) cc_final: 0.7431 (mtpt) REVERT: U 44 ASP cc_start: 0.7361 (t70) cc_final: 0.7142 (t70) REVERT: U 51 GLU cc_start: 0.8148 (tt0) cc_final: 0.7902 (tt0) REVERT: U 52 LYS cc_start: 0.8792 (mtmm) cc_final: 0.8469 (mtmm) REVERT: U 97 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7398 (tp30) REVERT: U 118 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7353 (mt0) REVERT: U 156 TYR cc_start: 0.8510 (m-80) cc_final: 0.8278 (m-80) REVERT: U 190 GLU cc_start: 0.7330 (tp30) cc_final: 0.7106 (tp30) REVERT: W 39 ASP cc_start: 0.8337 (m-30) cc_final: 0.8106 (m-30) REVERT: W 68 MET cc_start: 0.8695 (mtm) cc_final: 0.8479 (ttm) REVERT: W 86 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.8342 (ttt-90) REVERT: W 196 LYS cc_start: 0.8819 (tptm) cc_final: 0.8519 (tptp) REVERT: X 76 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8315 (mt-10) REVERT: X 170 LYS cc_start: 0.8092 (mtmt) cc_final: 0.7110 (tmmt) REVERT: X 199 LYS cc_start: 0.8759 (mttm) cc_final: 0.8485 (mttt) REVERT: Y 145 LYS cc_start: 0.8485 (mmtm) cc_final: 0.8249 (mmtp) REVERT: Y 151 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7329 (mp0) REVERT: Y 186 THR cc_start: 0.8499 (p) cc_final: 0.8183 (t) REVERT: Z 53 GLN cc_start: 0.8206 (pt0) cc_final: 0.7919 (pt0) REVERT: a 142 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: a 144 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8478 (pp) REVERT: a 172 ARG cc_start: 0.7804 (mtt180) cc_final: 0.7550 (mmt90) REVERT: b 144 TYR cc_start: 0.8285 (m-80) cc_final: 0.7922 (m-80) REVERT: b 159 ASP cc_start: 0.8089 (m-30) cc_final: 0.7847 (m-30) REVERT: b 163 LYS cc_start: 0.8391 (tmtp) cc_final: 0.8110 (tttt) outliers start: 62 outliers final: 22 residues processed: 1341 average time/residue: 1.7243 time to fit residues: 2836.4722 Evaluate side-chains 1013 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 987 time to evaluate : 5.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain H residue 8 CYS Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 142 GLU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 224 HIS Chi-restraints excluded: chain N residue 99 ARG Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain V residue 8 CYS Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain W residue 225 THR Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 142 GLU Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 224 HIS Chi-restraints excluded: chain b residue 99 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 508 optimal weight: 1.9990 chunk 456 optimal weight: 0.9990 chunk 253 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 307 optimal weight: 8.9990 chunk 243 optimal weight: 0.0570 chunk 471 optimal weight: 0.6980 chunk 182 optimal weight: 0.5980 chunk 286 optimal weight: 5.9990 chunk 351 optimal weight: 5.9990 chunk 546 optimal weight: 5.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN B 69 ASN B 78 ASN B 180 GLN C 26 GLN C 41 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 GLN D 55 GLN D 107 ASN E 99 HIS E 114 GLN E 134 GLN F 152 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN G 91 GLN ** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 HIS G 218 ASN G 222 GLN H 48 ASN H 179 GLN I 109 GLN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 61 GLN K 143 HIS K 173 HIS L 72 GLN L 181 GLN M 92 HIS N 146 GLN N 200 GLN ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 ASN P 69 ASN P 78 ASN P 180 GLN Q 26 GLN Q 41 ASN ** Q 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 145 GLN ** R 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 107 ASN S 99 HIS S 114 GLN S 134 GLN T 152 GLN ** T 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 ASN U 91 GLN ** U 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 121 HIS U 218 ASN U 222 GLN V 48 ASN V 179 GLN ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 61 GLN Y 143 HIS Y 173 HIS Z 72 GLN Z 181 GLN a 92 HIS a 169 HIS b 146 GLN b 200 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 48690 Z= 0.263 Angle : 0.596 9.964 65898 Z= 0.314 Chirality : 0.045 0.201 7420 Planarity : 0.005 0.054 8514 Dihedral : 6.971 86.966 6936 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.65 % Allowed : 14.08 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.11), residues: 6062 helix: 1.22 (0.10), residues: 2268 sheet: -0.92 (0.12), residues: 1502 loop : 0.17 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 156 HIS 0.006 0.001 HIS K 143 PHE 0.016 0.002 PHE X 70 TYR 0.017 0.002 TYR a 115 ARG 0.007 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1016 time to evaluate : 5.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.7695 (ptm-80) cc_final: 0.6693 (tpt170) REVERT: A 30 GLN cc_start: 0.7287 (mt0) cc_final: 0.7061 (mt0) REVERT: A 55 LYS cc_start: 0.7156 (tmtm) cc_final: 0.6907 (tttm) REVERT: A 113 MET cc_start: 0.9082 (mtp) cc_final: 0.8838 (mtt) REVERT: A 209 ASP cc_start: 0.6994 (m-30) cc_final: 0.6768 (m-30) REVERT: A 229 LYS cc_start: 0.7537 (mptt) cc_final: 0.7005 (mtpt) REVERT: B 47 GLU cc_start: 0.6834 (tm-30) cc_final: 0.6544 (tm-30) REVERT: B 116 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8044 (mtt) REVERT: B 184 ASP cc_start: 0.7346 (m-30) cc_final: 0.7038 (m-30) REVERT: C 171 GLN cc_start: 0.7797 (tp40) cc_final: 0.7329 (mt0) REVERT: C 223 LYS cc_start: 0.8005 (mptt) cc_final: 0.7652 (tptt) REVERT: C 236 MET cc_start: 0.6474 (mmm) cc_final: 0.5456 (mmm) REVERT: D 3 ASP cc_start: 0.6425 (t0) cc_final: 0.6103 (t0) REVERT: D 172 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6691 (mt-10) REVERT: E 20 ARG cc_start: 0.7856 (mtm110) cc_final: 0.7220 (mpt90) REVERT: E 62 SER cc_start: 0.7979 (p) cc_final: 0.7411 (m) REVERT: F 93 LEU cc_start: 0.8573 (tt) cc_final: 0.8142 (mt) REVERT: G 29 LYS cc_start: 0.7652 (mttp) cc_final: 0.7365 (mtpt) REVERT: G 51 GLU cc_start: 0.8211 (tt0) cc_final: 0.7900 (tt0) REVERT: G 97 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7335 (tp30) REVERT: G 118 GLN cc_start: 0.7879 (tm-30) cc_final: 0.7379 (mt0) REVERT: G 156 TYR cc_start: 0.8623 (m-80) cc_final: 0.8371 (m-80) REVERT: G 200 GLU cc_start: 0.6606 (mm-30) cc_final: 0.6384 (mp0) REVERT: H 150 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8389 (tpp) REVERT: I 144 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7694 (m110) REVERT: J 170 LYS cc_start: 0.7896 (mtmt) cc_final: 0.6923 (tmmt) REVERT: K 145 LYS cc_start: 0.8412 (mmtm) cc_final: 0.8177 (mmtp) REVERT: K 151 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7316 (mp0) REVERT: L 24 GLN cc_start: 0.7684 (mp10) cc_final: 0.7443 (mp-120) REVERT: L 53 GLN cc_start: 0.7941 (pt0) cc_final: 0.7708 (pt0) REVERT: L 86 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7866 (mm-30) REVERT: M 129 LYS cc_start: 0.8396 (mmtm) cc_final: 0.8116 (mmtp) REVERT: M 144 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8535 (pp) REVERT: N 159 ASP cc_start: 0.8093 (m-30) cc_final: 0.7809 (m-30) REVERT: O 7 ARG cc_start: 0.7689 (ptm-80) cc_final: 0.6696 (tpt170) REVERT: O 30 GLN cc_start: 0.7290 (mt0) cc_final: 0.7066 (mt0) REVERT: O 55 LYS cc_start: 0.7155 (tmtm) cc_final: 0.6909 (tttm) REVERT: O 113 MET cc_start: 0.9083 (mtp) cc_final: 0.8839 (mtt) REVERT: O 209 ASP cc_start: 0.6989 (m-30) cc_final: 0.6765 (m-30) REVERT: O 229 LYS cc_start: 0.7535 (mptt) cc_final: 0.7006 (mtpt) REVERT: P 47 GLU cc_start: 0.6862 (tm-30) cc_final: 0.6557 (tm-30) REVERT: P 116 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8043 (mtt) REVERT: P 184 ASP cc_start: 0.7350 (m-30) cc_final: 0.7042 (m-30) REVERT: Q 171 GLN cc_start: 0.7797 (tp40) cc_final: 0.7327 (mt0) REVERT: Q 223 LYS cc_start: 0.8004 (mptt) cc_final: 0.7650 (tptt) REVERT: Q 236 MET cc_start: 0.6467 (mmm) cc_final: 0.5445 (mmm) REVERT: R 3 ASP cc_start: 0.6422 (t0) cc_final: 0.6099 (t0) REVERT: R 172 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.7011 (mt-10) REVERT: S 20 ARG cc_start: 0.7853 (mtm110) cc_final: 0.7216 (mpt90) REVERT: S 62 SER cc_start: 0.7985 (p) cc_final: 0.7419 (m) REVERT: T 93 LEU cc_start: 0.8586 (tt) cc_final: 0.8154 (mt) REVERT: U 29 LYS cc_start: 0.7650 (mttp) cc_final: 0.7365 (mtpt) REVERT: U 51 GLU cc_start: 0.8224 (tt0) cc_final: 0.7925 (tt0) REVERT: U 97 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7337 (tp30) REVERT: U 118 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7380 (mt0) REVERT: U 156 TYR cc_start: 0.8622 (m-80) cc_final: 0.8368 (m-80) REVERT: U 200 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6401 (mp0) REVERT: V 150 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8390 (tpp) REVERT: W 144 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7693 (m110) REVERT: X 170 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7145 (tmmt) REVERT: Y 145 LYS cc_start: 0.8411 (mmtm) cc_final: 0.8176 (mmtp) REVERT: Y 151 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7317 (mp0) REVERT: Z 24 GLN cc_start: 0.7672 (mp10) cc_final: 0.7430 (mp-120) REVERT: Z 86 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7867 (mm-30) REVERT: a 144 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8536 (pp) REVERT: b 159 ASP cc_start: 0.8090 (m-30) cc_final: 0.7809 (m-30) outliers start: 136 outliers final: 53 residues processed: 1092 average time/residue: 1.6670 time to fit residues: 2251.5605 Evaluate side-chains 980 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 917 time to evaluate : 5.