Starting phenix.real_space_refine on Wed Mar 4 07:17:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lfm_0877/03_2026/6lfm_0877.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lfm_0877/03_2026/6lfm_0877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lfm_0877/03_2026/6lfm_0877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lfm_0877/03_2026/6lfm_0877.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lfm_0877/03_2026/6lfm_0877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lfm_0877/03_2026/6lfm_0877.map" } resolution = 3.5 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= 0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1821 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6510 2.51 5 N 1744 2.21 5 O 1855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10181 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1805 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2579 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 582 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "E" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 551 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "R" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2451 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 295} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1750 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.11, per 1000 atoms: 0.21 Number of scatterers: 10181 At special positions: 0 Unit cell: (87.3602, 123.414, 156.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1855 8.00 N 1744 7.00 C 6510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 34 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 50 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 34 " distance=2.04 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 50 " distance=2.04 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.04 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 0.75 Conformation dependent library (CDL) restraints added in 423.8 milliseconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2448 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 19 sheets defined 35.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.561A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 17 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.866A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.107A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.612A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.196A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.228A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 removed outlier: 3.524A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 352 removed outlier: 4.319A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 removed outlier: 4.062A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 23 removed outlier: 3.946A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.510A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.567A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'D' and resid 18 through 22 removed outlier: 4.085A pdb=" N ILE D 22 " --> pdb=" O PRO D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 70 removed outlier: 4.728A pdb=" N GLU D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS D 64 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 66 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'R' and resid 46 through 60 removed outlier: 4.255A pdb=" N VAL R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 75 removed outlier: 3.513A pdb=" N LEU R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASN R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU R 68 " --> pdb=" O LEU R 64 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET R 70 " --> pdb=" O ASN R 66 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU R 74 " --> pdb=" O MET R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 98 removed outlier: 4.136A pdb=" N LEU R 87 " --> pdb=" O THR R 83 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU R 88 " --> pdb=" O ASP R 84 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 111 removed outlier: 3.649A pdb=" N SER R 107 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS R 108 " --> pdb=" O TRP R 104 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 136 removed outlier: 4.032A pdb=" N CYS R 119 " --> pdb=" O GLY R 115 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER R 123 " --> pdb=" O CYS R 119 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU R 124 " --> pdb=" O LYS R 120 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN R 129 " --> pdb=" O LEU R 125 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR R 131 " --> pdb=" O GLU R 127 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE R 134 " --> pdb=" O PHE R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 147 Processing helix chain 'R' and resid 155 through 161 removed outlier: 4.499A pdb=" N ARG R 159 " --> pdb=" O LEU R 155 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU R 161 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 177 Processing helix chain 'R' and resid 177 through 182 removed outlier: 3.639A pdb=" N LEU R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 214 removed outlier: 3.644A pdb=" N ILE R 213 " --> pdb=" O MET R 209 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU R 214 " --> pdb=" O LEU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 219 Processing helix chain 'R' and resid 220 through 229 Processing helix chain 'R' and resid 230 through 241 Processing helix chain 'R' and resid 245 through 279 removed outlier: 3.819A pdb=" N ALA R 249 " --> pdb=" O GLN R 245 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG R 251 " --> pdb=" O HIS R 247 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA R 255 " --> pdb=" O ARG R 251 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL R 257 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU R 262 " --> pdb=" O LEU R 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU R 265 " --> pdb=" O LEU R 261 " (cutoff:3.500A) Proline residue: R 266 - end of helix removed outlier: 3.725A pdb=" N LEU R 272 " --> pdb=" O ASN R 268 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR