Starting phenix.real_space_refine on Mon Nov 18 19:27:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3l_27159/11_2024/8d3l_27159.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3l_27159/11_2024/8d3l_27159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3l_27159/11_2024/8d3l_27159.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3l_27159/11_2024/8d3l_27159.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3l_27159/11_2024/8d3l_27159.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3l_27159/11_2024/8d3l_27159.cif" } resolution = 3.49 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= 0.028 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: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 Fe 8 7.16 5 P 63 5.49 5 S 106 5.16 5 C 10874 2.51 5 N 3066 2.21 5 O 3366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17485 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2768 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 331} Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2758 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 11, 'TRANS': 330} Chain: "C" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2768 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 331} Chain: "D" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2758 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 11, 'TRANS': 330} Chain: "E" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 771 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "F" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 771 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "G" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 671 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Chain: "H" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 653 Classifications: {'DNA': 32} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 31} Chain: "I" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1775 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain: "J" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1770 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 8, 'TRANS': 208} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14084 SG CYS I 21 44.947 62.454 123.034 1.00 8.72 S ATOM 15460 SG CYS I 190 44.559 60.728 119.782 1.00 10.07 S ATOM 15460 SG CYS I 190 44.559 60.728 119.782 1.00 10.07 S ATOM 15482 SG CYS I 193 48.647 61.031 119.637 1.00 10.89 S ATOM 15525 SG CYS I 199 47.994 58.265 120.908 1.00 7.81 S ATOM 15525 SG CYS I 199 47.994 58.265 120.908 1.00 7.81 S ATOM 14084 SG CYS I 21 44.947 62.454 123.034 1.00 8.72 S ATOM 15460 SG CYS I 190 44.559 60.728 119.782 1.00 10.07 S ATOM 15482 SG CYS I 193 48.647 61.031 119.637 1.00 10.89 S ATOM 15854 SG CYS J 21 43.498 43.198 61.747 1.00 3.29 S ATOM 17295 SG CYS J 199 42.009 47.355 61.495 1.00 4.28 S ATOM 17252 SG CYS J 193 45.117 45.989 64.802 1.00 3.36 S ATOM 17295 SG CYS J 199 42.009 47.355 61.495 1.00 4.28 S ATOM 15854 SG CYS J 21 43.498 43.198 61.747 1.00 3.29 S ATOM 17230 SG CYS J 190 42.383 43.388 65.022 1.00 5.47 S ATOM 17252 SG CYS J 193 45.117 45.989 64.802 1.00 3.36 S ATOM 17230 SG CYS J 190 42.383 43.388 65.022 1.00 5.47 S Time building chain proxies: 11.29, per 1000 atoms: 0.65 Number of scatterers: 17485 At special positions: 0 Unit cell: (112.381, 116.006, 175.822, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 8 26.01 Mn 2 24.99 S 106 16.00 P 63 15.00 O 3366 8.00 N 3066 7.00 C 10874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.02 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 I 301 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 190 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 199 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 21 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 193 " pdb=" SF4 J 301 " pdb="FE2 SF4 J 301 " - pdb=" SG CYS J 199 " pdb="FE1 SF4 J 301 " - pdb=" SG CYS J 21 " pdb="FE3 SF4 J 301 " - pdb=" SG CYS J 193 " pdb="FE4 SF4 J 301 " - pdb=" SG CYS J 190 " Number of angles added : 24 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3754 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 19 sheets defined 49.6% alpha, 16.3% beta 20 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 88 through 99 removed outlier: 3.546A pdb=" N GLU A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 130 removed outlier: 3.544A pdb=" N SER A 104 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 154 removed outlier: 3.574A pdb=" N PHE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 4.273A pdb=" N ASP A 178 " --> pdb=" O ASN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 201 through 225 removed outlier: 3.635A pdb=" N MET A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 266 removed outlier: 4.851A pdb=" N GLU A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLY A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 285 through 301 removed outlier: 3.590A pdb=" N GLN A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.526A pdb=" N GLU B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 