Starting phenix.real_space_refine on Wed Feb 4 08:03:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l79_62871/02_2026/9l79_62871_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l79_62871/02_2026/9l79_62871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l79_62871/02_2026/9l79_62871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l79_62871/02_2026/9l79_62871.map" model { file = "/net/cci-nas-00/data/ceres_data/9l79_62871/02_2026/9l79_62871_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l79_62871/02_2026/9l79_62871_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.180 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 S 64 5.16 5 C 6028 2.51 5 N 1628 2.21 5 O 1740 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9461 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2040 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 7, 'TRANS': 262} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 4, 'TYR:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2482 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 86 Chain: "G" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 430 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1752 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "S" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1774 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 948 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8WL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.27, per 1000 atoms: 0.24 Number of scatterers: 9461 At special positions: 0 Unit cell: (102.34, 117.82, 133.3, 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) S 64 16.00 F 1 9.00 O 1740 8.00 N 1628 7.00 C 6028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 155 " distance=2.03 Simple disulfide: pdb=" SG CYS R 251 " - pdb=" SG CYS R 254 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 0.74 Conformation dependent library (CDL) restraints added in 294.0 milliseconds 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2306 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 30.9% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'R' and resid 8 through 34 removed outlier: 3.527A pdb=" N ALA R 12 " --> pdb=" O GLY R 8 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL R 13 " --> pdb=" O VAL R 9 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER R 16 " --> pdb=" O ALA R 12 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU R 17 " --> pdb=" O VAL R 13 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE R 18 " --> pdb=" O LEU R 14 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR R 23 " --> pdb=" O ILE R 19 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL R 27 " --> pdb=" O THR R 23 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA R 28 " --> pdb=" O LEU R 24 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 60 removed outlier: 4.210A pdb=" N PHE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR R 44 " --> pdb=" O SER R 40 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA R 48 " --> pdb=" O THR R 44 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU R 53 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE R 54 " --> pdb=" O ALA R 50 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY R 55 " --> pdb=" O ASP R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 92 removed outlier: 3.681A pdb=" N ARG R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA R 83 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL R 85 " --> pdb=" O ARG R 81 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR R 86 " --> pdb=" O MET R 82 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER R 92 " --> pdb=" O SER R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 109 removed outlier: 3.685A pdb=" N VAL R 96 " --> pdb=" O SER R 92 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE R 101 " --> pdb=" O MET R 97 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE R 107 " --> pdb=" O ARG R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 117 removed outlier: 3.890A pdb=" N LEU R 114 " --> pdb=" O PRO R 110 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS R 115 " --> pdb=" O PHE R 111 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE R 116 " --> pdb=" O ARG R 112 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET R 117 " --> pdb=" O TYR R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 139 removed outlier: 3.800A pdb=" N ALA R 122 " --> pdb=" O SER R 118 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY R 123 " --> pdb=" O GLY R 119 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP R 130 " --> pdb=" O ILE R 126 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU R 131 " --> pdb=" O ALA R 127 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL R 132 " --> pdb=" O GLY R 128 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY R 137 " --> pdb=" O SER R 133 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU R 139 " --> pdb=" O