Starting phenix.real_space_refine on Wed Feb 14 08:23:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlj_36399/02_2024/8jlj_36399_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlj_36399/02_2024/8jlj_36399.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlj_36399/02_2024/8jlj_36399_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlj_36399/02_2024/8jlj_36399_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlj_36399/02_2024/8jlj_36399_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlj_36399/02_2024/8jlj_36399.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlj_36399/02_2024/8jlj_36399.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlj_36399/02_2024/8jlj_36399_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlj_36399/02_2024/8jlj_36399_neut_updated.pdb" } resolution = 3.1 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= -0.002 sd= 0.120 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: 5 Type Number sf(0) Gaussians I 1 10.91 5 S 63 5.16 5 C 5676 2.51 5 N 1525 2.21 5 O 1653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "Y GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1928 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2596 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2147 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1784 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'UJF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.97, per 1000 atoms: 0.56 Number of scatterers: 8918 At special positions: 0 Unit cell: (90.95, 125.8, 128.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) I 1 52.95 S 63 16.00 O 1653 8.00 N 1525 7.00 C 5676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 181 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.9 seconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 34.5% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.610A pdb=" N GLN A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.515A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.613A pdb=" N VAL A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 299 through 317 removed outlier: 3.593A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 357 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.536A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.896A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 48 removed outlier: 4.023A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE R 33 " --> pdb=" O MET R 29 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU R 37 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL R 38 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 85 removed outlier: 4.069A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU R 61 " --> pdb=" O THR R 57 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Proline residue: R 77 - end of helix Processing helix chain 'R' and resid 95 through 125 Processing helix chain 'R' and resid 130 through 133 No H-bonds generated for 'chain 'R' and resid 130 through 133' Processing helix chain 'R' and resid 136 through 160 removed outlier: 3.849A pdb=" N VAL R 141 " --> pdb=" O SER R 137 " (cutoff:3.500A) Proline residue: R 150 - end of helix removed outlier: 3.642A pdb=" N TYR R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE R 155 " --> pdb=" O ALA R 151 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY R 156 " --> pdb=" O VAL R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 175 Processing helix chain 'R' and resid 187 through 197 Processing helix chain 'R' and resid 199 through 224 removed outlier: 3.977A pdb=" N VAL R 204 " --> pdb=" O ILE R 200 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET R 205 " --> pdb=" O PRO R 201 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE R 214 " --> pdb=" O TYR R 210 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 274 removed outlier: 3.805A pdb=" N GLY R 251 " --> pdb=" O ALA R 247 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) Proline residue: R 263 - end of helix removed outlier: 3.528A pdb=" N THR R 268 " --> pdb=" O PHE R 264 " (cutoff:3.500A) Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 