63 " --> pdb=" O TYR B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 99 removed outlier: 3.734A pdb=" N ARG B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 130 removed outlier: 3.522A pdb=" N SER B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 129 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 155 removed outlier: 3.954A pdb=" N GLN B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 178 removed outlier: 3.760A pdb=" N VAL B 176 " --> pdb=" O ASN B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 189 Processing helix chain 'B' and resid 202 through 225 removed outlier: 3.822A pdb=" N PHE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 219 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 249 Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.840A pdb=" N ALA B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 285 through 300 Processing helix chain 'B' and resid 317 through 331 removed outlier: 3.877A pdb=" N ALA B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 63 removed outlier: 3.655A pdb=" N GLU C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG C 63 " --> pdb=" O TYR C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 100 Processing helix chain 'C' and resid 101 through 130 Processing helix chain 'C' and resid 135 through 155 removed outlier: 3.584A pdb=" N PHE C 139 " --> pdb=" O ASN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 181 removed outlier: 3.563A pdb=" N GLN C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN C 172 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 203 removed outlier: 3.952A pdb=" N ASN C 203 " --> pdb=" O ASP C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 200 through 203' Processing helix chain 'C' and resid 204 through 223 Processing helix chain 'C' and resid 241 through 252 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 285 through 301 Processing helix chain 'C' and resid 316 through 331 removed outlier: 4.486A pdb=" N TYR C 320 " --> pdb=" O GLY C 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'D' and resid 87 through 98 removed outlier: 3.580A pdb=" N SER D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 130 removed outlier: 3.573A pdb=" N SER D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS D 130 " --> pdb=" O MET D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 155 removed outlier: 3.897A pdb=" N PHE D 139 " --> pdb=" O ASN D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 172 removed outlier: 3.914A pdb=" N LEU D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 removed outlier: 4.183A pdb=" N GLN D 179 " --> pdb=" O LYS D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 225 removed outlier: 3.587A pdb=" N VAL D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 248 through 256 removed outlier: 4.122A pdb=" N GLY D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 266 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 285 through 302 removed outlier: 3.670A pdb=" N GLU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 331 removed outlier: 4.474A pdb=" N TYR D 320 " --> pdb=" O GLY D 316 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 29 Processing helix chain 'E' and resid 44 through 59 Processing helix chain 'E' and resid 74 through 77 Processing helix chain 'F' and resid 15 through 30 removed outlier: 3.549A pdb=" N ASN F 29 " --> pdb=" O LYS F 25 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'I' and resid 12 through 21 removed outlier: 4.226A pdb=" N GLN I 16 " --> pdb=" O LEU I 12 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS I 17 " --> pdb=" O SER I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 30 removed outlier: 3.775A pdb=" N ALA I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 50 Processing helix chain 'I' and resid 119 through 135 Processing helix chain 'I' and resid 158 through 179 Processing helix chain 'I' and resid 188 through 192 removed outlier: 3.828A pdb=" N ASN I 191 " --> pdb=" O PRO I 188 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN I 192 " --> pdb=" O PHE I 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 188 through 192' Processing helix chain 'I' and resid 195 through 200 Processing helix chain 'I' and resid 201 through 205 removed outlier: 3.597A pdb=" N MET I 204 " --> pdb=" O PRO I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 218 removed outlier: 3.542A pdb=" N TYR I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 20 removed outlier: 3.641A pdb=" N GLN J 16 " --> pdb=" O SER J 13 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS J 17 " --> pdb=" O GLY J 14 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE J 18 " --> pdb=" O LEU J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 30 removed outlier: 4.014A pdb=" N ALA J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 51 removed outlier: 4.191A pdb=" N GLU J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 134 removed outlier: 3.648A pdb=" N LEU J 124 " --> pdb=" O ASP J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 