R 275 " --> pdb=" O LEU R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 315 removed outlier: 3.502A pdb=" N ILE R 301 " --> pdb=" O ASP R 297 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N HIS R 306 " --> pdb=" O LEU R 302 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER R 307 " --> pdb=" O GLY R 303 " (cutoff:3.500A) Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 332 removed outlier: 3.623A pdb=" N LEU R 326 " --> pdb=" O ARG R 322 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE R 328 " --> pdb=" O GLY R 324 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 4.051A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 56 removed outlier: 3.614A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.790A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.845A 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 'S' and resid 208 through 212 removed outlier: 3.656A pdb=" N ASP S 211 " --> pdb=" O GLU S 208 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 208 through 212' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.730A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 226 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.958A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.797A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.753A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 4.597A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 150 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR B 159 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.556A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.864A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.850A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.810A pdb=" N VAL D 41 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS D 42 " --> pdb=" O GLU D 24 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU E 24 " --> pdb=" O LYS E 42 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 184 through 185 Processing sheet with id=AB3, first strand: chain 'S' and resid 3 through 4 Processing sheet with id=AB4, first strand: chain 'S' and resid 17 through 21 removed outlier: 3.673A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 45 through 50 removed outlier: 6.709A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 135 through 136 removed outlier: 4.024A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 144 through 148 Processing sheet with id=AB8, first strand: chain 'S' and resid 162 through 163 Processing sheet with id=AB9, first strand: chain 'S' and resid 165 through 166 Processing sheet with id=AC1, first strand: chain 'S' and resid 177 through 178 removed outlier: 3.630A pdb=" N ASN S 182 " --> pdb=" O TYR S 178 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1023 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: 1.50 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3266 1.34 - 1.46: 2534 1.46 - 1.59: 4490 1.59 - 1.71: 0 1.71 - 1.84: 100 Bond restraints: 10390 Sorted by residual: bond pdb=" C10 CLR R 401 " pdb=" C5 CLR R 401 " ideal model delta sigma weight residual 1.519 1.402 0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C4 CLR R 401 " pdb=" C5 CLR R 401 " ideal model delta sigma weight residual 1.506 1.391 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C6 CLR R 401 " pdb=" C7 CLR R 401 " ideal model delta sigma weight residual 1.492 1.388 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 1.332 1.395 -0.063 2.00e-02 2.50e+03 9.83e+00 bond pdb=" CB VAL B 187 " pdb=" CG2 VAL B 187 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.64e+00 ... (remaining 10385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 13610 2.72 - 5.44: 402 5.44 - 8.16: 50 8.16 - 10.88: 12 10.88 - 13.60: 5 Bond angle restraints: 14079 Sorted by residual: angle pdb=" N PRO R 30 " pdb=" CA PRO R 30 " pdb=" C PRO R 30 " ideal model delta sigma weight residual 110.70 116.54 -5.84 1.22e+00 6.72e-01 2.29e+01 angle pdb=" CA MET A 240 " pdb=" CB MET A 240 " pdb=" CG MET A 240 " ideal model delta sigma weight residual 114.10 123.46 -9.36 2.00e+00 2.50e-01 2.19e+01 angle pdb=" CA PRO R 30 " pdb=" C PRO R 30 " pdb=" N PRO R 31 " ideal model delta sigma weight residual 117.93 123.42 -5.49 1.20e+00 6.94e-01 2.09e+01 angle pdb=" C CYS A 3 " pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 121.54 129.90 -8.36 1.91e+00 2.74e-01 1.92e+01 angle pdb=" C SER R 190 " pdb=" N ASN R 191 " pdb=" CA ASN R 191 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 ... (remaining 14074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5506 17.56 - 35.11: 621 35.11 - 52.67: 110 52.67 - 70.22: 20 70.22 - 87.78: 16 Dihedral angle restraints: 6273 sinusoidal: 2489 harmonic: 3784 Sorted by residual: dihedral pdb=" CA TYR S 178 " pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta harmonic sigma weight residual 180.00 -132.53 -47.47 0 5.00e+00 4.00e-02 9.01e+01 dihedral pdb=" CB CYS E 9 " pdb=" SG CYS E 9 " pdb=" SG CYS E 50 " pdb=" CB CYS E 50 " ideal model delta sinusoidal sigma weight residual -86.00 -168.56 82.56 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CA GLU R 45 " pdb=" C GLU R 45 " pdb=" N ILE R 46 " pdb=" CA ILE R 46 " ideal model delta harmonic sigma weight residual -180.00 -136.73 -43.27 0 5.00e+00 4.00e-02 7.49e+01 ... (remaining 6270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1434 0.100 - 0.200: 173 0.200 - 0.300: 11 0.300 - 0.400: 2 0.400 - 0.500: 1 Chirality restraints: 1621 Sorted by residual: chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.82 0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" C10 CLR R 401 " pdb=" C1 CLR R 401 " pdb=" C5 CLR R 401 " pdb=" C9 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.85 -2.45 -0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" C17 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C16 CLR R 401 " pdb=" C20 CLR R 401 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 1618 not shown) Planarity restraints: 1768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 30 " -0.067 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO R 31 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO R 31 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 31 