LEU R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 173 removed outlier: 4.114A pdb=" N VAL R 166 " --> pdb=" O HIS R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 206 removed outlier: 3.564A pdb=" N LEU R 180 " --> pdb=" O PRO R 176 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP R 187 " --> pdb=" O PHE R 183 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU R 189 " --> pdb=" O TYR R 185 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS R 190 " --> pdb=" O CYS R 186 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET R 194 " --> pdb=" O LYS R 190 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER R 196 " --> pdb=" O ALA R 192 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN R 198 " --> pdb=" O MET R 194 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE R 199 " --> pdb=" O HIS R 195 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS R 204 " --> pdb=" O ARG R 200 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA R 205 " --> pdb=" O LYS R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 236 removed outlier: 3.799A pdb=" N VAL R 229 " --> pdb=" O ARG R 225 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU R 230 " --> pdb=" O THR R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 252 removed outlier: 3.624A pdb=" N VAL R 247 " --> pdb=" O ILE R 243 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL R 249 " --> pdb=" O GLY R 245 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA R 250 " --> pdb=" O ILE R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 269 removed outlier: 4.141A pdb=" N GLY R 268 " --> pdb=" O LEU R 264 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL R 269 " --> pdb=" O TRP R 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 264 through 269' Processing helix chain 'R' and resid 270 through 273 Processing helix chain 'R' and resid 274 through 279 removed outlier: 3.654A pdb=" N ILE R 278 " --> pdb=" O LEU R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 293 removed outlier: 3.907A pdb=" N GLN R 289 " --> pdb=" O GLU R 285 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU R 290 " --> pdb=" O VAL R 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.957A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.653A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.749A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.555A pdb=" N ARG A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 29 " --> pdb=" O MET A 25 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.882A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 238' Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.873A pdb=" N ALA A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 removed outlier: 4.291A pdb=" N LEU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 340 removed outlier: 4.999A pdb=" N ILE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP A 333 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 removed outlier: 3.589A pdb=" N ARG A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 370 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 373 " --> pdb=" O CYS A 369 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 381 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.708A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.510A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.509A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.758A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.686A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.293A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.917A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.693A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.923A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.799A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.024A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.815A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.473A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.606A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET S 83 " --> pdb=" O ARG S 18 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.521A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU S 117 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.635A pdb=" N THR S 129 " --> pdb=" O ARG S 148 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 143 through 146 removed outlier: 3.789A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE S 204 " --> pdb=" O VAL S 143 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER S 192 " --> pdb=" O THR S 203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 174 through 178 removed outlier: 6.856A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR S 163 " --> pdb=" O MET S 218 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.555A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.675A pdb=" N VAL N 37 " --> pdb=" O TYR N 95 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 