178 removed outlier: 3.996A pdb=" N LYS J 164 " --> pdb=" O ALA J 160 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN J 178 " --> pdb=" O HIS J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 192 Processing helix chain 'J' and resid 195 through 200 Processing helix chain 'J' and resid 207 through 219 removed outlier: 3.940A pdb=" N ARG J 211 " --> pdb=" O ARG J 207 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR J 212 " --> pdb=" O SER J 208 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 6.360A pdb=" N LEU A 8 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 44 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU A 70 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLY A 46 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 81 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 78 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ILE B 67 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASN B 6 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N VAL B 45 " --> pdb=" O ASN B 6 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 8 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE B 47 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL B 10 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.796A pdb=" N GLY A 34 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 276 removed outlier: 4.113A pdb=" N LEU A 283 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 305 Processing sheet with id=AA5, first strand: chain 'B' and resid 31 through 37 removed outlier: 6.596A pdb=" N LEU B 26 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG B 35 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 24 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 51 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 303 through 305 Processing sheet with id=AA7, first strand: chain 'C' and resid 7 through 10 removed outlier: 5.613A pdb=" N LEU C 8 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE C 44 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LEU C 70 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLY C 46 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG C 79 " --> pdb=" O VAL D 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 31 through 37 removed outlier: 5.909A pdb=" N LYS C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS C 28 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 17 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 303 through 305 Processing sheet with id=AB1, first strand: chain 'D' and resid 6 through 10 removed outlier: 7.535A pdb=" N ASN D 6 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE D 44 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU D 8 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLY D 46 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL D 10 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLU D 42 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N THR D 68 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE D 44 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU D 70 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY D 46 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 32 through 37 removed outlier: 3.915A pdb=" N GLY D 34 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 274 through 276 Processing sheet with id=AB4, first strand: chain 'D' and resid 303 through 305 Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.675A pdb=" N VAL E 34 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL E 38 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU E 2 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 79 through 81 removed outlier: 7.008A pdb=" N LEU F 2 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU F 40 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ARG F 33 " --> pdb=" O GLU F 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 10 through 11 removed outlier: 5.585A pdb=" N LEU I 10 " --> pdb=" O SER I 78 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ILE I 80 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N CYS I 81 " --> pdb=" O TYR I 109 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N TYR I 109 " --> pdb=" O CYS I 81 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR I 102 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE I 93 " --> pdb=" O TYR I 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 57 through 58 removed outlier: 4.027A pdb=" N GLU I 57 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR I 64 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU I 85 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG I 66 " --> pdb=" O VAL I 83 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL I 83 " --> pdb=" O ARG I 66 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N CYS I 81 " --> pdb=" O TYR I 109 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N TYR I 109 " --> pdb=" O CYS I 81 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS I 141 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR I 