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.052 5.00e-02 4.00e+02 7.79e-02 9.72e+00 pdb=" N PRO B 236 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 37 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO R 38 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO R 38 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 38 " 0.037 5.00e-02 4.00e+02 ... (remaining 1765 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2907 2.79 - 3.32: 8972 3.32 - 3.85: 16562 3.85 - 4.37: 18981 4.37 - 4.90: 32787 Nonbonded interactions: 80209 Sorted by model distance: nonbonded pdb=" OG SER B 227 " pdb=" OD1 ASP B 228 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP R 94 " pdb=" OG SER R 307 " model vdw 2.280 3.040 nonbonded pdb=" O SER S 192 " pdb=" OG1 THR S 203 " model vdw 2.289 3.040 nonbonded pdb=" ND1 HIS B 54 " pdb=" OG SER B 74 " model vdw 2.308 3.120 ... (remaining 80204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and resid 6 through 72) selection = chain 'E' } 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 group one per residue 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.510 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.012 0.117 10398 Z= 0.535 Angle : 1.142 13.598 14095 Z= 0.605 Chirality : 0.067 0.500 1621 Planarity : 0.007 0.098 1768 Dihedral : 15.319 87.776 3801 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.27 % Allowed : 9.39 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -5.60 (0.17), residues: 1284 helix: -4.47 (0.11), residues: 416 sheet: -3.43 (0.26), residues: 278 loop : -3.13 (0.21), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 98 TYR 0.028 0.003 TYR S 178 PHE 0.027 0.003 PHE R 97 TRP 0.032 0.003 TRP R 112 HIS 0.009 0.002 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.01201 (10390) covalent geometry : angle 1.13869 (14079) SS BOND : bond 0.00601 ( 8) SS BOND : angle 2.90629 ( 16) hydrogen bonds : bond 0.29868 ( 363) hydrogen bonds : angle 10.90968 ( 1023) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 345 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8374 (ttmt) REVERT: A 243 MET cc_start: 0.8947 (tpp) cc_final: 0.8312 (mmm) REVERT: A 318 GLU cc_start: 0.6789 (tp30) cc_final: 0.5927 (tp30) REVERT: A 341 ASP cc_start: 0.8144 (t0) cc_final: 0.7718 (t0) REVERT: A 346 ASN cc_start: 0.9324 (m-40) cc_final: 0.8991 (m110) REVERT: A 349 LYS cc_start: 0.9043 (tttm) cc_final: 0.8778 (ttpp) REVERT: B 13 GLN cc_start: 0.8750 (mm110) cc_final: 0.7874 (tm-30) REVERT: B 59 TYR cc_start: 0.9000 (m-80) cc_final: 0.8561 (m-80) REVERT: B 101 MET cc_start: 0.9055 (mtp) cc_final: 0.8838 (mtp) REVERT: B 111 TYR cc_start: 0.8978 (m-80) cc_final: 0.8747 (m-10) REVERT: B 172 GLU cc_start: 0.8215 (mp0) cc_final: 0.7943 (mm-30) REVERT: B 188 MET cc_start: 0.7983 (mmm) cc_final: 0.7496 (mmm) REVERT: B 259 GLN cc_start: 0.8380 (pt0) cc_final: 0.7676 (pt0) REVERT: C 13 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.8074 (ptm160) REVERT: C 18 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8403 (tm-30) REVERT: C 20 LYS cc_start: 0.8792 (mttp) cc_final: 0.8274 (ttmm) REVERT: C 27 ARG cc_start: 0.8270 (mtt90) cc_final: 0.7961 (mpt-90) REVERT: D 4 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7772 (mm-30) REVERT: D 13 TYR cc_start: 0.8083 (t80) cc_final: 0.7794 (t80) REVERT: D 20 LYS cc_start: 0.7231 (pptt) cc_final: 0.6983 (pptt) REVERT: D 25 LEU cc_start: 0.8591 (tp) cc_final: 0.8189 (tp) REVERT: D 29 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7245 (tm-30) REVERT: D 32 PRO cc_start: 0.8772 (Cg_endo) cc_final: 0.8543 (Cg_exo) REVERT: E 47 ARG cc_start: 0.6999 (mtt-85) cc_final: 0.6477 (ttm110) REVERT: E 63 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7732 (mp0) REVERT: E 67 LYS cc_start: 0.7782 (mttm) cc_final: 0.7569 (mptt) REVERT: R 50 PHE cc_start: 0.8251 (m-10) cc_final: 0.7968 (m-10) REVERT: R 55 TYR cc_start: 0.8515 (m-80) cc_final: 0.7479 (m-80) REVERT: R 127 GLU cc_start: 0.8892 (tp30) cc_final: 0.8456 (tp30) REVERT: R 174 LEU cc_start: 0.8792 (mm) cc_final: 0.8420 (mm) REVERT: R 228 LEU cc_start: 0.9161 (mm) cc_final: 0.8680 (mm) REVERT: R 287 GLU cc_start: 0.8674 (mm-30) cc_final: 0.7910 (pp20) REVERT: R 310 ASN cc_start: 0.8669 (t0) cc_final: 0.8430 (t0) REVERT: S 73 ASP cc_start: 0.7453 (t0) cc_final: 0.7234 (t0) REVERT: S 83 MET cc_start: 0.8794 (mtm) cc_final: 0.8304 (ptp) REVERT: S 95 TYR cc_start: 0.8723 (m-10) cc_final: 0.8505 (m-10) REVERT: S 125 ASP cc_start: 0.8998 (p0) cc_final: 0.8492 (p0) REVERT: S 130 GLN cc_start: 0.7710 (mt0) cc_final: 0.7296 (mt0) REVERT: S 210 GLU cc_start: 0.7862 (tp30) cc_final: 0.7507 (mm-30) outliers start: 3 outliers final: 0 residues processed: 348 average time/residue: 0.1216 time to fit residues: 56.4337 Evaluate side-chains 270 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS B 62 HIS B 75 GLN B 175 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN R 89 ASN R 150 HIS R 268 ASN R 323 HIS S 171 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.141639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107461 restraints weight = 17164.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.111413 restraints weight = 7901.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113929 restraints weight = 4950.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.115386 restraints weight = 3693.