837 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: 1.05 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1504 1.30 - 1.44: 2729 1.44 - 1.57: 5339 1.57 - 1.71: 0 1.71 - 1.84: 93 Bond restraints: 9665 Sorted by residual: bond pdb=" N30 8WL R 401 " pdb=" O32 8WL R 401 " ideal model delta sigma weight residual 1.214 1.400 -0.186 2.00e-02 2.50e+03 8.60e+01 bond pdb=" C12 8WL R 401 " pdb=" N11 8WL R 401 " ideal model delta sigma weight residual 1.334 1.463 -0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C16 8WL R 401 " pdb=" N17 8WL R 401 " ideal model delta sigma weight residual 1.347 1.457 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C PRO R 276 " pdb=" O PRO R 276 " ideal model delta sigma weight residual 1.235 1.166 0.069 1.30e-02 5.92e+03 2.82e+01 bond pdb=" C8 8WL R 401 " pdb=" C9 8WL R 401 " ideal model delta sigma weight residual 1.544 1.461 0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 9660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 13071 3.27 - 6.54: 49 6.54 - 9.80: 7 9.80 - 13.07: 0 13.07 - 16.34: 1 Bond angle restraints: 13128 Sorted by residual: angle pdb=" O24 8WL R 401 " pdb=" S22 8WL R 401 " pdb=" O25 8WL R 401 " ideal model delta sigma weight residual 117.77 101.43 16.34 3.00e+00 1.11e-01 2.97e+01 angle pdb=" C GLY R 153 " pdb=" N GLN R 154 " pdb=" CA GLN R 154 " ideal model delta sigma weight residual 122.82 113.63 9.19 2.12e+00 2.22e-01 1.88e+01 angle pdb=" C PRO R 276 " pdb=" CA PRO R 276 " pdb=" CB PRO R 276 " ideal model delta sigma weight residual 111.56 105.22 6.34 1.65e+00 3.67e-01 1.47e+01 angle pdb=" CA GLN R 154 " pdb=" C GLN R 154 " pdb=" O GLN R 154 " ideal model delta sigma weight residual 120.89 117.24 3.65 1.11e+00 8.12e-01 1.08e+01 angle pdb=" C10 8WL R 401 " pdb=" N11 8WL R 401 " pdb=" C33 8WL R 401 " ideal model delta sigma weight residual 116.31 106.88 9.43 3.00e+00 1.11e-01 9.88e+00 ... (remaining 13123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.69: 5500 28.69 - 57.37: 170 57.37 - 86.06: 22 86.06 - 114.74: 7 114.74 - 143.43: 1 Dihedral angle restraints: 5700 sinusoidal: 2115 harmonic: 3585 Sorted by residual: dihedral pdb=" C10 8WL R 401 " pdb=" C8 8WL R 401 " pdb=" C9 8WL R 401 " pdb=" C7 8WL R 401 " ideal model delta sinusoidal sigma weight residual 90.59 -125.98 -143.43 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -120.59 34.59 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" C33 8WL R 401 " pdb=" C34 8WL R 401 " pdb=" C8 8WL R 401 " pdb=" C7 8WL R 401 " ideal model delta sinusoidal sigma weight residual 151.84 -94.08 -114.08 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 5697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.973: 1499 0.973 - 1.946: 0 1.946 - 2.919: 0 2.919 - 3.892: 0 3.892 - 4.865: 1 Chirality restraints: 1500 Sorted by residual: chirality pdb=" C8 8WL R 401 " pdb=" C34 8WL R 401 " pdb=" C7 8WL R 401 " pdb=" C9 8WL R 401 " both_signs ideal model delta sigma weight residual False 2.58 -2.28 4.86 2.00e-01 2.50e+01 5.92e+02 chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA TYR S 223 " pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CB TYR S 223 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 1497 not shown) Planarity restraints: 1661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 139 " 0.039 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO R 140 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO R 140 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 140 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 223 " -0.019 2.00e-02 2.50e+03 1.35e-02 3.64e+00 pdb=" CG TYR S 223 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR S 223 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR S 223 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 223 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR S 223 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR S 223 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR S 223 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO S 41 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " 0.024 5.00e-02 4.00e+02 ... (remaining 1658 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1245 2.76 - 3.29: 8195 3.29 - 3.83: 13314 3.83 - 4.36: 15699 4.36 - 4.90: 28998 Nonbonded interactions: 67451 Sorted by model distance: nonbonded pdb=" NH1 ARG B 42 " pdb=" O ILE B 43 " model vdw 2.220 3.120 nonbonded pdb=" O GLY N 8 " pdb=" OG1 THR N 122 " model vdw 2.229 3.040 nonbonded pdb=" OD1 ASP B 186 " pdb=" NH2 ARG A 228 " model vdw 2.295 3.120 nonbonded pdb=" NH1 ARG R 262 " pdb=" O24 8WL R 401 " model vdw 2.313 3.120 nonbonded pdb=" O ILE R 18 " pdb=" ND2 ASN R 22 " model vdw 2.325 3.120 ... (remaining 67446 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 ========== 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: 1.050 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.270 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:8.