280 through 301 removed outlier: 3.918A pdb=" N PHE R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR R 291 " --> pdb=" O TYR R 287 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU R 292 " --> pdb=" O TRP R 288 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 306 through 309 No H-bonds generated for 'chain 'R' and resid 306 through 309' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'Y' and resid 7 through 23 removed outlier: 3.544A pdb=" N MET Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU Y 22 " --> pdb=" O GLN Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 30 through 47 removed outlier: 3.711A pdb=" N ALA Y 35 " --> pdb=" O SER Y 31 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR Y 40 " --> pdb=" O ASP Y 36 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS Y 41 " --> pdb=" O LEU Y 37 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU Y 42 " --> pdb=" O MET Y 38 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS Y 46 " --> pdb=" O GLU Y 42 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU Y 47 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 326 through 330 removed outlier: 7.508A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.024A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.925A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.580A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.065A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 263 through 265 removed outlier: 4.777A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.761A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.533A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.698A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU S 117 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 146 through 148 removed outlier: 7.013A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'S' and resid 174 through 176 358 hydrogen bonds defined for protein. 1038 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: 2.62 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.36: 2902 1.36 - 1.54: 6050 1.54 - 1.73: 69 1.73 - 1.91: 93 1.91 - 2.10: 1 Bond restraints: 9115 Sorted by residual: bond pdb=" CA THR A 33 " pdb=" C THR A 33 " ideal model delta sigma weight residual 1.526 1.608 -0.082 1.37e-02 5.33e+03 3.59e+01 bond pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta sigma weight residual 1.453 1.530 -0.077 1.31e-02 5.83e+03 3.42e+01 bond pdb=" C VAL R 204 " pdb=" N MET R 205 " ideal model delta sigma weight residual 1.335 1.262 0.072 1.25e-02 6.40e+03 3.33e+01 bond pdb=" C SER R 79 " pdb=" O SER R 79 " ideal model delta sigma weight residual 1.236 1.169 0.068 1.18e-02 7.18e+03 3.29e+01 bond pdb=" N MET R 205 " pdb=" CA MET R 205 " ideal model delta sigma weight residual 1.459 1.392 0.067 1.20e-02 6.94e+03 3.11e+01 ... (remaining 9110 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.98: 191 105.98 - 113.00: 4752 113.00 - 120.02: 3237 120.02 - 127.04: 4060 127.04 - 134.06: 105 Bond angle restraints: 12345 Sorted by residual: angle pdb=" N THR A 33 " pdb=" CA THR A 33 " pdb=" C THR A 33 " ideal model delta sigma weight residual 110.55 123.37 -12.82 1.35e+00 5.49e-01 9.01e+01 angle pdb=" N LEU A 360 " pdb=" CA LEU A 360 " pdb=" C LEU A 360 " ideal model delta sigma weight residual 114.12 103.86 10.26 1.39e+00 5.18e-01 5.45e+01 angle pdb=" C11 UJF R 401 " pdb=" C12 UJF R 401 " pdb=" I01 UJF R 401 " ideal model delta sigma weight residual 105.19 126.97 -21.78 3.00e+00 1.11e-01 5.27e+01 angle pdb=" N CYS R 260 " pdb=" CA CYS R 260 " pdb=" C CYS R 260 " ideal model delta sigma weight residual 113.01 121.35 -8.34 1.20e+00 6.94e-01 4.83e+01 angle pdb=" N THR R 83 " pdb=" CA THR R 83 " pdb=" C THR R 83 " ideal model delta sigma weight residual 111.28 104.31 6.97 1.09e+00 8.42e-01 4.09e+01 ... (remaining 12340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4936 17.85 - 35.69: 376 35.69 - 53.54: 65 53.54 - 71.38: 20 71.38 - 89.23: 7 Dihedral angle restraints: 5404 sinusoidal: 2117 harmonic: 3287 Sorted by residual: dihedral pdb=" C ASN R 40 " pdb=" N ASN R 40 " pdb=" CA ASN R 40 " pdb=" CB ASN R 40 " ideal model delta harmonic sigma weight residual -122.60 -135.35 12.75 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C THR A 33 " pdb=" N THR A 33 " pdb=" CA THR A 33 " pdb=" CB THR A 33 " ideal model delta harmonic sigma weight residual -122.00 -134.42 12.42 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" CA TYR S 235 " pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 5401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1181 0.077 - 0.155: 160 0.155 - 0.232: 28 0.232 - 0.310: 6 0.310 - 0.387: 3 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CB VAL R 208 " pdb=" CA VAL R 208 " pdb=" CG1 VAL R 208 " pdb=" CG2 VAL R 208 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA ASN R 40 " pdb=" N ASN R 40 " pdb=" C ASN R 40 " pdb=" CB ASN R 40 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA THR A 33 " pdb=" N THR A 33 " pdb=" C THR A 33 " pdb=" CB THR A 33 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 1375 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 20 " 0.024 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C GLU A 20 " -0.080 2.00e-02 2.50e+03 pdb=" O GLU A 20 " 0.028 2.00e-02 2.50e+03 pdb=" N LYS A 21 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 251 " -0.022 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C GLY R 251 " 0.074 2.00e-02 2.50e+03 pdb=" O GLY R 251 " -0.028 2.00e-02 2.50e+03 pdb=" N ILE R 252 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 293 " 0.022 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C ASN R 293 " -0.071 2.00e-02 2.50e+03 pdb=" O ASN R 293 " 0.026 2.00e-02 2.50e+03 pdb=" N SER R 294 " 0.024 2.00e-02 2.50e+03 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.80: 2205 2.80 - 3.34: 8266 3.34 - 3.88: 14561 3.88 - 4.42: 17396 4.42 - 4.96: 30288 Nonbonded interactions: 72716 Sorted by model distance: nonbonded pdb=" OE1 GLU A 311 " pdb=" NH2 ARG A 314 " model vdw 2.256 2.520 nonbonded pdb=" ND2 ASN R 163 " pdb=" O PHE R 184 " model vdw 2.266 2.520 nonbonded pdb=" OG SER S 17 " pdb=" O MET S 83 " model vdw 2.324 2.440 nonbonded pdb=" OD1 ASP A 226 " pdb=" OG SER A 228 " model vdw 2.340 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP Y 48 " model vdw 2.361 2.440 ... (remaining 72711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.260 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: 0.010 Extract box with map and model: 4.160 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.540 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.008 0.082 9115 Z= 0.509 Angle : 1.009 21.781 12345 Z= 0.682 Chirality : 0.059 0.387 1378 Planarity : 0.006 0.061 1565 Dihedral : 13.524 89.229 3277 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.82 % Allowed : 3.09 % Favored : 96.08 % Cbeta Deviations : 0.28 % 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: -0.40 (0.26), residues: 1116 helix: -0.23 (0.28), residues: 376 sheet: 1.34 (0.35), residues: 262 loop : -1.19 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 147 HIS 0.011 0.001 HIS A 324 PHE 0.039 0.002 PHE R 304 TYR 0.018 0.001 TYR R 213 ARG 0.003 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 169 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8363 (pt0) cc_final: 0.8120 (pt0) REVERT: B 186 ASP cc_start: 0.7640 (p0) cc_final: 0.7245 (p0) REVERT: R 165 LYS cc_start: 0.6515 (mttm) cc_final: 0.6295 (ptmt) REVERT: R 195 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7238 (mtm) REVERT: S 7 SER cc_start: 0.7338 (t) cc_final: 0.7018 (p) REVERT: S 20 LEU cc_start: 0.7457 (mt) cc_final: 0.7238 (mp) REVERT: S 70 ILE cc_start: 0.8041 (pt) cc_final: 0.7616 (tt) REVERT: S 89 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6414 (mp0) outliers start: 8 outliers final: 4 residues processed: 174 average time/residue: 0.2560 time to fit residues: 58.2569 Evaluate side-chains 129 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 MET Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 286 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.0770 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 