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain C residue 145 GLN Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 8 CYS Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain I residue 144 ASN Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 67 LYS Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 99 ARG Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 116 MET Chi-restraints excluded: chain P residue 159 THR Chi-restraints excluded: chain Q residue 145 GLN Chi-restraints excluded: chain R residue 172 GLU Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain U residue 90 GLU Chi-restraints excluded: chain U residue 178 GLU Chi-restraints excluded: chain V residue 8 CYS Chi-restraints excluded: chain V residue 46 CYS Chi-restraints excluded: chain V residue 150 MET Chi-restraints excluded: chain W residue 144 ASN Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain W residue 225 THR Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 109 LYS Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 99 ARG Chi-restraints excluded: chain b residue 184 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 303 optimal weight: 0.2980 chunk 169 optimal weight: 0.8980 chunk 454 optimal weight: 9.9990 chunk 372 optimal weight: 0.5980 chunk 150 optimal weight: 0.9990 chunk 547 optimal weight: 5.9990 chunk 591 optimal weight: 0.2980 chunk 487 optimal weight: 2.9990 chunk 543 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 439 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN B 32 GLN B 180 GLN C 41 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 GLN D 55 GLN F 152 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN H 48 ASN I 35 HIS K 61 GLN M 60 ASN N 77 HIS N 149 GLN ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 ASN P 32 GLN P 78 ASN P 180 GLN ** Q 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 145 GLN R 55 GLN T 152 GLN ** T 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 218 ASN V 48 ASN W 35 HIS W 52 ASN ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 61 GLN ** Z 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 60 ASN b 77 HIS b 149 GLN ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 48690 Z= 0.221 Angle : 0.559 11.862 65898 Z= 0.295 Chirality : 0.044 0.202 7420 Planarity : 0.004 0.053 8514 Dihedral : 6.705 89.695 6924 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.14 % Allowed : 16.63 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.11), residues: 6062 helix: 1.37 (0.10), residues: 2278 sheet: -0.74 (0.13), residues: 1482 loop : 0.17 (0.13), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Z 55 HIS 0.004 0.001 HIS b 88 PHE 0.021 0.002 PHE I 119 TYR 0.014 0.001 TYR K 97 ARG 0.008 0.001 ARG a 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 1020 time to evaluate : 5.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.7731 (ptm-80) cc_final: 0.6716 (tpt170) REVERT: A 55 LYS cc_start: 0.7150 (tmtm) cc_final: 0.6927 (tttm) REVERT: A 209 ASP cc_start: 0.6928 (m-30) cc_final: 0.6677 (m-30) REVERT: A 229 LYS cc_start: 0.7480 (mptt) cc_final: 0.6982 (mtpt) REVERT: B 47 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6430 (tm-30) REVERT: B 62 LYS cc_start: 0.8474 (mttt) cc_final: 0.8189 (mtmt) REVERT: B 184 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7023 (m-30) REVERT: C 171 GLN cc_start: 0.7735 (tp40) cc_final: 0.7292 (mt0) REVERT: C 223 LYS cc_start: 0.7919 (mptt) cc_final: 0.7617 (tptt) REVERT: C 236 MET cc_start: 0.6530 (mmm) cc_final: 0.5440 (mmm) REVERT: D 80 ASP cc_start: 0.8888 (m-30) cc_final: 0.8623 (m-30) REVERT: D 172 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6684 (mt-10) REVERT: E 20 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7075 (mpt90) REVERT: E 62 SER cc_start: 0.8008 (p) cc_final: 0.7800 (p) REVERT: E 157 HIS cc_start: 0.7197 (OUTLIER) cc_final: 0.6888 (t70) REVERT: F 93 LEU cc_start: 0.8533 (tt) cc_final: 0.8108 (mt) REVERT: F 126 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7927 (ptt90) REVERT: G 29 LYS cc_start: 0.7479 (mttp) cc_final: 0.7256 (mtpt) REVERT: G 51 GLU cc_start: 0.8132 (tt0) cc_final: 0.7870 (tt0) REVERT: G 97 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7204 (tp30) REVERT: G 118 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7285 (mt0) REVERT: G 156 TYR cc_start: 0.8619 (m-80) cc_final: 0.8352 (m-80) REVERT: H 125 LYS cc_start: 0.8481 (mtpt) cc_final: 0.8275 (mtpt) REVERT: I 68 MET cc_start: 0.8594 (mtm) cc_final: 0.8380 (ttm) REVERT: I 95 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: J 170 LYS cc_start: 0.7876 (mtmt) cc_final: 0.7041 (pttp) REVERT: J 205 MET cc_start: 0.8995 (mmm) cc_final: 0.8754 (mmm) REVERT: K 40 ASP cc_start: 0.8090 (m-30) cc_final: 0.7871 (m-30) REVERT: K 58 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7683 (mm-30) REVERT: K 145 LYS cc_start: 0.8401 (mmtm) cc_final: 0.8171 (mmtp) REVERT: K 151 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7243 (mp0) REVERT: L 24 GLN cc_start: 0.7446 (mp10) cc_final: 0.7209 (mp-120) REVERT: L 89 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7594 (mtm-85) REVERT: M 18 MET cc_start: 0.5243 (mpm) cc_final: 0.4988 (mpm) REVERT: M 144 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8456 (pp) REVERT: N 159 ASP cc_start: 0.8029 (m-30) cc_final: 0.7719 (m-30) REVERT: O 7 ARG cc_start: 0.7729 (ptm-80) cc_final: 0.6719 (tpt170) REVERT: O 55 LYS cc_start: 0.7149 (tmtm) cc_final: 0.6929 (tttm) REVERT: O 209 ASP cc_start: 0.6936 (m-30) cc_final: 0.6692 (m-30) REVERT: O 229 LYS cc_start: 0.7474 (mptt) cc_final: 0.6978 (mtpt) REVERT: P 47 GLU cc_start: 0.6687 (tm-30) cc_final: 0.6354 (tm-30) REVERT: P 62 LYS cc_start: 0.8475 (mttt) cc_final: 0.8183 (mtmt) REVERT: P 132 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8380 (mt) REVERT: P 184 ASP cc_start: 0.7355 (m-30) cc_final: 0.7024 (m-30) REVERT: Q 171 GLN cc_start: 0.7737 (tp40) cc_final: 0.7291 (mt0) REVERT: Q 223 LYS cc_start: 0.7909 (mptt) cc_final: 0.7611 (tptt) REVERT: Q 236 MET cc_start: 0.6528 (mmm) cc_final: 0.5434 (mmm) REVERT: R 80 ASP cc_start: 0.8897 (m-30) cc_final: 0.8643 (m-30) REVERT: R 172 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6683 (mt-10) REVERT: S 20 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7070 (mpt90) REVERT: S 62 SER cc_start: 0.8012 (p) cc_final: 0.7807 (p) REVERT: S 157 HIS cc_start: 0.7197 (OUTLIER) cc_final: 0.6882 (t70) REVERT: T 93 LEU cc_start: 0.8532 (tt) cc_final: 0.8106 (mt) REVERT: T 126 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7927 (ptt90) REVERT: U 29 LYS cc_start: 0.7480 (mttp) cc_final: 0.7262 (mtpt) REVERT: U 51 GLU cc_start: 0.8136 (tt0) cc_final: 0.7875 (tt0) REVERT: U 97 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7200 (tp30) REVERT: U 118 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7286 (mt0) REVERT: U 156 TYR cc_start: 0.8612 (m-80) cc_final: 0.8384 (m-80) REVERT: V 125 LYS cc_start: 0.8483 (mtpt) cc_final: 0.8277 (mtpt) REVERT: W 68 MET cc_start: 0.8595 (mtm) cc_final: 0.8386 (ttm) REVERT: W 95 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8129 (mt0) REVERT: X 144 GLU cc_start: 0.6434 (mt-10) cc_final: 0.6155 (mp0) REVERT: X 170 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7149 (tmmt) REVERT: X 205 MET cc_start: 0.8986 (mmm) cc_final: 0.8754 (mmm) REVERT: Y 40 ASP cc_start: 0.8099 (m-30) cc_final: 0.7874 (m-30) REVERT: Y 58 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7686 (mm-30) REVERT: Y 145 LYS cc_start: 0.8398 (mmtm) cc_final: 0.8168 (mmtp) REVERT: Y 151 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7236 (mp0) REVERT: Z 24 GLN cc_start: 0.7409 (mp10) cc_final: 0.7174 (mp-120) REVERT: Z 89 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7595 (mtm-85) REVERT: Z 175 SER cc_start: 0.8995 (t) cc_final: 0.8794 (m) REVERT: a 18 MET cc_start: 0.5236 (mpm) cc_final: 0.4986 (mpm) REVERT: a 142 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: a 144 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8229 (pp) REVERT: b 159 ASP cc_start: 0.8031 (m-30) cc_final: 0.7723 (m-30) outliers start: 161 outliers final: 63 residues processed: 1115 average time/residue: 1.6424 time to fit residues: 2272.7436 Evaluate side-chains 1000 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 922 time to evaluate : 5.