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.186 9672 Z= 0.210 Angle : 0.610 16.338 13142 Z= 0.311 Chirality : 0.132 4.865 1500 Planarity : 0.004 0.060 1661 Dihedral : 14.398 143.430 3373 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.31 % Allowed : 0.10 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.22), residues: 1223 helix: -1.63 (0.25), residues: 311 sheet: -0.42 (0.28), residues: 347 loop : -2.04 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.032 0.001 TYR S 223 PHE 0.016 0.001 PHE A 305 TRP 0.016 0.001 TRP N 47 HIS 0.006 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9665) covalent geometry : angle 0.60737 (13128) SS BOND : bond 0.00724 ( 7) SS BOND : angle 1.69165 ( 14) hydrogen bonds : bond 0.36708 ( 296) hydrogen bonds : angle 8.05328 ( 837) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 0.332 Fit side-chains REVERT: A 24 LYS cc_start: 0.8362 (mttt) cc_final: 0.8155 (mttt) REVERT: A 282 ASN cc_start: 0.8177 (t0) cc_final: 0.7972 (t0) outliers start: 3 outliers final: 1 residues processed: 145 average time/residue: 0.6394 time to fit residues: 97.9711 Evaluate side-chains 119 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 248 GLN B 176 GLN A 261 ASN A 347 HIS S 174 GLN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.169701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.129822 restraints weight = 10880.688| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.93 r_work: 0.3290 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9672 Z= 0.205 Angle : 0.717 10.469 13142 Z= 0.377 Chirality : 0.047 0.223 1500 Planarity : 0.005 0.061 1661 Dihedral : 8.292 113.141 1374 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.25 % Allowed : 9.61 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.23), residues: 1223 helix: -0.56 (0.28), residues: 318 sheet: -0.20 (0.27), residues: 339 loop : -2.28 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.046 0.002 TYR S 223 PHE 0.018 0.002 PHE A 212 TRP 0.022 0.002 TRP N 47 HIS 0.014 0.002 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 9665) covalent geometry : angle 0.71237 (13128) SS BOND : bond 0.01848 ( 7) SS BOND : angle 2.70770 ( 14) hydrogen bonds : bond 0.08821 ( 296) hydrogen bonds : angle 5.10692 ( 837) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.389 Fit side-chains REVERT: B 96 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7478 (mtm-85) REVERT: G 47 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8004 (mt-10) outliers start: 22 outliers final: 9 residues processed: 129 average time/residue: 0.5989 time to fit residues: 81.6157 Evaluate side-chains 121 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 194 MET Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 0.0000 chunk 39 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 22 ASN R 109 GLN R 248 GLN R 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.175886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.127730 restraints weight = 10904.881| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.51 r_work: 0.3365 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9672 Z= 0.107 Angle : 0.534 9.302 13142 Z= 0.279 Chirality : 0.041 0.145 1500 Planarity : 0.004 0.051 1661 Dihedral : 7.499 120.606 1372 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.35 % Allowed : 12.88 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.23), residues: 1223 helix: 0.13 (0.29), residues: 335 sheet: 0.12 (0.28), residues: 325 loop : -2.25 (0.23), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.026 0.001 TYR S 223 PHE 0.017 0.001 PHE A 305 TRP 0.014 0.001 TRP N 47 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 9665) covalent geometry : angle 0.53298 (13128) SS BOND : bond 0.00582 ( 7) SS BOND : angle 1.06977 ( 14) hydrogen bonds : bond 0.05123 ( 296) hydrogen bonds : angle 4.36303 ( 837) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.407 Fit side-chains REVERT: R 32 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6518 (tt) REVERT: G 47 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: A 31 GLN cc_start: 0.7517 (mt0) cc_final: 0.6682 (pt0) REVERT: A 334 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6965 (mm-30) REVERT: S 85 SER cc_start: 0.8340 (t) cc_final: 0.8130 (t) outliers start: 23 outliers final: 8 residues processed: 128 average time/residue: 0.6180 time to fit residues: 84.0102 Evaluate side-chains 120 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 195 HIS Chi-restraints excluded: chain R residue 201 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 29 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 248 GLN R 283 GLN R 289 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.174273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132990 restraints weight = 10947.072| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.56 r_work: 0.3352 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9672 Z= 0.116 Angle : 0.557 9.172 13142 Z= 0.289 