143 " --> pdb=" O PRO I 106 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU I 108 " --> pdb=" O TYR I 143 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE I 145 " --> pdb=" O GLU I 108 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 10 through 11 removed outlier: 5.608A pdb=" N LEU J 10 " --> pdb=" O SER J 78 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE J 80 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N CYS J 81 " --> pdb=" O TYR J 109 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N TYR J 109 " --> pdb=" O CYS J 81 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY J 100 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU J 95 " --> pdb=" O GLY J 100 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR J 102 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE J 93 " --> pdb=" O TYR J 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 63 through 72 removed outlier: 6.805A pdb=" N THR J 64 " --> pdb=" O GLU J 85 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLU J 85 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG J 66 " --> pdb=" O VAL J 83 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL J 83 " --> pdb=" O ARG J 66 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N CYS J 81 " --> pdb=" O TYR J 109 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N TYR J 109 " --> pdb=" O CYS J 81 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TYR J 143 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE J 145 " --> pdb=" O PRO J 106 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU J 108 " --> pdb=" O PHE J 145 " (cutoff:3.500A) 802 hydrogen bonds defined for protein. 2313 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 5.64 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 7519 1.42 - 1.64: 10230 1.64 - 1.85: 169 1.85 - 2.07: 1 2.07 - 2.29: 24 Bond restraints: 17943 Sorted by residual: bond pdb=" CA TYR E 7 " pdb=" C TYR E 7 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.21e-02 6.83e+03 1.98e+01 bond pdb=" CA TYR F 7 " pdb=" C TYR F 7 " ideal model delta sigma weight residual 1.523 1.488 0.034 1.25e-02 6.40e+03 7.61e+00 bond pdb=" CA ALA C 204 " pdb=" CB ALA C 204 " ideal model delta sigma weight residual 1.532 1.491 0.040 1.57e-02 4.06e+03 6.62e+00 bond pdb=" CA ASN C 203 " pdb=" C ASN C 203 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.31e-02 5.83e+03 6.48e+00 bond pdb=" C TYR E 7 " pdb=" O TYR E 7 " ideal model delta sigma weight residual 1.234 1.204 0.030 1.28e-02 6.10e+03 5.64e+00 ... (remaining 17938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 24353 3.21 - 6.41: 103 6.41 - 9.62: 7 9.62 - 12.83: 1 12.83 - 16.04: 1 Bond angle restraints: 24465 Sorted by residual: angle pdb=" N ASN C 203 " pdb=" CA ASN C 203 " pdb=" C ASN C 203 " ideal model delta sigma weight residual 113.89 97.85 16.04 1.58e+00 4.01e-01 1.03e+02 angle pdb=" N PRO C 197 " pdb=" CA PRO C 197 " pdb=" C PRO C 197 " ideal model delta sigma weight residual 110.70 99.98 10.72 1.22e+00 6.72e-01 7.72e+01 angle pdb=" C ARG C 196 " pdb=" N PRO C 197 " pdb=" CA PRO C 197 " ideal model delta sigma weight residual 120.38 115.00 5.38 1.03e+00 9.43e-01 2.73e+01 angle pdb=" N ALA C 204 " pdb=" CA ALA C 204 " pdb=" C ALA C 204 " ideal model delta sigma weight residual 113.12 106.98 6.14 1.25e+00 6.40e-01 2.41e+01 angle pdb=" CA GLU E 62 " pdb=" CB GLU E 62 " pdb=" CG GLU E 62 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 ... (remaining 24460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.55: 10068 30.55 - 61.11: 634 61.11 - 91.66: 31 91.66 - 122.22: 0 122.22 - 152.77: 4 Dihedral angle restraints: 10737 sinusoidal: 4910 harmonic: 5827 Sorted by residual: dihedral pdb=" C ARG C 196 " pdb=" N ARG C 196 " pdb=" CA ARG C 196 " pdb=" CB ARG C 196 " ideal model delta harmonic sigma weight residual -122.60 -135.44 12.84 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" N ARG C 196 " pdb=" C ARG C 196 " pdb=" CA ARG C 196 " pdb=" CB ARG C 196 " ideal model delta harmonic sigma weight residual 122.80 135.24 -12.44 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" CA ARG A 196 " pdb=" C ARG A 196 " pdb=" N PRO A 197 " pdb=" CA PRO A 197 " ideal model delta harmonic sigma weight residual 180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 10734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2632 0.108 - 0.216: 52 0.216 - 0.323: 2 0.323 - 0.431: 0 0.431 - 0.539: 1 Chirality restraints: 2687 Sorted by residual: chirality pdb=" CA ARG C 196 " pdb=" N ARG C 196 " pdb=" C ARG C 196 " pdb=" CB ARG C 196 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" CA ASP C 200 " pdb=" N ASP C 200 " pdb=" C ASP C 200 " pdb=" CB ASP C 200 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ARG C 195 " pdb=" N ARG C 195 " pdb=" C ARG C 195 " pdb=" CB ARG C 195 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2684 not shown) Planarity restraints: 2912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 196 " -0.077 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO A 197 