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 157 HIS Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 99 ARG Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 159 THR Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 172 GLU Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 157 HIS Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 126 ARG Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 35 SER Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 178 GLU Chi-restraints excluded: chain V residue 46 CYS Chi-restraints excluded: chain W residue 39 ASP Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain W residue 225 THR Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 109 LYS Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 142 GLU Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain b residue 99 ARG Chi-restraints excluded: chain b residue 184 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 541 optimal weight: 2.9990 chunk 411 optimal weight: 7.9990 chunk 284 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 367 optimal weight: 0.7980 chunk 549 optimal weight: 0.6980 chunk 581 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 520 optimal weight: 0.0470 chunk 156 optimal weight: 0.8980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN B 180 GLN D 24 HIS D 55 GLN F 152 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 ASN G 218 ASN H 48 ASN H 111 GLN H 179 GLN I 35 HIS K 37 GLN K 61 GLN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 HIS N 89 ASN N 149 GLN ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 30 GLN ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 78 ASN P 180 GLN ** Q 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 HIS R 55 GLN T 152 GLN ** T 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 229 GLN U 166 ASN U 218 ASN V 48 ASN V 111 GLN V 179 GLN W 35 HIS ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 61 GLN ** Z 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 77 HIS b 89 ASN b 149 GLN b 200 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 48690 Z= 0.241 Angle : 0.561 11.927 65898 Z= 0.296 Chirality : 0.045 0.188 7420 Planarity : 0.004 0.056 8514 Dihedral : 6.604 89.532 6920 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.08 % Allowed : 17.65 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.11), residues: 6062 helix: 1.43 (0.10), residues: 2280 sheet: -0.69 (0.13), residues: 1480 loop : 0.21 (0.14), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 55 HIS 0.004 0.001 HIS E 157 PHE 0.016 0.002 PHE X 70 TYR 0.014 0.002 TYR M 115 ARG 0.009 0.001 ARG U 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1147 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 989 time to evaluate : 5.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.7746 (ptm-80) cc_final: 0.6707 (ttt180) REVERT: A 55 LYS cc_start: 0.7199 (tmtm) cc_final: 0.6954 (tttm) REVERT: A 209 ASP cc_start: 0.6974 (m-30) cc_final: 0.6714 (m-30) REVERT: A 229 LYS cc_start: 0.7476 (mptt) cc_final: 0.6985 (mtpt) REVERT: B 62 LYS cc_start: 0.8409 (mttt) cc_final: 0.8092 (mtmt) REVERT: B 184 ASP cc_start: 0.7377 (m-30) cc_final: 0.7041 (m-30) REVERT: C 171 GLN cc_start: 0.7706 (tp40) cc_final: 0.7255 (mt0) REVERT: C 223 LYS cc_start: 0.7905 (mptt) cc_final: 0.7633 (tptt) REVERT: C 236 MET cc_start: 0.6508 (mmm) cc_final: 0.5523 (mmm) REVERT: D 80 ASP cc_start: 0.8885 (m-30) cc_final: 0.8622 (m-30) REVERT: E 20 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7113 (mpt90) REVERT: E 62 SER cc_start: 0.8040 (p) cc_final: 0.7817 (p) REVERT: F 86 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7685 (tttt) REVERT: F 93 LEU cc_start: 0.8495 (tt) cc_final: 0.8072 (mt) REVERT: G 29 LYS cc_start: 0.7475 (mttp) cc_final: 0.7260 (mtpt) REVERT: G 51 GLU cc_start: 0.8130 (tt0) cc_final: 0.7879 (tt0) REVERT: G 97 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7185 (tp30) REVERT: G 118 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7261 (mt0) REVERT: H 106 ASP cc_start: 0.8353 (p0) cc_final: 0.8142 (p0) REVERT: I 68 MET cc_start: 0.8666 (mtm) cc_final: 0.8443 (ttm) REVERT: I 95 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8133 (mt0) REVERT: J 102 SER cc_start: 0.8541 (t) cc_final: 0.8201 (p) REVERT: J 119 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7924 (mm-30) REVERT: J 144 GLU cc_start: 0.6523 (mt-10) cc_final: 0.6244 (mp0) REVERT: J 170 LYS cc_start: 0.7907 (mtmt) cc_final: 0.7069 (pttp) REVERT: K 58 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7554 (mp0) REVERT: K 145 LYS cc_start: 0.8390 (mmtm) cc_final: 0.8170 (mmtp) REVERT: K 151 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7232 (mp0) REVERT: L 24 GLN cc_start: 0.7349 (mp10) cc_final: 0.7126 (mp10) REVERT: L 145 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: M 142 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: M 144 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8224 (pp) REVERT: N 126 ASP cc_start: 0.8970 (p0) cc_final: 0.8714 (p0) REVERT: N 128 TYR cc_start: 0.8592 (m-80) cc_final: 0.8374 (m-80) REVERT: N 159 ASP cc_start: 0.7979 (m-30) cc_final: 0.7649 (m-30) REVERT: O 7 ARG cc_start: 0.7746 (ptm-80) cc_final: 0.6705 (ttt180) REVERT: O 55 LYS cc_start: 0.7203 (tmtm) cc_final: 0.6970 (tttm) REVERT: O 209 ASP cc_start: 0.6974 (m-30) cc_final: 0.6720 (m-30) REVERT: O 229 LYS cc_start: 0.7469 (mptt) cc_final: 0.6983 (mtpt) REVERT: P 47 GLU cc_start: 0.6692 (tm-30) cc_final: 0.6380 (tm-30) REVERT: P 62 LYS cc_start: 0.8423 (mttt) cc_final: 0.8195 (mtmt) REVERT: P 184 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.7040 (m-30) REVERT: Q 171 GLN cc_start: 0.7708 (tp40) cc_final: 0.7252 (mt0) REVERT: Q 223 LYS cc_start: 0.7907 (mptt) cc_final: 0.7636 (tptt) REVERT: Q 236 MET cc_start: 0.6512 (mmm) cc_final: 0.5522 (mmm) REVERT: S 20 ARG cc_start: 0.7717 (mtm110) cc_final: 0.7111 (mpt90) REVERT: S 62 SER cc_start: 0.8044 (p) cc_final: 0.7822 (p) REVERT: T 86 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7683 (tttt) REVERT: T 93 LEU cc_start: 0.8492 (tt) cc_final: 0.8069 (mt) REVERT: U 29 LYS cc_start: 0.7497 (mttp) cc_final: 0.7280 (mtpt) REVERT: U 51 GLU cc_start: 0.8136 (tt0) cc_final: 0.7886 (tt0) REVERT: U 97 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7174 (tp30) REVERT: U 118 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7250 (mt0) REVERT: V 106 ASP cc_start: 0.8350 (p0) cc_final: 0.8143 (p0) REVERT: W 68 MET cc_start: 0.8660 (mtm) cc_final: 0.8438 (ttm) REVERT: W 95 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: X 144 GLU cc_start: 0.6415 (mt-10) cc_final: 0.6137 (mp0) REVERT: X 170 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7201 (tmmt) REVERT: Y 58 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7553 (mp0) REVERT: Y 145 LYS cc_start: 0.8386 (mmtm) cc_final: 0.8168 (mmtp) REVERT: Y 151 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7231 (mp0) REVERT: Z 24 GLN cc_start: 0.7322 (mp10) cc_final: 0.7099 (mp10) REVERT: Z 145 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: a 142 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7204 (tm-30) REVERT: a 144 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8254 (pp) REVERT: b 126 ASP cc_start: 0.8975 (p0) cc_final: 0.8766 (p0) REVERT: b 159 ASP cc_start: 0.7983 (m-30) cc_final: 0.7652 (m-30) outliers start: 158 outliers final: 69 residues processed: 1082 average time/residue: 1.6856 time to fit residues: 2268.5512 Evaluate side-chains 1019 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 938 time to evaluate : 5.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 157 HIS Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 8 CYS Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 142 GLU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 99 ARG Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 159 THR Chi-restraints excluded: chain P residue 184 ASP Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 157 HIS Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 86 LYS Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 35 SER Chi-restraints excluded: chain U residue 90 GLU Chi-restraints excluded: chain U residue 178 GLU Chi-restraints excluded: chain V residue 8 CYS Chi-restraints excluded: chain V residue 46 CYS Chi-restraints excluded: chain W residue 39 ASP Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain W residue 225 THR Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 109 LYS Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 67 LYS Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 142 GLU Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain b residue 99 ARG Chi-restraints excluded: chain b residue 184 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 484 optimal weight: 0.8980 chunk 330 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 433 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 496 optimal weight: 1.9990 chunk 402 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 297 optimal weight: 1.9990 chunk 522 optimal weight: 3.9990 chunk 146 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN B 180 GLN D 24 HIS D 55 GLN F 152 GLN F 229 GLN G 218 ASN H 48 ASN H 179 GLN I 35 HIS K 61 GLN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 HIS N 149 GLN ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 ASN P 180 GLN ** Q 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 HIS R 55 GLN T 152 GLN U 218 ASN V 48 ASN V 179 GLN W 35 HIS ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 61 GLN ** Z 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 77 HIS b 149 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 48690 Z= 0.251 Angle : 0.564 12.513 65898 Z= 0.298 Chirality : 0.045 0.175 7420 Planarity : 0.004 0.055 8514 Dihedral : 6.611 89.637 6920 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.51 % Allowed : 17.90 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.11), residues: 6062 helix: 1.42 (0.10), residues: 2282 sheet: -0.68 (0.13), residues: 1484 loop : 0.20 (0.14), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 55 HIS 0.004 0.001 HIS N 88 PHE 0.016 0.002 PHE J 70 TYR 0.014 0.002 TYR a 115 ARG 0.007 0.001 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 972 time to evaluate : 5.