Chirality : 0.042 0.158 1500 Planarity : 0.004 0.050 1661 Dihedral : 7.318 124.525 1372 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.45 % Allowed : 14.72 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.23), residues: 1223 helix: 0.41 (0.29), residues: 335 sheet: 0.10 (0.27), residues: 337 loop : -2.20 (0.23), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.030 0.001 TYR S 223 PHE 0.016 0.001 PHE A 305 TRP 0.015 0.001 TRP N 47 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9665) covalent geometry : angle 0.55470 (13128) SS BOND : bond 0.01014 ( 7) SS BOND : angle 1.51249 ( 14) hydrogen bonds : bond 0.05308 ( 296) hydrogen bonds : angle 4.17810 ( 837) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.369 Fit side-chains REVERT: R 32 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6522 (tt) REVERT: A 31 GLN cc_start: 0.7827 (mt0) cc_final: 0.7019 (pt0) REVERT: A 227 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.6100 (mt0) REVERT: A 334 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7239 (mm-30) REVERT: S 85 SER cc_start: 0.8345 (t) cc_final: 0.8144 (t) outliers start: 24 outliers final: 11 residues processed: 130 average time/residue: 0.5892 time to fit residues: 81.7093 Evaluate side-chains 124 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 194 MET Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 110 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 118 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 248 GLN R 283 GLN R 289 GLN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.174340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135264 restraints weight = 10995.301| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.59 r_work: 0.3325 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9672 Z= 0.115 Angle : 0.547 9.536 13142 Z= 0.286 Chirality : 0.042 0.152 1500 Planarity : 0.004 0.049 1661 Dihedral : 7.174 128.700 1372 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.76 % Allowed : 15.85 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.23), residues: 1223 helix: 0.56 (0.29), residues: 338 sheet: 0.26 (0.28), residues: 330 loop : -2.22 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.017 0.001 TYR S 223 PHE 0.016 0.001 PHE A 305 TRP 0.014 0.001 TRP N 47 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9665) covalent geometry : angle 0.54480 (13128) SS BOND : bond 0.00994 ( 7) SS BOND : angle 1.43975 ( 14) hydrogen bonds : bond 0.05091 ( 296) hydrogen bonds : angle 4.08599 ( 837) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.364 Fit side-chains REVERT: R 32 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6646 (tt) REVERT: B 96 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7339 (mtm-85) REVERT: A 31 GLN cc_start: 0.7798 (mt0) cc_final: 0.7124 (pt0) REVERT: A 227 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.5944 (mt0) REVERT: A 334 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7090 (mm-30) REVERT: S 223 TYR cc_start: 0.6001 (OUTLIER) cc_final: 0.5232 (t80) REVERT: N 38 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8055 (ptt180) outliers start: 27 outliers final: 16 residues processed: 129 average time/residue: 0.5768 time to fit residues: 79.2040 Evaluate side-chains 131 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 194 MET Chi-restraints excluded: chain R residue 195 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 38 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 68 optimal weight: 0.0030 chunk 107 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 115 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 248 GLN R 283 GLN R 289 GLN B 32 GLN S 130 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.172894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.132938 restraints weight = 10967.297| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.65 r_work: 0.3293 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9672 Z= 0.137 Angle : 0.587 10.168 13142 Z= 0.308 Chirality : 0.043 0.170 1500 Planarity : 0.004 0.049 1661 Dihedral : 7.188 131.697 1372 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.17 % Allowed : 16.46 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.23), residues: 1223 helix: 0.49 (0.29), residues: 338 sheet: 0.02 (0.27), residues: 347 loop : -2.18 (0.24), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 72 TYR 0.020 0.001 TYR S 223 PHE 0.017 0.001 PHE A 212 TRP 0.016 0.001 TRP N 47 HIS 0.010 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9665) covalent geometry : angle 0.58443 (13128) SS BOND : bond 0.01258 ( 7) SS BOND : angle 1.87629 ( 14) hydrogen bonds : bond 0.05747 ( 296) hydrogen bonds : angle 4.19437 ( 837) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.253 Fit side-chains REVERT: R 32 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6735 (tt) REVERT: B 96 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7339 (mtm-85) REVERT: A 31 GLN cc_start: 0.7749 (mt0) cc_final: 0.7058 (pt0) REVERT: A 227 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.5960 (mt0) REVERT: A 334 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7030 (mm-30) REVERT: S 223 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.5461 (t80) REVERT: N 38 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8065 (ptt180) outliers start: 31 outliers final: 14 residues processed: 126 average time/residue: 0.5545 time to fit residues: 74.1643 Evaluate side-chains 125 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 194 MET Chi-restraints excluded: chain R residue 195 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 38 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 87 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 47 optimal weight: 6.9990 chunk 120 optimal weight: 0.0040 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 248 GLN R 283 GLN R 289 GLN B 32 GLN S 130 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.176462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127430 restraints weight = 10961.788| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.56 r_work: 0.3359 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9672 Z= 0.100 Angle : 0.516 9.733 13142 Z= 0.271 Chirality : 0.041 0.138 1500 Planarity : 0.004 0.048 1661 Dihedral : 6.864 136.263 1372 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.86 % Allowed : 16.87 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.23), residues: 1223 helix: 0.77 (0.30), residues: 338 sheet: 0.31 (0.28), residues: 325 loop : -2.20 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.013 0.001 TYR S 223 PHE 0.018 0.001 PHE A 305 TRP 0.013 0.001 TRP N 47 HIS 0.010 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 9665) covalent geometry : angle 0.51477 (13128) SS BOND : bond 0.00720 ( 7) SS BOND : angle 1.13317 ( 14) hydrogen bonds : bond 0.04287 ( 296) hydrogen bonds : angle 3.94093 ( 837) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.387 Fit side-chains REVERT: R 32 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6506 (tt) REVERT: R 139 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6781 (tp) REVERT: A 31 GLN cc_start: 0.7457 (mt0) cc_final: 0.6815 (pt0) REVERT: A 227 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.5699 (mt0) REVERT: A 334 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6833 (mm-30) REVERT: S 223 TYR cc_start: 0.5573 (OUTLIER) cc_final: 0.4934 (t80) REVERT: N 38 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7866 (ptt180) outliers start: 28 outliers final: 17 residues processed: 133 average time/residue: 0.5565 time to fit residues: 79.0846 Evaluate side-chains 135 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 194 MET Chi-restraints excluded: chain R residue 195 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 38 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 9 optimal weight: 0.0050 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 248 GLN R 283 GLN R 289 GLN B 32 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.168786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.119397 restraints weight = 10836.093| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.53 r_work: 0.3255 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9672 Z= 0.222 Angle : 0.724 12.086 13142 Z= 0.377 Chirality : 0.047 0.214 1500 Planarity : 0.005 0.067 1661 Dihedral : 7.349 135.905 1372 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.76 % Allowed : 18.10 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.23), residues: 1223 helix: 0.18 (0.29), residues: 338 sheet: -0.03 (0.27), residues: 349 loop : -2.26 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.023 0.002 TYR S 223 PHE 0.022 0.002 PHE A 212 TRP 0.018 0.002 TRP N 47 HIS 0.012 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 9665) covalent geometry : angle 0.71808 (13128) SS BOND : bond 0.02085 ( 7) SS BOND : angle 2.95595 ( 14) hydrogen bonds : bond 0.07474 ( 296) hydrogen bonds : angle 4.43522 ( 837) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.381 Fit side-chains REVERT: B 96 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7424 (mtm-85) REVERT: A 31 GLN cc_start: 0.7798 (mt0) cc_final: 0.6999 (pt0) REVERT: A 227 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.6085 (mt0) REVERT: A 287 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6537 (tp) REVERT: A 334 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7077 (mm-30) REVERT: S 223 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.5864 (t80) outliers start: 27 outliers final: 13 residues processed: 126 average time/residue: 0.6307 time to fit residues: 84.2543 Evaluate side-chains 125 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 194 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 43 optimal weight: 0.0980 chunk 33 optimal weight: 0.0050 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 283 GLN R 289 