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO A 197 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 197 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 92 " -0.041 5.00e-02 4.00e+02 6.29e-02 6.32e+00 pdb=" N PRO F 93 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 93 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 93 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 306 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO C 307 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " 0.029 5.00e-02 4.00e+02 ... (remaining 2909 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 34 2.38 - 3.01: 9346 3.01 - 3.64: 25220 3.64 - 4.27: 36507 4.27 - 4.90: 61931 Nonbonded interactions: 133038 Sorted by model distance: nonbonded pdb=" OP1 DG H 29 " pdb="MN MN I 302 " model vdw 1.752 2.320 nonbonded pdb=" OD2 ASP I 82 " pdb="MN MN I 302 " model vdw 2.032 2.320 nonbonded pdb=" OG SER C 84 " pdb=" OH TYR D 229 " model vdw 2.137 3.040 nonbonded pdb=" OP1 DG G 29 " pdb="MN MN J 302 " model vdw 2.141 2.320 nonbonded pdb=" OG SER I 218 " pdb=" OE1 GLU I 219 " model vdw 2.191 3.040 ... (remaining 133033 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' and resid 1 through 342) selection = chain 'B' selection = (chain 'C' and resid 1 through 342) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 3 through 219 or resid 301 through 302)) selection = chain 'J' } 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: 8.670 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 47.280 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 17943 Z= 0.196 Angle : 0.617 16.036 24465 Z= 0.348 Chirality : 0.041 0.539 2687 Planarity : 0.005 0.116 2912 Dihedral : 17.744 152.772 6983 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.99 % Favored : 93.75 % Rotamer: Outliers : 0.23 % Allowed : 0.74 % Favored : 99.03 % Cbeta Deviations : 0.05 % 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: -0.39 (0.19), residues: 1985 helix: 1.15 (0.18), residues: 911 sheet: -0.20 (0.32), residues: 258 loop : -1.97 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 296 HIS 0.010 0.001 HIS D 130 PHE 0.026 0.001 PHE D 232 TYR 0.027 0.001 TYR E 7 ARG 0.006 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 260 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 MET cc_start: 0.5562 (mpp) cc_final: 0.4210 (mmt) REVERT: D 178 ASP cc_start: 0.7391 (t0) cc_final: 0.7070 (t0) REVERT: D 197 PRO cc_start: 0.3979 (Cg_exo) cc_final: 0.3654 (Cg_endo) REVERT: D 200 ASP cc_start: 0.6884 (m-30) cc_final: 0.6484 (p0) outliers start: 4 outliers final: 0 residues processed: 262 average time/residue: 0.3295 time to fit residues: 128.1935 Evaluate side-chains 200 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 8.9990 chunk 153 optimal weight: 0.0020 chunk 84 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN C 39 HIS ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN J 24 GLN J 71 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17943 Z= 0.229 Angle : 0.578 7.434 24465 Z= 0.311 Chirality : 0.040 0.148 2687 Planarity : 0.005 0.115 2912 Dihedral : 16.968 154.091 2901 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.55 % Favored : 93.25 % Rotamer: Outliers : 1.03 % Allowed : 8.29 % Favored : 90.69 % 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: 0.10 (0.19), residues: 1985 helix: 1.82 (0.18), residues: 912 sheet: -0.05 (0.33), residues: 242 loop : -2.03 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 342 HIS 0.005 0.001 HIS C 39 PHE 0.015 0.001 PHE J 20 TYR 0.018 0.001 TYR C 95 ARG 0.003 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 1.989 Fit side-chains REVERT: B 180 MET cc_start: 0.5632 (mpp) cc_final: 0.4193 (mmt) REVERT: D 125 ARG cc_start: 0.7046 (tpp-160) cc_final: 0.6736 (tmt170) REVERT: D 197 PRO cc_start: 0.3653 (Cg_exo) cc_final: 0.3336 (Cg_endo) REVERT: D 200 ASP cc_start: 0.6806 (m-30) cc_final: 0.6224 (p0) REVERT: E 62 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8107 (pm20) REVERT: I 48 LYS cc_start: 0.7968 (tptt) cc_final: 0.7640 (mttt) outliers start: 18 outliers final: 13 residues processed: 215 average time/residue: 0.3150 time to fit residues: 101.7241 Evaluate side-chains 205 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain I residue 130 CYS Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 198 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 0.0870 chunk 56 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 198 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 182 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN C 39 HIS ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17943 Z= 0.185 Angle : 0.557 16.227 24465 Z= 0.293 Chirality : 0.038 0.145 2687 Planarity : 0.004 0.114 2912 Dihedral : 16.981 155.148 2901 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.99 % Favored : 93.85 % Rotamer: Outliers : 1.09 % Allowed : 11.77 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 1985 helix: 2.04 (0.18), residues: 911 sheet: 0.08 (0.33), residues: 248 loop : -2.06 