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.7755 (ptm-80) cc_final: 0.6703 (ttt180) REVERT: A 55 LYS cc_start: 0.7247 (tmtm) cc_final: 0.7022 (tttm) REVERT: A 88 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7679 (mtp) REVERT: A 209 ASP cc_start: 0.6971 (m-30) cc_final: 0.6724 (m-30) REVERT: A 229 LYS cc_start: 0.7508 (mptt) cc_final: 0.7033 (mtpt) REVERT: B 62 LYS cc_start: 0.8421 (mttt) cc_final: 0.8174 (mtmt) REVERT: B 184 ASP cc_start: 0.7395 (m-30) cc_final: 0.7046 (m-30) REVERT: C 171 GLN cc_start: 0.7750 (tp40) cc_final: 0.7290 (mt0) REVERT: C 179 LYS cc_start: 0.8215 (ptmt) cc_final: 0.7938 (ptmm) REVERT: C 223 LYS cc_start: 0.7866 (mptt) cc_final: 0.7597 (tptt) REVERT: C 236 MET cc_start: 0.6527 (mmm) cc_final: 0.5521 (mmm) REVERT: D 54 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7222 (mt) REVERT: E 20 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7079 (mpt90) REVERT: E 62 SER cc_start: 0.8062 (p) cc_final: 0.7825 (p) REVERT: F 86 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7677 (tttt) REVERT: F 93 LEU cc_start: 0.8505 (tt) cc_final: 0.8078 (mt) REVERT: G 29 LYS cc_start: 0.7509 (mttp) cc_final: 0.7299 (mtpt) REVERT: G 51 GLU cc_start: 0.8155 (tt0) cc_final: 0.7898 (tt0) REVERT: G 97 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7164 (tp30) REVERT: G 156 TYR cc_start: 0.8605 (m-80) cc_final: 0.8336 (m-80) REVERT: G 178 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6695 (tm-30) REVERT: I 68 MET cc_start: 0.8679 (mtm) cc_final: 0.8459 (ttm) REVERT: I 86 ARG cc_start: 0.8410 (ttm-80) cc_final: 0.8187 (ttt-90) REVERT: I 95 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: J 102 SER cc_start: 0.8604 (t) cc_final: 0.8269 (p) REVERT: J 144 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6257 (mp0) REVERT: J 170 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7071 (pttp) REVERT: K 39 ASP cc_start: 0.7491 (t0) cc_final: 0.7240 (t0) REVERT: K 145 LYS cc_start: 0.8390 (mmtm) cc_final: 0.8149 (mmtp) REVERT: L 24 GLN cc_start: 0.7342 (mp10) cc_final: 0.7136 (mp10) REVERT: L 145 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: M 18 MET cc_start: 0.5124 (OUTLIER) cc_final: 0.4740 (mpm) REVERT: M 142 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: M 144 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8234 (pp) REVERT: N 159 ASP cc_start: 0.7980 (m-30) cc_final: 0.7658 (m-30) REVERT: O 7 ARG cc_start: 0.7754 (ptm-80) cc_final: 0.6704 (ttt180) REVERT: O 55 LYS cc_start: 0.7238 (tmtm) cc_final: 0.7025 (tttm) REVERT: O 88 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7681 (mtp) REVERT: O 209 ASP cc_start: 0.6956 (m-30) cc_final: 0.6735 (m-30) REVERT: O 229 LYS cc_start: 0.7505 (mptt) cc_final: 0.7039 (mtpt) REVERT: P 62 LYS cc_start: 0.8421 (mttt) cc_final: 0.8177 (mtmt) REVERT: P 184 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.7029 (m-30) REVERT: Q 171 GLN cc_start: 0.7752 (tp40) cc_final: 0.7288 (mt0) REVERT: Q 179 LYS cc_start: 0.8213 (ptmt) cc_final: 0.7938 (ptmm) REVERT: Q 223 LYS cc_start: 0.7871 (mptt) cc_final: 0.7597 (tptt) REVERT: Q 236 MET cc_start: 0.6511 (mmm) cc_final: 0.5518 (mmm) REVERT: R 54 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7241 (mt) REVERT: S 20 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7078 (mpt90) REVERT: S 62 SER cc_start: 0.8065 (p) cc_final: 0.7829 (p) REVERT: T 86 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7679 (tttt) REVERT: T 93 LEU cc_start: 0.8506 (tt) cc_final: 0.8082 (mt) REVERT: U 29 LYS cc_start: 0.7521 (mttp) cc_final: 0.7311 (mtpt) REVERT: U 51 GLU cc_start: 0.8151 (tt0) cc_final: 0.7895 (tt0) REVERT: U 97 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7166 (tp30) REVERT: U 156 TYR cc_start: 0.8604 (m-80) cc_final: 0.8355 (m-80) REVERT: U 178 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6709 (tm-30) REVERT: U 193 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7730 (ttp80) REVERT: W 68 MET cc_start: 0.8681 (mtm) cc_final: 0.8461 (ttm) REVERT: W 95 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8153 (mt0) REVERT: X 75 LEU cc_start: 0.8713 (tp) cc_final: 0.8442 (mt) REVERT: X 102 SER cc_start: 0.8606 (t) cc_final: 0.8260 (p) REVERT: X 144 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6145 (mp0) REVERT: X 170 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7189 (tmmt) REVERT: Y 39 ASP cc_start: 0.7491 (t0) cc_final: 0.7239 (t0) REVERT: Y 145 LYS cc_start: 0.8387 (mmtm) cc_final: 0.8147 (mmtp) REVERT: Z 24 GLN cc_start: 0.7324 (mp10) cc_final: 0.7115 (mp10) REVERT: Z 145 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: a 18 MET cc_start: 0.5131 (OUTLIER) cc_final: 0.4817 (mpm) REVERT: a 30 ASP cc_start: 0.8208 (p0) cc_final: 0.7863 (p0) REVERT: a 142 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: a 144 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8255 (pp) REVERT: b 159 ASP cc_start: 0.7984 (m-30) cc_final: 0.7662 (m-30) outliers start: 180 outliers final: 86 residues processed: 1074 average time/residue: 1.6502 time to fit residues: 2210.1613 Evaluate side-chains 1041 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 934 time to evaluate : 5.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 157 HIS Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 8 CYS Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 185 GLU Chi-restraints excluded: chain M residue 18 MET Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 142 GLU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain N residue 99 ARG Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 191 GLU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 159 THR Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 184 ASP Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 157 HIS Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 86 LYS Chi-restraints excluded: chain U residue 35 SER Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 178 GLU Chi-restraints excluded: chain V residue 8 CYS Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 46 CYS Chi-restraints excluded: chain V residue 102 VAL Chi-restraints excluded: chain W residue 39 ASP Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain W residue 225 THR Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 109 LYS Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 67 LYS Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 185 GLU Chi-restraints excluded: chain a residue 18 MET Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 126 SER Chi-restraints excluded: chain a residue 142 GLU Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain b residue 92 LYS Chi-restraints excluded: chain b residue 99 ARG Chi-restraints excluded: chain b residue 184 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 195 optimal weight: 6.9990 chunk 524 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 341 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 582 optimal weight: 7.9990 chunk 483 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 305 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN D 24 HIS D 28 GLN D 55 GLN F 152 GLN G 218 ASN G 230 GLN H 48 ASN H 179 GLN I 35 HIS ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 HIS N 149 GLN O 20 GLN ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 180 GLN ** Q 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 HIS R 55 GLN T 152 GLN U 218 ASN U 230 GLN V 48 ASN V 179 GLN W 35 HIS ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 122 GLN Y 61 GLN ** Z 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 77 HIS b 149 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 48690 Z= 0.316 Angle : 0.598 11.571 65898 Z= 0.317 Chirality : 0.046 0.196 7420 Planarity : 0.005 0.057 8514 Dihedral : 6.745 89.673 6920 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.65 % Allowed : 18.16 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.11), residues: 6062 helix: 1.31 (0.10), residues: 2272 sheet: -0.75 (0.13), residues: 1496 loop : 0.19 (0.14), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 156 HIS 0.005 0.001 HIS C 118 PHE 0.016 0.002 PHE J 133 TYR 0.020 0.002 TYR E 68 ARG 0.010 0.001 ARG C 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 967 time to evaluate : 5.