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116527 restraints weight = 3078.610| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10398 Z= 0.174 Angle : 0.688 8.904 14095 Z= 0.363 Chirality : 0.044 0.230 1621 Planarity : 0.006 0.076 1768 Dihedral : 6.300 41.307 1474 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.92 % Allowed : 17.59 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.35 (0.19), residues: 1284 helix: -2.80 (0.19), residues: 427 sheet: -2.92 (0.27), residues: 284 loop : -2.80 (0.22), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 159 TYR 0.027 0.002 TYR A 302 PHE 0.017 0.001 PHE R 218 TRP 0.028 0.001 TRP R 112 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00380 (10390) covalent geometry : angle 0.68626 (14079) SS BOND : bond 0.00377 ( 8) SS BOND : angle 1.51141 ( 16) hydrogen bonds : bond 0.04139 ( 363) hydrogen bonds : angle 6.08196 ( 1023) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 321 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8867 (t70) cc_final: 0.8501 (t0) REVERT: A 243 MET cc_start: 0.8784 (tpp) cc_final: 0.8268 (tpp) REVERT: A 302 TYR cc_start: 0.8733 (t80) cc_final: 0.8449 (t80) REVERT: A 341 ASP cc_start: 0.8471 (t0) cc_final: 0.8079 (t0) REVERT: A 346 ASN cc_start: 0.9281 (m-40) cc_final: 0.8932 (m110) REVERT: A 349 LYS cc_start: 0.9015 (tttm) cc_final: 0.8785 (ttpp) REVERT: B 59 TYR cc_start: 0.8817 (m-80) cc_final: 0.8616 (m-80) REVERT: B 105 TYR cc_start: 0.9019 (t80) cc_final: 0.8610 (t80) REVERT: B 157 ILE cc_start: 0.9020 (tt) cc_final: 0.8749 (tt) REVERT: B 159 THR cc_start: 0.9127 (p) cc_final: 0.8856 (p) REVERT: B 188 MET cc_start: 0.8351 (mmm) cc_final: 0.8076 (mmm) REVERT: B 211 TRP cc_start: 0.9242 (m100) cc_final: 0.8733 (m100) REVERT: B 259 GLN cc_start: 0.8187 (pt0) cc_final: 0.7571 (pt0) REVERT: B 297 TRP cc_start: 0.8895 (m100) cc_final: 0.8681 (m100) REVERT: C 13 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.8046 (ptp-110) REVERT: C 20 LYS cc_start: 0.8867 (mttp) cc_final: 0.8575 (ttmm) REVERT: C 25 ILE cc_start: 0.9010 (mp) cc_final: 0.8604 (mp) REVERT: C 27 ARG cc_start: 0.8380 (mtt90) cc_final: 0.8145 (mtt90) REVERT: C 32 LYS cc_start: 0.9032 (ttmt) cc_final: 0.8711 (ttpp) REVERT: D 4 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7513 (mm-30) REVERT: D 13 TYR cc_start: 0.7923 (t80) cc_final: 0.7708 (t80) REVERT: D 29 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7030 (tm-30) REVERT: D 32 PRO cc_start: 0.8623 (Cg_endo) cc_final: 0.8397 (Cg_exo) REVERT: D 68 ARG cc_start: 0.8333 (mmm160) cc_final: 0.7925 (mmm-85) REVERT: E 47 ARG cc_start: 0.6958 (mtt-85) cc_final: 0.6396 (ttm110) REVERT: E 63 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7723 (mp0) REVERT: R 50 PHE cc_start: 0.8180 (m-10) cc_final: 0.7861 (m-10) REVERT: R 55 TYR cc_start: 0.8054 (m-80) cc_final: 0.7328 (m-80) REVERT: R 126 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8229 (ttmm) REVERT: R 127 GLU cc_start: 0.8791 (tp30) cc_final: 0.7747 (tp30) REVERT: R 163 LYS cc_start: 0.8125 (mppt) cc_final: 0.7521 (mptt) REVERT: R 184 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7793 (tpp80) REVERT: R 198 GLU cc_start: 0.5474 (OUTLIER) cc_final: 0.5094 (mt-10) REVERT: R 224 LEU cc_start: 0.8679 (tp) cc_final: 0.8325 (tp) REVERT: R 227 MET cc_start: 0.7929 (mtp) cc_final: 0.7586 (ttm) REVERT: R 228 LEU cc_start: 0.9128 (mm) cc_final: 0.8792 (mm) REVERT: R 287 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8051 (pp20) REVERT: R 306 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.7822 (t70) REVERT: R 310 ASN cc_start: 0.8526 (t0) cc_final: 0.8281 (t0) REVERT: R 314 TYR cc_start: 0.8837 (m-80) cc_final: 0.8529 (m-80) REVERT: R 323 HIS cc_start: 0.8143 (m90) cc_final: 0.7885 (m-70) REVERT: R 327 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.8037 (ptmt) REVERT: S 73 ASP cc_start: 0.7469 (t0) cc_final: 0.6813 (t0) REVERT: S 95 TYR cc_start: 0.8732 (m-10) cc_final: 0.8442 (m-10) REVERT: S 221 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8927 (mt) outliers start: 32 outliers final: 18 residues processed: 337 average time/residue: 0.1111 time to fit residues: 51.6235 Evaluate side-chains 310 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 288 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 327 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 119 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 88 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 62 optimal weight: 40.0000 chunk 84 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 295 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN R 89 ASN R 150 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.141813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107484 restraints weight = 17154.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.111402 restraints weight = 7923.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.113926 restraints weight = 4991.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115387 restraints weight = 3724.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116515 restraints weight = 3118.478| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10398 Z= 0.163 Angle : 0.645 7.719 14095 Z= 0.336 Chirality : 0.044 0.180 1621 Planarity : 0.005 0.070 1768 Dihedral : 5.795 39.212 1474 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.01 % Allowed : 18.96 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.45 (0.21), residues: 1284 helix: -1.77 (0.22), residues: 429 sheet: -2.62 (0.28), residues: 274 loop : -2.40 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 62 TYR 0.022 0.001 TYR B 59 PHE 0.014 0.001 PHE R 97 TRP 0.025 0.002 TRP R 112 HIS 0.003 0.001 HIS R 247 Details of bonding type rmsd covalent geometry : bond 0.00371 (10390) covalent geometry : angle 0.64321 (14079) SS BOND : bond 0.00164 ( 8) SS BOND : angle 1.50779 ( 16) hydrogen bonds : bond 0.03602 ( 363) hydrogen bonds : angle 5.45941 ( 1023) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 300 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8851 (t70) cc_final: 0.8457 (t0) REVERT: A 29 LYS cc_start: 0.8947 (ttmt) cc_final: 0.8451 (ttmt) REVERT: A 243 MET cc_start: 0.8722 (tpp) cc_final: 0.8439 (tpp) REVERT: A 341 ASP cc_start: 0.8561 (t0) cc_final: 0.8228 (t0) REVERT: A 349 LYS cc_start: 0.9003 (tttm) cc_final: 0.8764 (ttpp) REVERT: B 10 GLU cc_start: 0.7860 (tp30) cc_final: 0.7641 (tp30) REVERT: B 59 TYR cc_start: 0.8906 (m-80) cc_final: 0.8467 (m-80) REVERT: B 105 TYR cc_start: 0.9070 (t80) cc_final: 0.8597 (t80) REVERT: B 188 MET cc_start: 0.8311 (mmm) cc_final: 0.8087 (mmm) REVERT: B 211 TRP cc_start: 0.9045 (m100) cc_final: 0.8219 (m100) REVERT: B 226 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7353 (mp0) REVERT: B 258 ASP cc_start: 0.8007 (t0) cc_final: 0.7275 (t0) REVERT: C 13 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.8171 (ptp-110) REVERT: C 20 LYS cc_start: 0.8829 (mttp) cc_final: 0.8574 (ttmm) REVERT: C 25 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8641 (mp) REVERT: C 27 ARG cc_start: 0.8233 (mtt90) cc_final: 0.7928 (mtt90) REVERT: D 6 ARG cc_start: 