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 296 HIS 0.003 0.001 HIS D 130 PHE 0.025 0.001 PHE D 111 TYR 0.015 0.001 TYR J 175 ARG 0.003 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 1.854 Fit side-chains REVERT: B 125 ARG cc_start: 0.7305 (tmm-80) cc_final: 0.6821 (ttt90) REVERT: B 180 MET cc_start: 0.5474 (mpp) cc_final: 0.5155 (mmt) REVERT: D 197 PRO cc_start: 0.3791 (Cg_exo) cc_final: 0.3495 (Cg_endo) REVERT: D 200 ASP cc_start: 0.6876 (m-30) cc_final: 0.6454 (p0) REVERT: D 342 TRP cc_start: 0.8195 (OUTLIER) cc_final: 0.7595 (m-10) REVERT: E 62 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7981 (pm20) REVERT: I 48 LYS cc_start: 0.7878 (tptt) cc_final: 0.7629 (mttt) outliers start: 19 outliers final: 7 residues processed: 213 average time/residue: 0.3124 time to fit residues: 99.8143 Evaluate side-chains 200 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 62 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN C 30 GLN C 39 HIS C 306 HIS C 322 GLN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 GLN J 32 GLN J 71 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17943 Z= 0.298 Angle : 0.620 9.353 24465 Z= 0.331 Chirality : 0.042 0.150 2687 Planarity : 0.005 0.112 2912 Dihedral : 17.285 156.846 2901 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.25 % Favored : 92.59 % Rotamer: Outliers : 1.43 % Allowed : 15.09 % Favored : 83.49 % 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: 0.06 (0.19), residues: 1985 helix: 1.84 (0.18), residues: 912 sheet: 0.10 (0.33), residues: 237 loop : -2.15 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 342 HIS 0.005 0.001 HIS J 180 PHE 0.035 0.002 PHE D 232 TYR 0.018 0.001 TYR C 320 ARG 0.005 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 1.925 Fit side-chains REVERT: B 125 ARG cc_start: 0.7427 (tmm-80) cc_final: 0.6984 (ttt90) REVERT: B 180 MET cc_start: 0.5695 (mpp) cc_final: 0.4069 (mmt) REVERT: D 180 MET cc_start: 0.6578 (mmm) cc_final: 0.6375 (tpp) REVERT: D 200 ASP cc_start: 0.6972 (m-30) cc_final: 0.6412 (p0) REVERT: D 342 TRP cc_start: 0.8459 (OUTLIER) cc_final: 0.7812 (m-10) REVERT: E 38 VAL cc_start: 0.8596 (p) cc_final: 0.8342 (t) REVERT: E 62 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: I 48 LYS cc_start: 0.8005 (tptt) cc_final: 0.7655 (mttt) outliers start: 25 outliers final: 18 residues processed: 216 average time/residue: 0.3095 time to fit residues: 100.9308 Evaluate side-chains 206 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain I residue 130 CYS Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain J residue 198 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 166 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 39 HIS C 322 GLN ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17943 Z= 0.324 Angle : 0.638 9.218 24465 Z= 0.340 Chirality : 0.042 0.152 2687 Planarity : 0.005 0.111 2912 Dihedral : 17.381 158.513 2901 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.05 % Favored : 92.70 % Rotamer: Outliers : 2.17 % Allowed : 16.57 % Favored : 81.26 % 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: -0.14 (0.19), residues: 1985 helix: 1.69 (0.18), residues: 911 sheet: -0.12 (0.32), residues: 245 loop : -2.25 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 165 HIS 0.005 0.001 HIS J 180 PHE 0.024 0.002 PHE D 232 TYR 0.018 0.002 TYR D 255 ARG 0.005 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 2.122 Fit side-chains REVERT: A 190 PHE cc_start: 0.7783 (t80) cc_final: 0.7217 (t80) REVERT: B 125 ARG cc_start: 0.7421 (tmm-80) cc_final: 0.6998 (ttt90) REVERT: B 180 MET cc_start: 0.5746 (mpp) cc_final: 0.4099 (mmt) REVERT: D 41 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8355 (mp) REVERT: D 200 ASP cc_start: 0.7171 (m-30) cc_final: 0.6726 (p0) REVERT: D 342 TRP cc_start: 0.8523 (OUTLIER) cc_final: 0.7871 (m-10) REVERT: E 38 VAL cc_start: 0.8555 (p) cc_final: 0.8256 (t) REVERT: E 62 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: I 48 LYS cc_start: 0.8026 (tptt) cc_final: 0.7677 (mttt) REVERT: I 147 ASN cc_start: 0.7733 (t0) cc_final: 0.7495 (t0) outliers start: 38 outliers final: 19 residues processed: 220 average time/residue: 0.3188 time to fit residues: 106.6313 Evaluate side-chains 206 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 71 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 0.9980 chunk 175 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 30 GLN C 39 HIS ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN J 71 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17943 Z= 0.301 Angle : 0.621 8.945 24465 Z= 0.332 Chirality : 0.041 0.156 2687 Planarity : 0.005 0.111 2912 Dihedral : 17.403 159.770 2901 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.56 % Favored : 92.24 % Rotamer: Outliers : 2.51 % Allowed : 17.26 % 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: -0.19 (0.19), residues: 1985 helix: 1.66 (0.18), residues: 911 sheet: -0.17 (0.32), residues: 244 loop : -2.27 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 165 HIS 0.005 0.001 HIS