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.7813 (ptm-80) cc_final: 0.6750 (ttt180) REVERT: A 54 ASP cc_start: 0.5959 (OUTLIER) cc_final: 0.5577 (t0) REVERT: A 55 LYS cc_start: 0.7267 (tmtm) cc_final: 0.6976 (tttm) REVERT: A 88 MET cc_start: 0.8715 (pp-130) cc_final: 0.7689 (mtp) REVERT: A 229 LYS cc_start: 0.7565 (mptt) cc_final: 0.7023 (mtpt) REVERT: B 62 LYS cc_start: 0.8426 (mttt) cc_final: 0.8155 (mtmt) REVERT: B 132 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8387 (mt) REVERT: B 184 ASP cc_start: 0.7419 (m-30) cc_final: 0.7059 (m-30) REVERT: C 102 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: C 171 GLN cc_start: 0.7779 (tp40) cc_final: 0.7291 (mt0) REVERT: C 223 LYS cc_start: 0.7852 (mptt) cc_final: 0.7587 (tptt) REVERT: C 236 MET cc_start: 0.6556 (mmm) cc_final: 0.5404 (mmm) REVERT: D 41 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6808 (ttt) REVERT: D 54 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7255 (mt) REVERT: D 172 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6872 (mt-10) REVERT: E 62 SER cc_start: 0.8111 (p) cc_final: 0.7876 (p) REVERT: F 86 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7710 (tttt) REVERT: F 93 LEU cc_start: 0.8566 (tt) cc_final: 0.8136 (mt) REVERT: F 110 ASP cc_start: 0.8388 (m-30) cc_final: 0.8122 (m-30) REVERT: G 29 LYS cc_start: 0.7698 (mttp) cc_final: 0.7485 (mtpm) REVERT: G 51 GLU cc_start: 0.8179 (tt0) cc_final: 0.7919 (tt0) REVERT: G 97 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7170 (tp30) REVERT: G 156 TYR cc_start: 0.8621 (m-80) cc_final: 0.8355 (m-80) REVERT: G 178 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6744 (tm-30) REVERT: I 95 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: J 102 SER cc_start: 0.8642 (t) cc_final: 0.8335 (p) REVERT: J 170 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7136 (pttp) REVERT: K 39 ASP cc_start: 0.7408 (t0) cc_final: 0.7163 (t0) REVERT: K 58 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: L 89 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.7200 (mtm-85) REVERT: L 145 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: M 18 MET cc_start: 0.5408 (OUTLIER) cc_final: 0.5146 (mpm) REVERT: M 50 HIS cc_start: 0.8040 (t-90) cc_final: 0.7832 (t-90) REVERT: M 144 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8512 (pp) REVERT: N 159 ASP cc_start: 0.8137 (m-30) cc_final: 0.7857 (m-30) REVERT: O 7 ARG cc_start: 0.7811 (ptm-80) cc_final: 0.7597 (ptt-90) REVERT: O 54 ASP cc_start: 0.5978 (OUTLIER) cc_final: 0.5603 (t0) REVERT: O 55 LYS cc_start: 0.7293 (tmtm) cc_final: 0.6998 (tttm) REVERT: O 88 MET cc_start: 0.8716 (pp-130) cc_final: 0.7692 (mtp) REVERT: O 229 LYS cc_start: 0.7551 (mptt) cc_final: 0.7015 (mtpt) REVERT: P 62 LYS cc_start: 0.8433 (mttt) cc_final: 0.8163 (mtmt) REVERT: P 184 ASP cc_start: 0.7421 (m-30) cc_final: 0.7060 (m-30) REVERT: Q 102 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: Q 171 GLN cc_start: 0.7782 (tp40) cc_final: 0.7289 (mt0) REVERT: Q 223 LYS cc_start: 0.7853 (mptt) cc_final: 0.7591 (tptt) REVERT: Q 236 MET cc_start: 0.6530 (mmm) cc_final: 0.5393 (mmm) REVERT: R 54 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7254 (mt) REVERT: R 172 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6873 (mt-10) REVERT: S 62 SER cc_start: 0.8103 (p) cc_final: 0.7870 (p) REVERT: T 86 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7703 (tttt) REVERT: T 93 LEU cc_start: 0.8564 (tt) cc_final: 0.8135 (mt) REVERT: U 29 LYS cc_start: 0.7676 (mttp) cc_final: 0.7466 (mtpm) REVERT: U 51 GLU cc_start: 0.8180 (tt0) cc_final: 0.7924 (tt0) REVERT: U 97 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7179 (tp30) REVERT: U 178 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6738 (tm-30) REVERT: W 95 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8164 (mt0) REVERT: X 75 LEU cc_start: 0.8728 (tp) cc_final: 0.8478 (mt) REVERT: X 102 SER cc_start: 0.8642 (t) cc_final: 0.8329 (p) REVERT: X 170 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7196 (tmmt) REVERT: Y 39 ASP cc_start: 0.7405 (t0) cc_final: 0.7160 (t0) REVERT: Y 58 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: Z 24 GLN cc_start: 0.7506 (mp10) cc_final: 0.7302 (mp10) REVERT: Z 89 ARG cc_start: 0.7603 (mtm-85) cc_final: 0.7206 (mtm-85) REVERT: Z 145 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: a 18 MET cc_start: 0.5422 (OUTLIER) cc_final: 0.5180 (mpm) REVERT: a 30 ASP cc_start: 0.8348 (p0) cc_final: 0.8002 (p0) REVERT: a 50 HIS cc_start: 0.8035 (t-90) cc_final: 0.7831 (t-90) REVERT: a 142 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7226 (tm-30) REVERT: a 144 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8259 (pp) REVERT: b 159 ASP cc_start: 0.8137 (m-30) cc_final: 0.7857 (m-30) outliers start: 187 outliers final: 84 residues processed: 1083 average time/residue: 1.6224 time to fit residues: 2176.8062 Evaluate side-chains 1042 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 932 time to evaluate : 5.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 145 GLN Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 8 CYS Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain M residue 18 MET Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 118 ASN Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain N residue 99 ARG Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 191 GLU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 159 THR Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 145 GLN Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 172 GLU Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 56 SER Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 182 LEU Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 86 LYS Chi-restraints excluded: chain T residue 126 ARG Chi-restraints excluded: chain U residue 35 SER Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 178 GLU Chi-restraints excluded: chain V residue 8 CYS Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 46 CYS Chi-restraints excluded: chain W residue 39 ASP Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain W residue 225 THR Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 58 GLU Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 109 LYS Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 67 LYS Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain a residue 18 MET Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 118 ASN Chi-restraints excluded: chain a residue 126 SER Chi-restraints excluded: chain a residue 142 GLU Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain b residue 92 LYS Chi-restraints excluded: chain b residue 99 ARG Chi-restraints excluded: chain b residue 184 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 561 optimal weight: 0.0030 chunk 65 optimal weight: 4.9990 chunk 331 optimal weight: 0.8980 chunk 425 optimal weight: 0.4980 chunk 329 optimal weight: 2.9990 chunk 490 optimal weight: 0.9980 chunk 325 optimal weight: 0.9980 chunk 580 optimal weight: 0.8980 chunk 363 optimal weight: 4.9990 chunk 353 optimal weight: 6.9990 chunk 267 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN B 180 GLN C 26 GLN D 24 HIS D 55 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN G 218 ASN H 48 ASN I 35 HIS I 52 ASN ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 118 ASN N 77 HIS N 149 GLN ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 ASN P 180 GLN Q 26 GLN R 24 HIS R 55 GLN ** R 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 115 GLN T 152 GLN U 11 ASN U 218 ASN V 48 ASN W 35 HIS Y 61 GLN ** Z 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 ASN b 77 HIS b 149 GLN ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 48690 Z= 0.214 Angle : 0.556 12.888 65898 Z= 0.294 Chirality : 0.044 0.169 7420 Planarity : 0.004 0.054 8514 Dihedral : 6.585 89.751 6920 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.06 % Allowed : 19.52 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.11), residues: 6062 helix: 1.41 (0.11), residues: 2274 sheet: -0.69 (0.13), residues: 1496 loop : 0.24 (0.14), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Z 55 HIS 0.006 0.001 HIS E 157 PHE 0.017 0.002 PHE X 70 TYR 0.019 0.002 TYR M 108 ARG 0.011 0.001 ARG C 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1141 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 984 time to evaluate : 5.