0.8604 (ttp-170) cc_final: 0.8204 (ptm160) REVERT: D 29 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7168 (tm-30) REVERT: D 68 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7751 (mmm-85) REVERT: E 47 ARG cc_start: 0.6883 (mtt-85) cc_final: 0.6397 (ttm110) REVERT: E 63 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7948 (mt-10) REVERT: R 50 PHE cc_start: 0.7951 (m-10) cc_final: 0.7552 (m-10) REVERT: R 55 TYR cc_start: 0.8079 (m-80) cc_final: 0.7575 (m-80) REVERT: R 59 PHE cc_start: 0.8475 (t80) cc_final: 0.8255 (t80) REVERT: R 61 LEU cc_start: 0.8222 (tp) cc_final: 0.7952 (tp) REVERT: R 126 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8038 (ttpp) REVERT: R 163 LYS cc_start: 0.8117 (mppt) cc_final: 0.7570 (mptt) REVERT: R 184 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7766 (tpp80) REVERT: R 198 GLU cc_start: 0.5557 (OUTLIER) cc_final: 0.5093 (mt-10) REVERT: R 224 LEU cc_start: 0.8660 (tp) cc_final: 0.8308 (tp) REVERT: R 227 MET cc_start: 0.7911 (mtp) cc_final: 0.7580 (ttm) REVERT: R 228 LEU cc_start: 0.9133 (mm) cc_final: 0.8793 (mm) REVERT: R 287 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8054 (pp20) REVERT: R 306 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.7941 (t70) REVERT: R 314 TYR cc_start: 0.8896 (m-80) cc_final: 0.8480 (m-80) REVERT: R 323 HIS cc_start: 0.8199 (m90) cc_final: 0.7601 (m170) REVERT: S 6 GLU cc_start: 0.7519 (pm20) cc_final: 0.6152 (pm20) REVERT: S 73 ASP cc_start: 0.7491 (t0) cc_final: 0.6890 (t0) REVERT: S 95 TYR cc_start: 0.8598 (m-10) cc_final: 0.8370 (m-10) REVERT: S 109 ASP cc_start: 0.8341 (p0) cc_final: 0.8098 (p0) REVERT: S 128 MET cc_start: 0.8715 (mmm) cc_final: 0.7945 (mmm) REVERT: S 130 GLN cc_start: 0.7367 (mt0) cc_final: 0.7034 (mt0) REVERT: S 221 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9068 (mt) outliers start: 44 outliers final: 27 residues processed: 325 average time/residue: 0.1051 time to fit residues: 47.2264 Evaluate side-chains 314 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 125 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 106 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 346 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN R 150 HIS S 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.146074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.113213 restraints weight = 17216.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.116751 restraints weight = 8723.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.117829 restraints weight = 5170.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.118661 restraints weight = 4310.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.118999 restraints weight = 3931.317| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10398 Z= 0.116 Angle : 0.608 7.927 14095 Z= 0.311 Chirality : 0.042 0.192 1621 Planarity : 0.004 0.068 1768 Dihedral : 5.292 38.959 1474 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.19 % Allowed : 20.51 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.90 (0.22), residues: 1284 helix: -1.09 (0.24), residues: 428 sheet: -2.38 (0.28), residues: 293 loop : -2.21 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 62 TYR 0.027 0.001 TYR A 302 PHE 0.023 0.001 PHE S 200 TRP 0.023 0.001 TRP R 112 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00260 (10390) covalent geometry : angle 0.60646 (14079) SS BOND : bond 0.00228 ( 8) SS BOND : angle 1.23945 ( 16) hydrogen bonds : bond 0.03074 ( 363) hydrogen bonds : angle 5.05061 ( 1023) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 309 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8872 (t70) cc_final: 0.8439 (t0) REVERT: A 29 LYS cc_start: 0.8971 (ttmt) cc_final: 0.8427 (ttmt) REVERT: A 46 LYS cc_start: 0.8316 (tttt) cc_final: 0.8062 (tmtt) REVERT: A 341 ASP cc_start: 0.8520 (t0) cc_final: 0.8236 (t0) REVERT: B 59 TYR cc_start: 0.8787 (m-80) cc_final: 0.8476 (m-80) REVERT: B 82 TRP cc_start: 0.8838 (m100) cc_final: 0.8566 (m100) REVERT: B 105 TYR cc_start: 0.9022 (t80) cc_final: 0.8751 (t80) REVERT: B 157 ILE cc_start: 0.8792 (tt) cc_final: 0.8396 (tt) REVERT: B 211 TRP cc_start: 0.9045 (m100) cc_final: 0.8461 (m100) REVERT: B 234 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8581 (m-80) REVERT: B 258 ASP cc_start: 0.7746 (t0) cc_final: 0.7093 (t0) REVERT: B 259 GLN cc_start: 0.7945 (pt0) cc_final: 0.7539 (pt0) REVERT: B 261 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9031 (mm) REVERT: C 13 ARG cc_start: 0.8541 (ttm-80) cc_final: 0.8272 (ptp-110) REVERT: C 25 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8677 (mp) REVERT: D 6 ARG cc_start: 0.8534 (ttp-170) cc_final: 0.8260 (ptm160) REVERT: D 29 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7216 (tm-30) REVERT: E 47 ARG cc_start: 0.6604 (mtt-85) cc_final: 0.6396 (ttm110) REVERT: R 50 PHE cc_start: 0.7959 (m-10) cc_final: 0.7545 (m-10) REVERT: R 55 TYR cc_start: 0.7819 (m-80) cc_final: 0.7482 (m-80) REVERT: R 59 PHE cc_start: 0.8452 (t80) cc_final: 0.8225 (t80) REVERT: R 61 LEU cc_start: 0.8125 (tp) cc_final: 0.7910 (tp) REVERT: R 126 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8003 (ttpp) REVERT: R 157 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7680 (mm110) REVERT: R 163 LYS cc_start: 0.8146 (mppt) cc_final: 0.7648 (mptt) REVERT: R 224 LEU cc_start: 0.8748 (tp) cc_final: 0.8371 (tp) REVERT: R 227 MET cc_start: 0.7883 (mtp) cc_final: 0.7575 (ttm) REVERT: R 228 LEU cc_start: 0.9120 (mm) cc_final: 0.8869 (mm) REVERT: R 264 TRP cc_start: 0.8212 (m100) cc_final: 0.7826 (m100) REVERT: R 277 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7434 (ttp) REVERT: R 287 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7974 (pp20) REVERT: R 306 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7601 (t70) REVERT: R 323 HIS cc_start: 0.8211 (m90) cc_final: 0.7696 (m170) REVERT: S 109 ASP cc_start: 0.8144 (p0) cc_final: 0.7935 (p0) REVERT: S 128 MET cc_start: 0.8600 (mmm) cc_final: 0.7820 (mmm) REVERT: S 130 GLN cc_start: 0.7547 (mt0) cc_final: 0.7196 (mt0) outliers start: 46 outliers final: 27 residues processed: 334 average time/residue: 0.1115 time to fit residues: 50.9967 Evaluate side-chains 320 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 288 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 10 optimal weight: 0.0980 chunk 121 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 0.0870 chunk 33 optimal weight: 0.0010 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 0.