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126846 restraints weight = 10982.782| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.57 r_work: 0.3351 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9672 Z= 0.105 Angle : 0.542 9.623 13142 Z= 0.283 Chirality : 0.041 0.138 1500 Planarity : 0.004 0.048 1661 Dihedral : 6.841 140.521 1372 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.25 % Allowed : 19.12 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.23), residues: 1223 helix: 0.68 (0.30), residues: 334 sheet: 0.34 (0.28), residues: 328 loop : -2.25 (0.23), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.013 0.001 TYR S 223 PHE 0.021 0.001 PHE A 305 TRP 0.016 0.001 TRP N 47 HIS 0.013 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 9665) covalent geometry : angle 0.54134 (13128) SS BOND : bond 0.00735 ( 7) SS BOND : angle 1.14145 ( 14) hydrogen bonds : bond 0.04420 ( 296) hydrogen bonds : angle 4.02232 ( 837) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.386 Fit side-chains REVERT: R 32 LEU cc_start: 0.6889 (mt) cc_final: 0.6574 (tt) REVERT: R 139 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6863 (tp) REVERT: A 31 GLN cc_start: 0.7456 (mt0) cc_final: 0.6791 (pt0) REVERT: A 227 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.5765 (mt0) REVERT: A 334 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6809 (mm-30) REVERT: S 223 TYR cc_start: 0.5571 (OUTLIER) cc_final: 0.4908 (t80) outliers start: 22 outliers final: 10 residues processed: 126 average time/residue: 0.5948 time to fit residues: 79.9252 Evaluate side-chains 125 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 194 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 109 optimal weight: 0.0040 chunk 119 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 6 optimal weight: 0.0670 chunk 33 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 0.0000 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 283 GLN R 289 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.179659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131291 restraints weight = 10994.800| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.50 r_work: 0.3408 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9672 Z= 0.094 Angle : 0.510 10.059 13142 Z= 0.264 Chirality : 0.040 0.135 1500 Planarity : 0.004 0.049 1661 Dihedral : 6.495 147.775 1372 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.53 % Allowed : 19.53 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.24), residues: 1223 helix: 1.07 (0.30), residues: 335 sheet: 0.39 (0.28), residues: 333 loop : -2.16 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 103 TYR 0.010 0.001 TYR S 223 PHE 0.022 0.001 PHE A 305 TRP 0.014 0.001 TRP N 47 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 9665) covalent geometry : angle 0.50888 (13128) SS BOND : bond 0.00550 ( 7) SS BOND : angle 0.96108 ( 14) hydrogen bonds : bond 0.03563 ( 296) hydrogen bonds : angle 3.75632 ( 837) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.358 Fit side-chains REVERT: R 139 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6695 (tp) REVERT: B 16 ASN cc_start: 0.7486 (m-40) cc_final: 0.7278 (m110) REVERT: A 31 GLN cc_start: 0.7490 (mt0) cc_final: 0.6891 (pt0) REVERT: A 334 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6825 (mm-30) REVERT: S 223 TYR cc_start: 0.5206 (OUTLIER) cc_final: 0.4717 (t80) outliers start: 15 outliers final: 8 residues processed: 121 average time/residue: 0.6146 time to fit residues: 79.3376 Evaluate side-chains 120 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain N residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.0370 chunk 54 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 0.0370 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 248 GLN R 283 GLN R 289 GLN B 32 GLN B 237 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.178610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.129433 restraints weight = 10903.847| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.55 r_work: 0.3384 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9672 Z= 0.100 Angle : 0.522 10.159 13142 Z= 0.272 Chirality : 0.041 0.138 1500 Planarity : 0.004 0.049 1661 Dihedral : 6.471 151.631 1372 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.12 % Allowed : 19.73 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.24), residues: 1223 helix: 1.14 (0.30), residues: 330 sheet: 0.50 (0.28), residues: 329 loop : -2.11 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 332 TYR 0.013 0.001 TYR S 223 PHE 0.020 0.001 PHE A 305 TRP 0.014 0.001 TRP N 47 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 9665) covalent geometry : angle 0.52108 (13128) SS BOND : bond 0.00727 ( 7) SS BOND : angle 1.15781 ( 14) hydrogen bonds : bond 0.03907 ( 296) hydrogen bonds : angle 3.77302 ( 837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3200.36 seconds wall clock time: 55 minutes 1.97 seconds (3301.97 seconds total)