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.7726 (ptm-80) cc_final: 0.6660 (ttt180) REVERT: A 54 ASP cc_start: 0.5832 (OUTLIER) cc_final: 0.5561 (t0) REVERT: A 55 LYS cc_start: 0.7249 (tmtm) cc_final: 0.7015 (tttm) REVERT: A 88 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7690 (mtp) REVERT: A 229 LYS cc_start: 0.7478 (mptt) cc_final: 0.7059 (mtpt) REVERT: B 62 LYS cc_start: 0.8395 (mttt) cc_final: 0.8041 (mtmt) REVERT: B 116 MET cc_start: 0.8369 (mtt) cc_final: 0.7978 (mtt) REVERT: B 184 ASP cc_start: 0.7386 (m-30) cc_final: 0.7043 (m-30) REVERT: C 171 GLN cc_start: 0.7765 (tp40) cc_final: 0.7311 (mt0) REVERT: C 223 LYS cc_start: 0.7785 (mptt) cc_final: 0.7574 (tptt) REVERT: C 236 MET cc_start: 0.6579 (mmm) cc_final: 0.5555 (mmm) REVERT: D 216 THR cc_start: 0.8379 (p) cc_final: 0.8125 (t) REVERT: E 62 SER cc_start: 0.8037 (p) cc_final: 0.7823 (p) REVERT: G 51 GLU cc_start: 0.8147 (tt0) cc_final: 0.7888 (tt0) REVERT: G 97 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7120 (tp30) REVERT: G 178 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6730 (tm-30) REVERT: H 186 LYS cc_start: 0.8220 (mttm) cc_final: 0.7659 (mtmm) REVERT: I 39 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7808 (t0) REVERT: I 91 MET cc_start: 0.8541 (mtm) cc_final: 0.8233 (mpp) REVERT: I 95 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8114 (mt0) REVERT: J 75 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8409 (mt) REVERT: J 102 SER cc_start: 0.8607 (t) cc_final: 0.8297 (p) REVERT: J 144 GLU cc_start: 0.6487 (mt-10) cc_final: 0.6227 (mp0) REVERT: J 170 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7051 (pttp) REVERT: J 205 MET cc_start: 0.8994 (mmm) cc_final: 0.8782 (mmm) REVERT: K 46 MET cc_start: 0.8639 (mtp) cc_final: 0.8164 (mtp) REVERT: L 89 ARG cc_start: 0.7422 (mtm-85) cc_final: 0.6895 (mtm-85) REVERT: L 145 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: M 144 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8434 (pp) REVERT: N 159 ASP cc_start: 0.7914 (m-30) cc_final: 0.7570 (m-30) REVERT: O 7 ARG cc_start: 0.7722 (ptm-80) cc_final: 0.6587 (ttt180) REVERT: O 88 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7688 (mtp) REVERT: O 229 LYS cc_start: 0.7479 (mptt) cc_final: 0.7064 (mtpt) REVERT: P 62 LYS cc_start: 0.8398 (mttt) cc_final: 0.8145 (mtmt) REVERT: P 116 MET cc_start: 0.8374 (mtt) cc_final: 0.7983 (mtt) REVERT: P 184 ASP cc_start: 0.7385 (m-30) cc_final: 0.7042 (m-30) REVERT: Q 171 GLN cc_start: 0.7763 (tp40) cc_final: 0.7302 (mt0) REVERT: Q 223 LYS cc_start: 0.7797 (mptt) cc_final: 0.7583 (tptt) REVERT: Q 236 MET cc_start: 0.6558 (mmm) cc_final: 0.5533 (mmm) REVERT: R 216 THR cc_start: 0.8373 (p) cc_final: 0.8148 (t) REVERT: U 51 GLU cc_start: 0.8151 (tt0) cc_final: 0.7932 (tt0) REVERT: U 178 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6727 (tm-30) REVERT: U 193 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7596 (ptt90) REVERT: V 186 LYS cc_start: 0.8216 (mttm) cc_final: 0.7654 (mtmm) REVERT: W 39 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7828 (t0) REVERT: W 91 MET cc_start: 0.8537 (mtm) cc_final: 0.8228 (mpp) REVERT: W 95 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: X 75 LEU cc_start: 0.8659 (tp) cc_final: 0.8426 (mt) REVERT: X 102 SER cc_start: 0.8601 (t) cc_final: 0.8294 (p) REVERT: X 144 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6038 (mp0) REVERT: X 170 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7152 (tmmt) REVERT: Y 46 MET cc_start: 0.8637 (mtp) cc_final: 0.8161 (mtp) REVERT: Z 89 ARG cc_start: 0.7427 (mtm-85) cc_final: 0.6903 (mtm-85) REVERT: Z 145 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: a 30 ASP cc_start: 0.8216 (p0) cc_final: 0.7868 (p0) REVERT: a 142 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: a 144 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8213 (pp) REVERT: b 159 ASP cc_start: 0.7915 (m-30) cc_final: 0.7569 (m-30) outliers start: 157 outliers final: 66 residues processed: 1078 average time/residue: 1.6434 time to fit residues: 2199.2537 Evaluate side-chains 1001 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 919 time to evaluate : 5.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 8 CYS Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain N residue 99 ARG Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 159 THR Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 126 ARG Chi-restraints excluded: chain U residue 35 SER Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 178 GLU Chi-restraints excluded: chain V residue 8 CYS Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 46 CYS Chi-restraints excluded: chain W residue 39 ASP Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain W residue 225 THR Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 109 LYS Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 126 SER Chi-restraints excluded: chain a residue 142 GLU Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain b residue 92 LYS Chi-restraints excluded: chain b residue 99 ARG Chi-restraints excluded: chain b residue 184 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 358 optimal weight: 0.1980 chunk 231 optimal weight: 2.9990 chunk 346 optimal weight: 7.9990 chunk 174 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 368 optimal weight: 5.9990 chunk 395 optimal weight: 8.9990 chunk 286 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 456 optimal weight: 8.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 49 GLN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 180 GLN C 26 GLN ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 HIS D 55 GLN F 152 GLN G 91 GLN G 218 ASN H 48 ASN I 35 HIS I 122 GLN ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN N 77 HIS N 149 GLN O 20 GLN O 49 GLN ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 GLN P 180 GLN Q 26 GLN Q 215 GLN R 24 HIS R 55 GLN T 152 GLN U 11 ASN U 91 GLN U 218 ASN V 48 ASN W 35 HIS ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 61 GLN ** Z 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 ASN b 77 HIS b 149 GLN ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 48690 Z= 0.374 Angle : 0.632 11.419 65898 Z= 0.335 Chirality : 0.047 0.205 7420 Planarity : 0.005 0.112 8514 Dihedral : 6.826 89.846 6920 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.02 % Allowed : 20.46 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.11), residues: 6062 helix: 1.20 (0.10), residues: 2272 sheet: -0.76 (0.13), residues: 1510 loop : 0.18 (0.14), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP W 142 HIS 0.007 0.001 HIS E 157 PHE 0.019 0.002 PHE X 133 TYR 0.021 0.002 TYR C 5 ARG 0.009 0.001 ARG U 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 930 time to evaluate : 5.729 Fit side-chains revert: symmetry clash REVERT: A 7 ARG cc_start: 0.7780 (ptm-80) cc_final: 0.6721 (tpp-160) REVERT: A 54 ASP cc_start: 0.6009 (OUTLIER) cc_final: 0.5666 (t0) REVERT: A 55 LYS cc_start: 0.7294 (tmtm) cc_final: 0.6976 (tttm) REVERT: A 88 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.7703 (mtp) REVERT: A 229 LYS cc_start: 0.7525 (mptt) cc_final: 0.7088 (mtpt) REVERT: B 184 ASP cc_start: 0.7422 (m-30) cc_final: 0.7064 (m-30) REVERT: C 102 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: C 171 GLN cc_start: 0.7775 (tp40) cc_final: 0.7298 (mt0) REVERT: C 223 LYS cc_start: 0.7893 (mptt) cc_final: 0.7628 (tptt) REVERT: C 236 MET cc_start: 0.6540 (mmm) cc_final: 0.5370 (mmm) REVERT: E 53 ARG cc_start: 0.7613 (mmt90) cc_final: 0.7329 (mmt90) REVERT: E 62 SER cc_start: 0.8117 (p) cc_final: 0.7892 (p) REVERT: F 86 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7708 (tttt) REVERT: F 93 LEU cc_start: 0.8611 (tt) cc_final: 0.8165 (mt) REVERT: G 51 GLU cc_start: 0.8173 (tt0) cc_final: 0.7915 (tt0) REVERT: G 97 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7255 (tp30) REVERT: G 156 TYR cc_start: 0.8622 (m-80) cc_final: 0.8364 (m-80) REVERT: G 178 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6771 (tm-30) REVERT: I 95 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: I 121 LYS cc_start: 0.9051 (tttt) cc_final: 0.8826 (tttt) REVERT: J 102 SER cc_start: 0.8684 (t) cc_final: 0.8403 (p) REVERT: J 170 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7068 (tmmt) REVERT: K 58 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: K 186 THR cc_start: 0.8366 (p) cc_final: 0.8077 (t) REVERT: L 89 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7092 (mtm-85) REVERT: L 145 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: M 50 HIS cc_start: 0.8092 (t-90) cc_final: 0.7875 (t-90) REVERT: M 144 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8556 (pp) REVERT: N 159 ASP cc_start: 0.8148 (m-30) cc_final: 0.7858 (m-30) REVERT: N 163 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7923 (tmmt) REVERT: O 7 ARG cc_start: 0.7756 (ptm-80) cc_final: 0.6664 (tpp-160) REVERT: O 54 ASP cc_start: 0.5972 (OUTLIER) cc_final: 0.5687 (t0) REVERT: O 88 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7693 (mtp) REVERT: O 229 LYS cc_start: 0.7527 (mptt) cc_final: 0.7092 (mtpt) REVERT: P 132 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8395 (mt) REVERT: P 184 ASP cc_start: 0.7421 (m-30) cc_final: 0.7062 (m-30) REVERT: Q 102 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: Q 171 GLN cc_start: 0.7765 (tp40) cc_final: 0.7282 (mt0) REVERT: Q 223 LYS cc_start: 0.7889 (mptt) cc_final: 0.7630 (tptt) REVERT: Q 236 MET cc_start: 0.6543 (mmm) cc_final: 0.5373 (mmm) REVERT: R 216 THR cc_start: 0.8439 (p) cc_final: 0.8171 (t) REVERT: S 53 ARG cc_start: 0.7615 (mmt90) cc_final: 0.7329 (mmt90) REVERT: T 86 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7710 (tttt) REVERT: T 93 LEU cc_start: 0.8608 (tt) cc_final: 0.8164 (mt) REVERT: U 51 GLU cc_start: 0.8179 (tt0) cc_final: 0.7929 (tt0) REVERT: U 178 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: W 95 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: W 121 LYS cc_start: 0.9045 (tttt) cc_final: 0.8818 (tttm) REVERT: X 75 LEU cc_start: 0.8734 (tp) cc_final: 0.8493 (mt) REVERT: X 102 SER cc_start: 0.8679 (t) cc_final: 0.8397 (p) REVERT: X 127 SER cc_start: 0.8220 (p) cc_final: 0.8018 (m) REVERT: X 144 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6140 (mp0) REVERT: X 170 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7196 (tmmt) REVERT: Y 58 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: Y 186 THR cc_start: 0.8365 (p) cc_final: 0.8076 (t) REVERT: Z 89 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7092 (mtm-85) REVERT: Z 145 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: a 50 HIS cc_start: 0.8094 (t-90) cc_final: 0.7878 (t-90) REVERT: a 142 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: a 144 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8271 (pp) REVERT: b 159 ASP cc_start: 0.8147 (m-30) cc_final: 0.7856 (m-30) REVERT: b 163 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7928 (tmmt) outliers start: 155 outliers final: 77 residues processed: 1026 average time/residue: 1.6778 time to fit residues: 2135.6912 Evaluate side-chains 997 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 895 time to evaluate : 5.