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 346 ASN D 8 GLN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN R 150 HIS R 247 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.148818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.116232 restraints weight = 17064.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.119226 restraints weight = 8732.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120324 restraints weight = 5362.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.121699 restraints weight = 4435.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.122098 restraints weight = 3786.446| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10398 Z= 0.107 Angle : 0.601 7.713 14095 Z= 0.306 Chirality : 0.042 0.160 1621 Planarity : 0.004 0.066 1768 Dihedral : 4.944 37.553 1474 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.28 % Allowed : 22.06 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.54 (0.22), residues: 1284 helix: -0.67 (0.25), residues: 431 sheet: -2.17 (0.28), residues: 298 loop : -2.12 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 62 TYR 0.023 0.001 TYR A 302 PHE 0.016 0.001 PHE S 200 TRP 0.026 0.001 TRP R 112 HIS 0.004 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00237 (10390) covalent geometry : angle 0.60078 (14079) SS BOND : bond 0.00207 ( 8) SS BOND : angle 0.96268 ( 16) hydrogen bonds : bond 0.02912 ( 363) hydrogen bonds : angle 4.84365 ( 1023) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 306 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8949 (t70) cc_final: 0.8479 (t0) REVERT: A 29 LYS cc_start: 0.8977 (ttmt) cc_final: 0.8695 (ttmm) REVERT: A 243 MET cc_start: 0.8598 (mmm) cc_final: 0.7946 (mmm) REVERT: A 287 TYR cc_start: 0.8383 (m-80) cc_final: 0.8072 (m-80) REVERT: A 305 CYS cc_start: 0.8471 (t) cc_final: 0.7848 (m) REVERT: A 341 ASP cc_start: 0.8494 (t0) cc_final: 0.8238 (t0) REVERT: B 59 TYR cc_start: 0.8892 (m-80) cc_final: 0.8643 (m-80) REVERT: B 82 TRP cc_start: 0.8717 (m100) cc_final: 0.8402 (m100) REVERT: B 157 ILE cc_start: 0.8771 (tt) cc_final: 0.8351 (tt) REVERT: B 211 TRP cc_start: 0.9006 (m100) cc_final: 0.8291 (m100) REVERT: B 234 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8470 (m-80) REVERT: B 252 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9217 (tt) REVERT: B 258 ASP cc_start: 0.7762 (t0) cc_final: 0.7230 (t0) REVERT: B 259 GLN cc_start: 0.7520 (pt0) cc_final: 0.7121 (pt0) REVERT: B 262 MET cc_start: 0.7446 (tpt) cc_final: 0.7190 (tpp) REVERT: C 13 ARG cc_start: 0.8646 (ttm-80) cc_final: 0.8327 (ptp-110) REVERT: C 25 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8503 (mp) REVERT: D 6 ARG cc_start: 0.8435 (ttp-170) cc_final: 0.8202 (ptm160) REVERT: D 13 TYR cc_start: 0.7704 (t80) cc_final: 0.7261 (t80) REVERT: D 29 GLU cc_start: 0.7685 (tm-30) cc_final: 0.6915 (tm-30) REVERT: D 66 LEU cc_start: 0.6986 (mm) cc_final: 0.6175 (pp) REVERT: E 47 ARG cc_start: 0.6660 (mtt-85) cc_final: 0.6404 (ttm110) REVERT: R 50 PHE cc_start: 0.7797 (m-10) cc_final: 0.7324 (m-10) REVERT: R 55 TYR cc_start: 0.7954 (m-80) cc_final: 0.7431 (m-80) REVERT: R 126 LYS cc_start: 0.8381 (ttmm) cc_final: 0.7903 (ttpp) REVERT: R 157 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7619 (mm110) REVERT: R 163 LYS cc_start: 0.8065 (mppt) cc_final: 0.7668 (mmtm) REVERT: R 224 LEU cc_start: 0.8631 (tp) cc_final: 0.8203 (tp) REVERT: R 227 MET cc_start: 0.7851 (mtp) cc_final: 0.7590 (ttm) REVERT: R 228 LEU cc_start: 0.9037 (mm) cc_final: 0.8783 (mm) REVERT: R 246 LYS cc_start: 0.8576 (ptmm) cc_final: 0.8201 (ptpp) REVERT: R 306 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7543 (t70) REVERT: R 323 HIS cc_start: 0.8262 (m90) cc_final: 0.8052 (m-70) REVERT: S 128 MET cc_start: 0.8621 (mmm) cc_final: 0.8073 (mmm) REVERT: S 130 GLN cc_start: 0.7519 (mt0) cc_final: 0.7159 (mt0) outliers start: 36 outliers final: 21 residues processed: 325 average time/residue: 0.1018 time to fit residues: 45.9711 Evaluate side-chains 310 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 285 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 18 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 74 optimal weight: 0.0060 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN R 150 HIS R 247 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.146898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.114399 restraints weight = 17285.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.117465 restraints weight = 8892.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.118616 restraints weight = 5381.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.119561 restraints weight = 4491.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119869 restraints weight = 4033.573| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10398 Z= 0.131 Angle : 0.619 8.343 14095 Z= 0.313 Chirality : 0.042 0.151 1621 Planarity : 0.004 0.075 1768 Dihedral : 4.919 37.212 1474 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.19 % Allowed : 23.43 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.38 (0.23), residues: 1284 helix: -0.51 (0.26), residues: 431 sheet: -2.15 (0.29), residues: 283 loop : -2.04 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 8 TYR 0.022 0.001 TYR A 302 PHE 0.020 0.001 PHE S 200 TRP 0.020 0.001 TRP R 112 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00301 (10390) covalent geometry : angle 0.61808 (14079) SS BOND : bond 0.00200 ( 8) SS BOND : angle 1.13066 ( 16) hydrogen bonds : bond 0.02789 ( 363) hydrogen bonds : angle 4.78666 ( 1023) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 283 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8937 (t70) cc_final: 0.8469 (t0) REVERT: A 29 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8797 (ttmm) REVERT: A 198 MET cc_start: 0.7501 (ttm) cc_final: 0.7284 (mtm) REVERT: A 243 MET cc_start: 0.8561 (mmm) cc_final: 0.7986 (mmm) REVERT: A 305 CYS cc_start: 0.8554 (t) cc_final: 0.7985 (m) REVERT: A 