D 306 PHE 0.033 0.002 PHE D 232 TYR 0.021 0.001 TYR D 255 ARG 0.004 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 1.946 Fit side-chains REVERT: A 190 PHE cc_start: 0.7774 (t80) cc_final: 0.7234 (t80) REVERT: B 125 ARG cc_start: 0.7398 (tmm-80) cc_final: 0.6986 (ttt90) REVERT: B 155 ASN cc_start: 0.7244 (OUTLIER) cc_final: 0.6049 (p0) REVERT: B 180 MET cc_start: 0.5809 (mpp) cc_final: 0.4080 (mmt) REVERT: D 41 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8348 (mp) REVERT: D 342 TRP cc_start: 0.8548 (OUTLIER) cc_final: 0.7929 (m-10) REVERT: E 38 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8255 (t) REVERT: E 62 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7964 (pm20) REVERT: I 68 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6187 (tpt) REVERT: I 147 ASN cc_start: 0.7861 (t0) cc_final: 0.7606 (t0) outliers start: 44 outliers final: 27 residues processed: 227 average time/residue: 0.3039 time to fit residues: 104.7143 Evaluate side-chains 217 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 186 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 111 optimal weight: 0.0980 chunk 142 optimal weight: 3.9990 chunk 110 optimal weight: 0.4980 chunk 164 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 194 optimal weight: 2.9990 chunk 121 optimal weight: 0.3980 chunk 118 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 39 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN E 35 GLN I 147 ASN J 71 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 17943 Z= 0.167 Angle : 0.551 12.176 24465 Z= 0.293 Chirality : 0.038 0.229 2687 Planarity : 0.004 0.110 2912 Dihedral : 17.153 160.108 2901 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.54 % Favored : 94.31 % Rotamer: Outliers : 1.89 % Allowed : 18.86 % Favored : 79.26 % 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: 0.14 (0.19), residues: 1985 helix: 1.92 (0.18), residues: 916 sheet: -0.20 (0.32), residues: 266 loop : -2.08 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 165 HIS 0.004 0.001 HIS D 130 PHE 0.029 0.001 PHE D 232 TYR 0.015 0.001 TYR D 255 ARG 0.007 0.000 ARG D 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 125 ARG cc_start: 0.7393 (tmm-80) cc_final: 0.6952 (ttt90) REVERT: D 200 ASP cc_start: 0.6854 (m-30) cc_final: 0.6526 (p0) REVERT: D 342 TRP cc_start: 0.8464 (OUTLIER) cc_final: 0.7625 (m-10) REVERT: E 38 VAL cc_start: 0.8445 (p) cc_final: 0.8165 (t) REVERT: E 62 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8009 (pm20) REVERT: I 68 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6086 (tpt) REVERT: I 129 MET cc_start: 0.8150 (mtt) cc_final: 0.7903 (ttm) REVERT: I 147 ASN cc_start: 0.7752 (t160) cc_final: 0.7520 (t0) outliers start: 33 outliers final: 19 residues processed: 227 average time/residue: 0.3117 time to fit residues: 106.1790 Evaluate side-chains 215 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 78 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 39 HIS ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN J 71 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17943 Z= 0.353 Angle : 0.658 10.174 24465 Z= 0.348 Chirality : 0.043 0.197 2687 Planarity : 0.005 0.109 2912 Dihedral : 17.428 160.771 2901 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.91 % Favored : 91.89 % Rotamer: Outliers : 2.46 % Allowed : 18.80 % Favored : 78.74 % 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: -0.19 (0.19), residues: 1985 helix: 1.65 (0.18), residues: 910 sheet: -0.21 (0.32), residues: 260 loop : -2.29 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 342 HIS 0.005 0.001 HIS D 39 PHE 0.035 0.002 PHE D 232 TYR 0.021 0.002 TYR C 320 ARG 0.005 0.000 ARG D 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 1.988 Fit side-chains REVERT: A 190 PHE cc_start: 0.7752 (t80) cc_final: 0.7167 (t80) REVERT: A 313 MET cc_start: 0.7755 (ptp) cc_final: 0.7455 (mtm) REVERT: B 1 MET cc_start: 0.7131 (mtp) cc_final: 0.6918 (mtp) REVERT: B 125 ARG cc_start: 0.7404 (tmm-80) cc_final: 0.6990 (ttt90) REVERT: B 155 ASN cc_start: 0.7239 (OUTLIER) cc_final: 0.6014 (p0) REVERT: B 180 MET cc_start: 0.5758 (mpp) cc_final: 0.4227 (mmt) REVERT: D 41 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8380 (mp) REVERT: D 342 TRP cc_start: 0.8609 (OUTLIER) cc_final: 0.7955 (m-10) REVERT: E 38 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8338 (t) REVERT: E 62 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8009 (pm20) REVERT: I 68 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6266 (tpt) REVERT: J 217 LEU cc_start: 0.4350 (OUTLIER) cc_final: 0.4054 (mm) outliers start: 43 outliers final: 25 residues processed: 225 average time/residue: 0.3045 time to fit residues: 103.0365 Evaluate side-chains 220 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain J residue 217 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 180 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 39 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN ** I 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 17943 