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 8 CYS Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 166 GLN Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 89 ARG Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 99 ARG Chi-restraints excluded: chain N residue 163 LYS Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 191 GLU Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 159 THR Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 86 LYS Chi-restraints excluded: chain T residue 126 ARG Chi-restraints excluded: chain U residue 35 SER Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 178 GLU Chi-restraints excluded: chain V residue 8 CYS Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 46 CYS Chi-restraints excluded: chain W residue 39 ASP Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain W residue 225 THR Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain Y residue 58 GLU Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 109 LYS Chi-restraints excluded: chain Y residue 166 GLN Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 89 ARG Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 126 SER Chi-restraints excluded: chain a residue 142 GLU Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain b residue 99 ARG Chi-restraints excluded: chain b residue 163 LYS Chi-restraints excluded: chain b residue 184 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 527 optimal weight: 4.9990 chunk 555 optimal weight: 0.8980 chunk 507 optimal weight: 3.9990 chunk 540 optimal weight: 0.5980 chunk 325 optimal weight: 0.9980 chunk 235 optimal weight: 0.3980 chunk 424 optimal weight: 3.9990 chunk 165 optimal weight: 0.3980 chunk 488 optimal weight: 2.9990 chunk 511 optimal weight: 0.9990 chunk 538 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN B 32 GLN B 180 GLN C 26 GLN C 29 ASN D 55 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN G 218 ASN G 230 GLN H 48 ASN H 179 GLN I 35 HIS ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 118 ASN N 77 HIS N 149 GLN ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 ASN P 32 GLN P 180 GLN Q 26 GLN Q 29 ASN R 24 HIS R 55 GLN ** R 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 GLN U 218 ASN U 230 GLN V 48 ASN V 179 GLN W 35 HIS ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 61 GLN ** Z 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 ASN a 118 ASN b 77 HIS b 149 GLN ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 48690 Z= 0.216 Angle : 0.573 12.908 65898 Z= 0.303 Chirality : 0.044 0.171 7420 Planarity : 0.004 0.063 8514 Dihedral : 6.633 89.851 6920 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.55 % Allowed : 21.39 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.11), residues: 6062 helix: 1.31 (0.11), residues: 2280 sheet: -0.68 (0.13), residues: 1436 loop : 0.14 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 55 HIS 0.005 0.001 HIS S 157 PHE 0.019 0.002 PHE X 101 TYR 0.023 0.002 TYR M 108 ARG 0.008 0.001 ARG a 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 944 time to evaluate : 5.425 Fit side-chains revert: symmetry clash REVERT: A 7 ARG cc_start: 0.7618 (ptm-80) cc_final: 0.6627 (tpp-160) REVERT: A 55 LYS cc_start: 0.7266 (tmtm) cc_final: 0.6978 (tttm) REVERT: A 88 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7694 (mtp) REVERT: A 229 LYS cc_start: 0.7400 (mptt) cc_final: 0.7078 (mtpt) REVERT: B 62 LYS cc_start: 0.8432 (mttt) cc_final: 0.8018 (mtmt) REVERT: B 80 ASP cc_start: 0.8238 (p0) cc_final: 0.7726 (p0) REVERT: B 116 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8446 (mtt) REVERT: B 184 ASP cc_start: 0.7385 (m-30) cc_final: 0.7040 (m-30) REVERT: C 171 GLN cc_start: 0.7751 (tp40) cc_final: 0.7328 (mt0) REVERT: C 236 MET cc_start: 0.6547 (mmm) cc_final: 0.5509 (mmm) REVERT: D 179 LYS cc_start: 0.8391 (mtmt) cc_final: 0.8155 (pttp) REVERT: D 185 GLU cc_start: 0.6912 (mp0) cc_final: 0.6701 (tt0) REVERT: D 216 THR cc_start: 0.8335 (p) cc_final: 0.8119 (t) REVERT: E 53 ARG cc_start: 0.7572 (mmt90) cc_final: 0.7306 (mmt90) REVERT: G 51 GLU cc_start: 0.8138 (tt0) cc_final: 0.7904 (tt0) REVERT: G 97 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7171 (tp30) REVERT: G 178 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: H 186 LYS cc_start: 0.8225 (mttm) cc_final: 0.7681 (mtmm) REVERT: I 39 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7836 (t0) REVERT: I 91 MET cc_start: 0.8549 (mtm) cc_final: 0.8253 (mpp) REVERT: I 95 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: J 15 MET cc_start: 0.8542 (ttm) cc_final: 0.8321 (ttt) REVERT: J 48 ASP cc_start: 0.7819 (m-30) cc_final: 0.7575 (m-30) REVERT: J 102 SER cc_start: 0.8624 (t) cc_final: 0.8348 (p) REVERT: J 144 GLU cc_start: 0.6565 (mt-10) cc_final: 0.6262 (mp0) REVERT: J 205 MET cc_start: 0.9000 (mmm) cc_final: 0.8791 (mmm) REVERT: K 46 MET cc_start: 0.8555 (mtp) cc_final: 0.8112 (mtp) REVERT: L 89 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.7052 (mtm-85) REVERT: L 145 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7463 (mt-10) REVERT: M 50 HIS cc_start: 0.7943 (t-90) cc_final: 0.7732 (t-90) REVERT: M 142 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: M 144 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8148 (pp) REVERT: N 1 MET cc_start: 0.4699 (OUTLIER) cc_final: 0.2166 (ptp) REVERT: N 159 ASP cc_start: 0.7921 (m-30) cc_final: 0.7573 (m-30) REVERT: N 182 LYS cc_start: 0.9239 (mttm) cc_final: 0.9014 (mttp) REVERT: O 7 ARG cc_start: 0.7592 (ptm-80) cc_final: 0.6555 (tpp-160) REVERT: O 88 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7707 (mtp) REVERT: O 229 LYS cc_start: 0.7403 (mptt) cc_final: 0.7084 (mtpt) REVERT: P 62 LYS cc_start: 0.8428 (mttt) cc_final: 0.8014 (mtmt) REVERT: P 80 ASP cc_start: 0.8233 (p0) cc_final: 0.7789 (p0) REVERT: P 116 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8454 (mtt) REVERT: P 184 ASP cc_start: 0.7381 (m-30) cc_final: 0.7038 (m-30) REVERT: Q 171 GLN cc_start: 0.7755 (tp40) cc_final: 0.7325 (mt0) REVERT: Q 236 MET cc_start: 0.6547 (mmm) cc_final: 0.5510 (mmm) REVERT: S 53 ARG cc_start: 0.7573 (mmt90) cc_final: 0.7315 (mmt90) REVERT: U 51 GLU cc_start: 0.8140 (tt0) cc_final: 0.7915 (tt0) REVERT: U 178 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6741 (tm-30) REVERT: U 193 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7507 (ptm-80) REVERT: V 186 LYS cc_start: 0.8223 (mttm) cc_final: 0.7680 (mtmm) REVERT: W 39 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7836 (t0) REVERT: W 91 MET cc_start: 0.8532 (mtm) cc_final: 0.8245 (mpp) REVERT: W 95 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8075 (mt0) REVERT: X 48 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7590 (m-30) REVERT: X 102 SER cc_start: 0.8568 (t) cc_final: 0.8320 (p) REVERT: X 144 GLU cc_start: 0.6550 (mt-10) cc_final: 0.5997 (mp0) REVERT: X 170 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7104 (tmmt) REVERT: Y 46 MET cc_start: 0.8551 (mtp) cc_final: 0.8106 (mtp) REVERT: Z 89 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7061 (mtm-85) REVERT: Z 145 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: a 30 ASP cc_start: 0.8201 (p0) cc_final: 0.7884 (p0) REVERT: a 50 HIS cc_start: 0.7942 (t-90) cc_final: 0.7732 (t-90) REVERT: a 142 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: a 144 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8191 (pp) REVERT: b 1 MET cc_start: 0.4713 (OUTLIER) cc_final: 0.2168 (ptp) REVERT: b 159 ASP cc_start: 0.7902 (m-30) cc_final: 0.7548 (m-30) outliers start: 131 outliers final: 66 residues processed: 1023 average time/residue: 1.6234 time to fit residues: 2068.7274 Evaluate side-chains 982 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 894 time to evaluate : 5.