341 ASP cc_start: 0.8573 (t0) cc_final: 0.8323 (t0) REVERT: B 59 TYR cc_start: 0.8917 (m-80) cc_final: 0.8656 (m-80) REVERT: B 82 TRP cc_start: 0.8681 (m100) cc_final: 0.7996 (m100) REVERT: B 147 SER cc_start: 0.9214 (OUTLIER) cc_final: 0.8702 (t) REVERT: B 157 ILE cc_start: 0.8910 (tt) cc_final: 0.8536 (tt) REVERT: B 211 TRP cc_start: 0.9064 (m100) cc_final: 0.8419 (m100) REVERT: B 234 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8603 (m-80) REVERT: B 258 ASP cc_start: 0.8040 (t0) cc_final: 0.7318 (t0) REVERT: B 259 GLN cc_start: 0.7652 (pt0) cc_final: 0.7222 (pt0) REVERT: C 13 ARG cc_start: 0.8645 (ttm-80) cc_final: 0.8324 (ptp-110) REVERT: C 25 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8778 (mp) REVERT: C 32 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8738 (ttpp) REVERT: D 6 ARG cc_start: 0.8552 (ttp-170) cc_final: 0.8241 (ptm160) REVERT: D 29 GLU cc_start: 0.7650 (tm-30) cc_final: 0.6960 (tm-30) REVERT: E 47 ARG cc_start: 0.6702 (mtt-85) cc_final: 0.6487 (ttm110) REVERT: R 55 TYR cc_start: 0.7973 (m-80) cc_final: 0.7530 (m-80) REVERT: R 126 LYS cc_start: 0.8450 (ttmm) cc_final: 0.8075 (ttpp) REVERT: R 127 GLU cc_start: 0.8698 (tp30) cc_final: 0.8155 (tp30) REVERT: R 157 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7620 (mm110) REVERT: R 163 LYS cc_start: 0.8053 (mppt) cc_final: 0.7625 (mmtm) REVERT: R 224 LEU cc_start: 0.8749 (tp) cc_final: 0.8439 (tp) REVERT: R 227 MET cc_start: 0.7912 (mtp) cc_final: 0.7651 (ttm) REVERT: R 228 LEU cc_start: 0.9016 (mm) cc_final: 0.8779 (mm) REVERT: R 229 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7242 (m-10) REVERT: R 246 LYS cc_start: 0.8477 (ptmm) cc_final: 0.8089 (ptpp) REVERT: R 287 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7900 (pp20) REVERT: R 306 HIS cc_start: 0.7978 (OUTLIER) cc_final: 0.7428 (t70) REVERT: R 323 HIS cc_start: 0.8106 (m90) cc_final: 0.7858 (m-70) REVERT: S 128 MET cc_start: 0.8695 (mmm) cc_final: 0.7906 (mmm) REVERT: S 130 GLN cc_start: 0.7573 (mt0) cc_final: 0.7223 (mt0) outliers start: 46 outliers final: 27 residues processed: 310 average time/residue: 0.1056 time to fit residues: 45.2061 Evaluate side-chains 302 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 85 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 40 optimal weight: 0.0070 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.146854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.112492 restraints weight = 17225.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116481 restraints weight = 7993.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119002 restraints weight = 5029.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.120665 restraints weight = 3769.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.121611 restraints weight = 3102.630| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10398 Z= 0.141 Angle : 0.627 9.388 14095 Z= 0.317 Chirality : 0.043 0.149 1621 Planarity : 0.004 0.072 1768 Dihedral : 4.924 37.209 1474 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.92 % Allowed : 24.43 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.18 (0.23), residues: 1284 helix: -0.31 (0.26), residues: 431 sheet: -2.00 (0.30), residues: 276 loop : -1.98 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 62 TYR 0.028 0.001 TYR A 302 PHE 0.019 0.001 PHE S 200 TRP 0.031 0.001 TRP R 112 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00324 (10390) covalent geometry : angle 0.62611 (14079) SS BOND : bond 0.00241 ( 8) SS BOND : angle 1.09461 ( 16) hydrogen bonds : bond 0.02821 ( 363) hydrogen bonds : angle 4.72843 ( 1023) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 273 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8879 (t70) cc_final: 0.8395 (t0) REVERT: A 29 LYS cc_start: 0.8982 (ttmt) cc_final: 0.8769 (ttmm) REVERT: A 198 MET cc_start: 0.7576 (ttm) cc_final: 0.7319 (mtm) REVERT: A 243 MET cc_start: 0.8487 (mmm) cc_final: 0.7951 (mmm) REVERT: A 255 ASN cc_start: 0.8369 (m-40) cc_final: 0.8142 (m-40) REVERT: A 305 CYS cc_start: 0.8515 (t) cc_final: 0.7959 (m) REVERT: A 341 ASP cc_start: 0.8568 (t0) cc_final: 0.8315 (t0) REVERT: B 82 TRP cc_start: 0.8754 (m100) cc_final: 0.7997 (m100) REVERT: B 147 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8743 (t) REVERT: B 157 ILE cc_start: 0.9040 (tt) cc_final: 0.8706 (tt) REVERT: B 188 MET cc_start: 0.8393 (mmm) cc_final: 0.7446 (mpp) REVERT: B 211 TRP cc_start: 0.9082 (m100) cc_final: 0.8363 (m100) REVERT: B 226 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7426 (mp0) REVERT: B 234 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8688 (m-80) REVERT: B 258 ASP cc_start: 0.7928 (t0) cc_final: 0.7231 (t0) REVERT: C 13 ARG cc_start: 0.8645 (ttm-80) cc_final: 0.8324 (ptp-110) REVERT: C 25 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8692 (mp) REVERT: C 32 LYS cc_start: 0.8974 (ttmt) cc_final: 0.8763 (ttpp) REVERT: D 29 GLU cc_start: 0.7673 (tm-30) cc_final: 0.6967 (tm-30) REVERT: E 47 ARG cc_start: 0.6812 (mtt-85) cc_final: 0.6537 (ttm110) REVERT: R 55 TYR cc_start: 0.8154 (m-80) cc_final: 0.7508 (m-80) REVERT: R 126 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8040 (ttpp) REVERT: R 127 GLU cc_start: 0.8611 (tp30) cc_final: 0.8038 (tp30) REVERT: R 157 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7566 (mm110) REVERT: R 163 LYS cc_start: 0.8032 (mppt) cc_final: 0.7593 (mmtm) REVERT: R 224 LEU cc_start: 0.8685 (tp) cc_final: 0.8390 (tp) REVERT: R 227 MET cc_start: 0.7923 (mtp) cc_final: 0.7640 (ttm) REVERT: R 228 LEU cc_start: 0.9025 (mm) cc_final: 0.8756 (mm) REVERT: R 229 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7448 (m-10) REVERT: R 246 LYS cc_start: 0.8595 (ptmm) cc_final: 0.8144 (ptpp) REVERT: R 287 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7824 (pp20) REVERT: R 306 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.7322 (t70) REVERT: R 323 HIS cc_start: 0.8111 (m90) cc_final: 0.7855 (m-70) REVERT: S 109 ASP cc_start: 0.8256 (p0) cc_final: 0.8054 (p0) REVERT: S 128 MET cc_start: 0.8689 (mmm) cc_final: 0.7934 (mmm) REVERT: S 130 GLN cc_start: 0.7521 (mt0) cc_final: 0.7178 (mt0) outliers start: 43 outliers final: 34 residues processed: 297 average time/residue: 0.1097 time to fit residues: 44.9006 Evaluate side-chains 301 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 262 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 4 optimal weight: 10.0000 chunk 110 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.144716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.110646 restraints weight = 16825.