197 HIS A 261 GLN B 75 GLN B 268 ASN B 293 ASN R 40 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9115 Z= 0.182 Angle : 0.592 10.802 12345 Z= 0.305 Chirality : 0.044 0.234 1378 Planarity : 0.004 0.037 1565 Dihedral : 4.766 44.175 1250 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.34 % Allowed : 8.35 % Favored : 90.31 % 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: 0.20 (0.26), residues: 1116 helix: 1.00 (0.28), residues: 385 sheet: 1.40 (0.34), residues: 259 loop : -1.37 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.007 0.002 HIS B 225 PHE 0.018 0.002 PHE A 189 TYR 0.016 0.002 TYR S 235 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8392 (pt0) cc_final: 0.8131 (pt0) REVERT: A 237 LEU cc_start: 0.8318 (mt) cc_final: 0.8028 (mm) REVERT: B 186 ASP cc_start: 0.7794 (p0) cc_final: 0.6922 (p0) REVERT: B 217 MET cc_start: 0.8118 (ppp) cc_final: 0.7420 (ppp) REVERT: R 81 VAL cc_start: 0.7503 (p) cc_final: 0.7258 (t) REVERT: R 217 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7221 (mmtm) REVERT: S 18 ARG cc_start: 0.8519 (ttm170) cc_final: 0.8282 (ttt90) REVERT: S 70 ILE cc_start: 0.8112 (pt) cc_final: 0.7809 (tt) REVERT: S 89 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6620 (mp0) outliers start: 13 outliers final: 10 residues processed: 143 average time/residue: 0.2842 time to fit residues: 54.2099 Evaluate side-chains 134 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain S residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9115 Z= 0.190 Angle : 0.571 10.927 12345 Z= 0.298 Chirality : 0.043 0.137 1378 Planarity : 0.004 0.039 1565 Dihedral : 4.512 45.811 1240 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.06 % Allowed : 10.52 % Favored : 87.42 % 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: 0.46 (0.26), residues: 1116 helix: 1.52 (0.28), residues: 385 sheet: 1.39 (0.33), residues: 265 loop : -1.46 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.007 0.001 HIS B 225 PHE 0.014 0.002 PHE B 199 TYR 0.031 0.002 TYR S 235 ARG 0.003 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.6662 (t80) REVERT: R 81 VAL cc_start: 0.7550 (p) cc_final: 0.7305 (t) REVERT: R 217 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7367 (tptt) outliers start: 20 outliers final: 13 residues processed: 144 average time/residue: 0.2565 time to fit residues: 49.8237 Evaluate side-chains 138 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 0.0770 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 96 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9115 Z= 0.124 Angle : 0.500 9.329 12345 Z= 0.258 Chirality : 0.041 0.130 1378 Planarity : 0.003 0.035 1565 Dihedral : 4.322 48.729 1240 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.65 % Allowed : 12.47 % Favored : 85.88 % 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: 0.67 (0.26), residues: 1116 helix: 1.76 (0.28), residues: 386 sheet: 1.25 (0.33), residues: 279 loop : -1.32 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS S 232 PHE 0.013 0.001 PHE B 199 TYR 0.015 0.001 TYR S 235 ARG 0.002 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: R 81 VAL cc_start: 0.7408 (p) cc_final: 0.7201 (t) REVERT: R 217 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7274 (mmtm) outliers start: 16 outliers final: 11 residues processed: 133 average time/residue: 0.2499 time to fit residues: 44.3923 Evaluate side-chains 134 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 30.0000 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9115 Z= 0.282 Angle : 0.651 11.703 12345 Z= 0.339 Chirality : 0.045 0.146 1378 Planarity : 0.005 0.056 1565 Dihedral : 4.814 50.233 1239 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.47 % Allowed : 13.71 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 0.43 (0.26), residues: 1116 helix: 1.52 (0.27), residues: 386 sheet: 1.28 (0.34), residues: 259 loop : -1.41 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.019 0.002 PHE B 151 TYR 0.035 0.002 TYR S 235 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.6742 (t80) REVERT: R 81 VAL cc_start: 