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 89 ARG Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 142 GLU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 99 ARG Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 116 MET Chi-restraints excluded: chain P residue 159 THR Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 62 SER Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain U residue 35 SER Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 178 GLU Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 46 CYS Chi-restraints excluded: chain W residue 39 ASP Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain W residue 225 THR Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 48 ASP Chi-restraints excluded: chain X residue 84 ASP Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 109 LYS Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 89 ARG Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 126 SER Chi-restraints excluded: chain a residue 142 GLU Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 99 ARG Chi-restraints excluded: chain b residue 184 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 355 optimal weight: 3.9990 chunk 571 optimal weight: 2.9990 chunk 348 optimal weight: 0.9990 chunk 271 optimal weight: 5.9990 chunk 397 optimal weight: 6.9990 chunk 599 optimal weight: 1.9990 chunk 551 optimal weight: 0.9980 chunk 477 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 368 optimal weight: 10.0000 chunk 292 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 180 GLN C 26 GLN ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 HIS D 55 GLN F 152 GLN G 11 ASN G 91 GLN G 175 GLN G 218 ASN H 48 ASN I 35 HIS I 215 ASN K 61 GLN L 53 GLN N 149 GLN ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 GLN P 180 GLN Q 26 GLN ** Q 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 HIS R 55 GLN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 GLN U 91 GLN U 218 ASN V 48 ASN W 35 HIS ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 61 GLN Z 53 GLN b 149 GLN ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 48690 Z= 0.356 Angle : 0.638 12.241 65898 Z= 0.338 Chirality : 0.047 0.262 7420 Planarity : 0.005 0.094 8514 Dihedral : 6.798 89.281 6920 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.15 % Allowed : 22.15 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.11), residues: 6062 helix: 1.17 (0.10), residues: 2270 sheet: -0.75 (0.12), residues: 1520 loop : 0.18 (0.14), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 156 HIS 0.005 0.001 HIS Q 118 PHE 0.022 0.002 PHE X 101 TYR 0.027 0.002 TYR B 95 ARG 0.010 0.001 ARG A 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 900 time to evaluate : 5.288 Fit side-chains REVERT: A 7 ARG cc_start: 0.7748 (ptm-80) cc_final: 0.6712 (tpp-160) REVERT: A 55 LYS cc_start: 0.7279 (tmtm) cc_final: 0.6977 (tttm) REVERT: A 88 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.7703 (mtp) REVERT: A 229 LYS cc_start: 0.7488 (mptt) cc_final: 0.7116 (mtpt) REVERT: B 184 ASP cc_start: 0.7412 (m-30) cc_final: 0.7066 (m-30) REVERT: C 102 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: C 171 GLN cc_start: 0.7769 (tp40) cc_final: 0.7321 (mt0) REVERT: C 189 ASP cc_start: 0.8154 (m-30) cc_final: 0.7897 (m-30) REVERT: C 236 MET cc_start: 0.6541 (mmm) cc_final: 0.5508 (mmm) REVERT: D 185 GLU cc_start: 0.7003 (mp0) cc_final: 0.6597 (tt0) REVERT: F 93 LEU cc_start: 0.8571 (tt) cc_final: 0.8144 (mt) REVERT: G 51 GLU cc_start: 0.8181 (tt0) cc_final: 0.7919 (tt0) REVERT: G 97 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7265 (tp30) REVERT: G 156 TYR cc_start: 0.8594 (m-80) cc_final: 0.8352 (m-80) REVERT: G 178 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6777 (tm-30) REVERT: I 91 MET cc_start: 0.8593 (mtm) cc_final: 0.8289 (mpp) REVERT: I 95 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: J 75 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8454 (mt) REVERT: J 102 SER cc_start: 0.8692 (t) cc_final: 0.8453 (p) REVERT: K 58 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7475 (mm-30) REVERT: K 186 THR cc_start: 0.8372 (p) cc_final: 0.8066 (t) REVERT: L 89 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7161 (mtm-85) REVERT: L 145 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: M 142 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: M 144 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8262 (pp) REVERT: N 1 MET cc_start: 0.5248 (OUTLIER) cc_final: 0.2365 (ptp) REVERT: N 159 ASP cc_start: 0.8129 (m-30) cc_final: 0.7819 (m-30) REVERT: O 7 ARG cc_start: 0.7693 (ptm-80) cc_final: 0.6654 (tpp-160) REVERT: O 88 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.7704 (mtp) REVERT: O 229 LYS cc_start: 0.7493 (mptt) cc_final: 0.7121 (mtpt) REVERT: P 80 ASP cc_start: 0.8311 (p0) cc_final: 0.8072 (p0) REVERT: P 116 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8452 (mtt) REVERT: P 184 ASP cc_start: 0.7410 (m-30) cc_final: 0.7062 (m-30) REVERT: Q 102 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: Q 171 GLN cc_start: 0.7774 (tp40) cc_final: 0.7319 (mt0) REVERT: Q 189 ASP cc_start: 0.8158 (m-30) cc_final: 0.7908 (m-30) REVERT: Q 236 MET cc_start: 0.6541 (mmm) cc_final: 0.5509 (mmm) REVERT: R 179 LYS cc_start: 0.8441 (mtmt) cc_final: 0.8157 (pttp) REVERT: T 93 LEU cc_start: 0.8563 (tt) cc_final: 0.8136 (mt) REVERT: T 119 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7557 (mtpt) REVERT: T 126 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8158 (tmm160) REVERT: U 51 GLU cc_start: 0.8165 (tt0) cc_final: 0.7920 (tt0) REVERT: U 178 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: W 91 MET cc_start: 0.8556 (mtm) cc_final: 0.8259 (mpp) REVERT: W 95 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: X 75 LEU cc_start: 0.8712 (tp) cc_final: 0.8468 (mt) REVERT: X 144 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6112 (mp0) REVERT: X 170 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7183 (tmmt) REVERT: Y 58 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7478 (mm-30) REVERT: Y 186 THR cc_start: 0.8373 (p) cc_final: 0.8064 (t) REVERT: Z 89 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7161 (mtm-85) REVERT: Z 145 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: a 50 HIS cc_start: 0.8083 (t-90) cc_final: 0.7876 (t-90) REVERT: a 142 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: a 144 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8242 (pp) REVERT: b 1 MET cc_start: 0.5211 (OUTLIER) cc_final: 0.2335 (ptp) REVERT: b 159 ASP cc_start: 0.8128 (m-30) cc_final: 0.7831 (m-30) outliers start: 110 outliers final: 61 residues processed: 969 average time/residue: 1.6575 time to fit residues: 1984.7885 Evaluate side-chains 973 residues out of total 5132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 889 time to evaluate : 5.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 89 ARG Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 142 GLU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 99 ARG Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 116 MET Chi-restraints excluded: chain P residue 159 THR Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 62 SER Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 119 LYS Chi-restraints excluded: chain T residue 126 ARG Chi-restraints excluded: chain U residue 35 SER Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 178 GLU Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 46 CYS Chi-restraints excluded: chain W residue 39 ASP Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain W residue 225 THR Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 109 LYS Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 89 ARG Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 142 GLU Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 99 ARG Chi-restraints excluded: chain b residue 184 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 379 optimal weight: 3.9990 chunk 508 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 440 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 478 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 491 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN B 32 GLN B 180 GLN ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 HIS D 55 GLN E 157 HIS F 152 GLN G 91 GLN G 199 HIS G 218 ASN H 48 ASN I 35 HIS K 61 GLN L 196 HIS N 89 ASN N 149 GLN ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 ASN P 32 GLN P 180 GLN Q 26 GLN R 24 HIS R 55 GLN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 HIS T 152 GLN U 91 GLN U 199 HIS U 218 ASN V 48 ASN W 35 HIS ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 61 GLN b 89 ASN b 149 GLN ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.146639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.120228 restraints weight = 50051.809| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.11 r_work: 0.3154 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 48690 Z= 0.419 Angle : 0.676 11.225 65898 Z= 0.359 Chirality : 0.048 0.247 7420 Planarity : 0.005 0.083 8514 Dihedral : 7.003 89.117 6920 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.30 % Allowed : 21.92 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.11), residues: 6062 helix: 0.98 (0.10), residues: 2268 sheet: -0.84 (0.13), residues: 1482 loop : 0.11 (0.13), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 154 HIS 0.006 0.001 HIS S 157 PHE 0.024 0.002 PHE X 101 TYR 0.030 0.002 TYR B 95 ARG 0.011 0.001 ARG A 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27870.60 seconds wall clock time: 486 minutes 6.34 seconds (29166.34 seconds total)