Z= 0.202 Angle : 0.580 10.428 24465 Z= 0.308 Chirality : 0.039 0.207 2687 Planarity : 0.004 0.108 2912 Dihedral : 17.264 162.199 2901 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.74 % Favored : 94.11 % Rotamer: Outliers : 1.94 % Allowed : 19.31 % Favored : 78.74 % 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: 0.01 (0.19), residues: 1985 helix: 1.82 (0.18), residues: 913 sheet: -0.15 (0.32), residues: 270 loop : -2.21 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 165 HIS 0.004 0.001 HIS C 39 PHE 0.030 0.001 PHE D 232 TYR 0.013 0.001 TYR D 255 ARG 0.006 0.000 ARG D 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 2.022 Fit side-chains REVERT: A 190 PHE cc_start: 0.7692 (t80) cc_final: 0.7189 (t80) REVERT: A 313 MET cc_start: 0.7670 (ptp) cc_final: 0.7404 (mtm) REVERT: B 1 MET cc_start: 0.7085 (mtp) cc_final: 0.6842 (mtp) REVERT: B 125 ARG cc_start: 0.7322 (tmm-80) cc_final: 0.6952 (ttt90) REVERT: B 155 ASN cc_start: 0.7185 (OUTLIER) cc_final: 0.5977 (p0) REVERT: B 180 MET cc_start: 0.5667 (mpp) cc_final: 0.4112 (mmt) REVERT: D 342 TRP cc_start: 0.8499 (OUTLIER) cc_final: 0.7736 (m-10) REVERT: E 38 VAL cc_start: 0.8423 (p) cc_final: 0.8138 (t) REVERT: E 62 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8006 (pm20) REVERT: I 68 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6163 (tpt) REVERT: J 68 MET cc_start: 0.5940 (OUTLIER) cc_final: 0.5389 (ttt) REVERT: J 217 LEU cc_start: 0.4317 (OUTLIER) cc_final: 0.4037 (mm) outliers start: 34 outliers final: 21 residues processed: 214 average time/residue: 0.3009 time to fit residues: 97.6067 Evaluate side-chains 215 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain J residue 68 MET Chi-restraints excluded: chain J residue 217 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 0.3980 chunk 191 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 39 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN D 183 GLN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** I 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17943 Z= 0.289 Angle : 0.620 9.844 24465 Z= 0.330 Chirality : 0.041 0.174 2687 Planarity : 0.005 0.108 2912 Dihedral : 17.391 163.007 2901 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.71 % Favored : 92.14 % Rotamer: Outliers : 2.06 % Allowed : 19.20 % Favored : 78.74 % 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: -0.13 (0.19), residues: 1985 helix: 1.73 (0.18), residues: 913 sheet: -0.14 (0.32), residues: 250 loop : -2.29 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 165 HIS 0.005 0.001 HIS C 39 PHE 0.033 0.002 PHE D 232 TYR 0.017 0.001 TYR C 320 ARG 0.005 0.000 ARG D 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 1.869 Fit side-chains REVERT: A 190 PHE cc_start: 0.7752 (t80) cc_final: 0.7207 (t80) REVERT: A 313 MET cc_start: 0.7735 (ptp) cc_final: 0.7475 (mtm) REVERT: B 1 MET cc_start: 0.7196 (mtp) cc_final: 0.6946 (mtp) REVERT: B 125 ARG cc_start: 0.7321 (tmm-80) cc_final: 0.6911 (ttt90) REVERT: B 155 ASN cc_start: 0.7197 (OUTLIER) cc_final: 0.5975 (p0) REVERT: B 180 MET cc_start: 0.5762 (mpp) cc_final: 0.4284 (mmt) REVERT: C 313 MET cc_start: 0.8117 (mtm) cc_final: 0.7827 (mtm) REVERT: D 342 TRP cc_start: 0.8572 (OUTLIER) cc_final: 0.7874 (m-10) REVERT: E 38 VAL cc_start: 0.8538 (p) cc_final: 0.8288 (t) REVERT: E 62 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: I 68 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6259 (tpt) REVERT: J 68 MET cc_start: 0.6080 (OUTLIER) cc_final: 0.5492 (ttt) REVERT: J 217 LEU cc_start: 0.4369 (OUTLIER) cc_final: 0.4040 (mm) outliers start: 36 outliers final: 25 residues processed: 215 average time/residue: 0.3143 time to fit residues: 102.1186 Evaluate side-chains 219 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain J residue 68 MET Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 217 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 49 optimal weight: 0.4980 chunk 147 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN D 172 ASN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.160375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124113 restraints weight = 23435.270| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.42 r_work: 0.3337 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.265 17943 Z= 0.383 Angle : 0.935 59.191 24465 Z= 0.555 Chirality : 0.049 1.176 2687 Planarity : 0.005 0.108 2912 Dihedral : 17.395 163.000 2901 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.66 % Favored : 92.14 % Rotamer: Outliers : 2.34 % Allowed : 18.80 % Favored : 78.86 % Cbeta Deviations : 0.11 % 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: -0.15 (0.19), residues: 1985 helix: 1.70 (0.18), residues: 913 sheet: -0.14 (0.32), residues: 250 loop : -2.30 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 342 HIS 0.005 0.001 HIS C 39 PHE 0.031 0.002 PHE D 232 TYR 0.016 0.001 TYR C 320 ARG 0.004 0.000 ARG D 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3499.34 seconds wall clock time: 65 minutes 9.60 seconds (3909.60 seconds total)