0.7449 (p) cc_final: 0.7204 (t) REVERT: R 200 ILE cc_start: 0.8533 (mm) cc_final: 0.8173 (mt) REVERT: R 217 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7200 (mmtm) REVERT: S 160 ARG cc_start: 0.7507 (ttt180) cc_final: 0.7306 (ttp-170) REVERT: S 235 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.5604 (t80) outliers start: 24 outliers final: 18 residues processed: 137 average time/residue: 0.2466 time to fit residues: 45.1862 Evaluate side-chains 141 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9115 Z= 0.199 Angle : 0.568 10.435 12345 Z= 0.295 Chirality : 0.043 0.141 1378 Planarity : 0.004 0.042 1565 Dihedral : 4.678 52.804 1239 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.89 % Allowed : 14.33 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 0.50 (0.26), residues: 1116 helix: 1.64 (0.27), residues: 386 sheet: 1.08 (0.32), residues: 285 loop : -1.41 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.015 0.002 PHE A 189 TYR 0.024 0.002 TYR S 235 ARG 0.002 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: B 219 ARG cc_start: 0.7843 (mtm110) cc_final: 0.7454 (mmm160) REVERT: B 234 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.6659 (t80) REVERT: R 81 VAL cc_start: 0.7438 (p) cc_final: 0.7216 (t) REVERT: R 200 ILE cc_start: 0.8536 (mm) cc_final: 0.8170 (mt) REVERT: R 217 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7145 (mmtm) REVERT: S 235 TYR cc_start: 0.6491 (OUTLIER) cc_final: 0.5661 (t80) outliers start: 28 outliers final: 20 residues processed: 140 average time/residue: 0.2634 time to fit residues: 49.7000 Evaluate side-chains 146 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 32 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9115 Z= 0.127 Angle : 0.487 8.999 12345 Z= 0.251 Chirality : 0.041 0.130 1378 Planarity : 0.003 0.035 1565 Dihedral : 4.374 54.048 1239 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.27 % Allowed : 15.57 % Favored : 82.16 % 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: 0.72 (0.26), residues: 1116 helix: 1.89 (0.28), residues: 382 sheet: 1.20 (0.33), residues: 285 loop : -1.32 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 197 PHE 0.013 0.001 PHE B 199 TYR 0.014 0.001 TYR S 235 ARG 0.002 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 306 TYR cc_start: 0.7535 (m-80) cc_final: 0.7161 (m-80) REVERT: B 219 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7462 (mmm160) REVERT: B 234 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.6628 (t80) REVERT: B 300 LEU cc_start: 0.8573 (mm) cc_final: 0.8316 (mt) REVERT: R 81 VAL cc_start: 0.7179 (p) cc_final: 0.6973 (t) REVERT: R 200 ILE cc_start: 0.8480 (mm) cc_final: 0.8112 (mt) REVERT: R 217 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7109 (mmtm) REVERT: S 235 TYR cc_start: 0.6226 (OUTLIER) cc_final: 0.5698 (t80) outliers start: 22 outliers final: 17 residues processed: 143 average time/residue: 0.2439 time to fit residues: 46.6841 Evaluate side-chains 143 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 0.0040 chunk 99 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9115 Z= 0.119 Angle : 0.486 8.896 12345 Z= 0.249 Chirality : 0.041 0.132 1378 Planarity : 0.003 0.034 1565 Dihedral : 4.254 54.068 1239 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.37 % Allowed : 15.36 % Favored : 82.27 % 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: 0.82 (0.26), residues: 1116 helix: 1.97 (0.28), residues: 383 sheet: 1.20 (0.33), residues: 285 loop : -1.23 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 266 PHE 0.012 0.001 PHE A 189 TYR 0.015 0.001 TYR S 235 ARG 0.001 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 237 LEU cc_start: 0.8206 (mt) cc_final: 0.7978 (mm) REVERT: A 306 TYR cc_start: 0.7510 (m-80) cc_final: 0.7222 (m-80) REVERT: B 130 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: B 219 ARG cc_start: 0.7813 (mtm110) cc_final: 0.7466 (mmm160) REVERT: B 234 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.6636 (t80) REVERT: R 81 VAL cc_start: 0.7098 (p) cc_final: 0.6894 (t) REVERT: R 217 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7108 (mmtm) REVERT: S 7 SER cc_start: 0.7826 (t) cc_final: 0.7286 (p) REVERT: S 235 TYR cc_start: 0.6215 (OUTLIER) cc_final: 0.5816 (t80) outliers start: 23 outliers final: 17 residues processed: 139 average time/residue: 0.2363 time to fit residues: 44.1705 Evaluate side-chains 144 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9115 Z= 0.194 Angle : 0.564 10.940 12345 Z= 0.291 Chirality : 0.043 0.140 1378 Planarity : 0.004 0.039 1565 Dihedral : 4.549 53.097 1239 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.37 % Allowed : 15.15 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 0.67 (0.26), residues: 1116 helix: 1.81 (0.28), residues: 382 sheet: 1.14 (0.32), residues: 284 loop : -1.28 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.015 0.002 PHE A 189 TYR 0.027 0.002 TYR S 235 ARG 0.002 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 237 LEU cc_start: 0.8256 (mt) cc_final: 0.7981 (mm) REVERT: A 306 TYR cc_start: 0.7582 (m-80) cc_final: 0.7319 (m-80) REVERT: B 234 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.6656 (t80) REVERT: R 81 VAL cc_start: 0.7169 (p) cc_final: 0.6953 (t) REVERT: R 200 ILE cc_start: 0.8530 (mm) cc_final: 0.8188 (mt) REVERT: R 217 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7139 (mmtm) REVERT: S 7 SER cc_start: 0.7934 (t) cc_final: 0.7372 (p) REVERT: S 235 TYR cc_start: 0.6699 (OUTLIER) cc_final: 0.5906 (t80) outliers start: 23 outliers final: 20 residues processed: 141 average time/residue: 0.2538 time to fit residues: 47.6069 Evaluate side-chains 150 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.3980 chunk 73 optimal weight: 0.3980 chunk 110 optimal weight: 0.0770 chunk 101 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 93 optimal weight: 0.0270 chunk 26 optimal weight: 0.8980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9115 Z= 0.107 Angle : 0.471 8.850 12345 Z= 0.241 Chirality : 0.040 0.128 1378 Planarity : 0.003 0.035 1565 Dihedral : 4.258 55.080 1239 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.16 % Allowed : 15.57 % Favored : 82.27 % 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: 0.87 (0.26), residues: 1116 helix: 2.02 (0.28), residues: 382 sheet: 1.04 (0.32), residues: 293 loop : -1.09 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE B 199 TYR 0.010 0.001 TYR R 153 ARG 0.002 0.000 ARG S 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.960 Fit side-chains REVERT: A 237 LEU cc_start: 0.8171 (mt) cc_final: 0.7935 (mm) REVERT: A 306 TYR cc_start: 0.7467 (m-80) cc_final: 0.6887 (m-80) REVERT: B 219 ARG cc_start: 0.7845 (mtm110) cc_final: 0.7481 (mmm160) REVERT: B 234 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.6626 (t80) REVERT: R 81 VAL cc_start: 0.7075 (p) cc_final: 0.6866 (t) REVERT: R 217 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7103 (mmtm) REVERT: S 7 SER cc_start: 0.7727 (t) cc_final: 0.7238 (p) REVERT: S 235 TYR cc_start: 0.6008 (OUTLIER) cc_final: 0.5702 (t80) outliers start: 21 outliers final: 14 residues processed: 143 average time/residue: 0.2349 time to fit residues: 45.3466 Evaluate side-chains 140 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.158308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.122206 restraints weight = 8536.352| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.54 r_work: 0.2912 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9115 Z= 0.142 Angle : 0.511 9.587 12345 Z= 0.263 Chirality : 0.041 0.134 1378 Planarity : 0.004 0.037 1565 Dihedral : 4.301 54.685 1239 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.06 % Allowed : 15.67 % Favored : 82.27 % 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: 0.78 (0.26), residues: 1116 helix: 1.91 (0.28), residues: 383 sheet: 0.99 (0.32), residues: 295 loop : -1.11 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 261 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE A 189 TYR 0.019 0.001 TYR S 235 ARG 0.002 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2237.92 seconds wall clock time: 41 minutes 9.15 seconds (2469.15 seconds total)