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114745 restraints weight = 7626.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117382 restraints weight = 4744.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119046 restraints weight = 3507.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.120083 restraints weight = 2885.408| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10398 Z= 0.134 Angle : 0.629 8.898 14095 Z= 0.316 Chirality : 0.043 0.151 1621 Planarity : 0.004 0.072 1768 Dihedral : 4.866 36.419 1474 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.38 % Allowed : 24.07 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.05 (0.23), residues: 1284 helix: -0.15 (0.26), residues: 431 sheet: -1.95 (0.30), residues: 278 loop : -1.93 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 62 TYR 0.019 0.001 TYR A 302 PHE 0.019 0.001 PHE S 200 TRP 0.026 0.001 TRP R 112 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00307 (10390) covalent geometry : angle 0.62853 (14079) SS BOND : bond 0.00239 ( 8) SS BOND : angle 1.01358 ( 16) hydrogen bonds : bond 0.02768 ( 363) hydrogen bonds : angle 4.68647 ( 1023) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8885 (t70) cc_final: 0.8406 (t0) REVERT: A 243 MET cc_start: 0.8484 (mmm) cc_final: 0.7949 (mmm) REVERT: A 255 ASN cc_start: 0.8398 (m-40) cc_final: 0.8165 (m-40) REVERT: A 305 CYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7998 (m) REVERT: A 341 ASP cc_start: 0.8547 (t0) cc_final: 0.8342 (t0) REVERT: B 82 TRP cc_start: 0.8761 (m100) cc_final: 0.7980 (m100) REVERT: B 147 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8763 (t) REVERT: B 157 ILE cc_start: 0.9052 (tt) cc_final: 0.8724 (tt) REVERT: B 188 MET cc_start: 0.8455 (mmm) cc_final: 0.7524 (mpp) REVERT: B 226 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7396 (mp0) REVERT: B 234 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8713 (m-80) REVERT: B 258 ASP cc_start: 0.7789 (t0) cc_final: 0.7209 (t0) REVERT: B 261 LEU cc_start: 0.9244 (mm) cc_final: 0.8960 (mm) REVERT: C 13 ARG cc_start: 0.8645 (ttm-80) cc_final: 0.8327 (ptp-110) REVERT: C 25 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8531 (mp) REVERT: C 32 LYS cc_start: 0.8969 (ttmt) cc_final: 0.8768 (ttpp) REVERT: D 6 ARG cc_start: 0.8682 (ttp-170) cc_final: 0.8163 (ptm160) REVERT: E 47 ARG cc_start: 0.6769 (mtt-85) cc_final: 0.6531 (ttm110) REVERT: R 55 TYR cc_start: 0.8128 (m-80) cc_final: 0.7528 (m-80) REVERT: R 96 LEU cc_start: 0.9037 (mp) cc_final: 0.8819 (mp) REVERT: R 126 LYS cc_start: 0.8498 (ttmm) cc_final: 0.8157 (ttpp) REVERT: R 127 GLU cc_start: 0.8604 (tp30) cc_final: 0.7986 (tp30) REVERT: R 163 LYS cc_start: 0.8016 (mppt) cc_final: 0.7584 (mmtm) REVERT: R 224 LEU cc_start: 0.8663 (tp) cc_final: 0.8365 (tp) REVERT: R 227 MET cc_start: 0.7906 (mtp) cc_final: 0.7629 (ttm) REVERT: R 228 LEU cc_start: 0.9027 (mm) cc_final: 0.8741 (mm) REVERT: R 229 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7376 (m-10) REVERT: R 246 LYS cc_start: 0.8604 (ptmm) cc_final: 0.8126 (ptpp) REVERT: R 287 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7731 (pp20) REVERT: R 304 ILE cc_start: 0.8988 (tp) cc_final: 0.8734 (tp) REVERT: R 306 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.7290 (t70) REVERT: R 323 HIS cc_start: 0.8105 (m90) cc_final: 0.7847 (m-70) REVERT: S 109 ASP cc_start: 0.8240 (p0) cc_final: 0.8037 (p0) REVERT: S 128 MET cc_start: 0.8685 (mmm) cc_final: 0.7936 (mmm) outliers start: 48 outliers final: 37 residues processed: 305 average time/residue: 0.1059 time to fit residues: 44.4276 Evaluate side-chains 317 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 274 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 90 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 60 optimal weight: 0.0570 chunk 102 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 75 GLN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.147430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.112306 restraints weight = 17068.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.116358 restraints weight = 7953.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.118960 restraints weight = 5022.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.120564 restraints weight = 3747.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.121663 restraints weight = 3115.816| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10398 Z= 0.134 Angle : 0.642 9.504 14095 Z= 0.324 Chirality : 0.043 0.152 1621 Planarity : 0.004 0.071 1768 Dihedral : 4.850 36.203 1474 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.47 % Allowed : 23.97 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.98 (0.23), residues: 1284 helix: -0.03 (0.26), residues: 431 sheet: -1.95 (0.30), residues: 285 loop : -1.91 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 62 TYR 0.029 0.001 TYR A 302 PHE 0.019 0.001 PHE S 200 TRP 0.025 0.001 TRP R 112 HIS 0.002 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00310 (10390) covalent geometry : angle 0.64159 (14079) SS BOND : bond 0.00217 ( 8) SS BOND : angle 0.96793 ( 16) hydrogen bonds : bond 0.02773 ( 363) hydrogen bonds : angle 4.64277 ( 1023) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 289 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8891 (t70) cc_final: 0.8417 (t0) REVERT: A 46 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7709 (tmtt) REVERT: A 243 MET cc_start: 0.8506 (mmm) cc_final: 0.7935 (mmm) REVERT: A 255 ASN cc_start: 0.8339 (m-40) cc_final: 0.8022 (m110) REVERT: A 305 CYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8006 (m) REVERT: A 341 ASP cc_start: 0.8540 (t0) cc_final: 0.8337 (t0) REVERT: B 19 ARG cc_start: 0.8088 (ttp-170) cc_final: 0.7696 (mtm180) REVERT: B 75 GLN cc_start: 0.7880 (mt0) cc_final: 0.7648 (mt0) REVERT: B 82 TRP cc_start: 0.8759 (m100) cc_final: 0.8033 (m100) REVERT: B 147 SER cc_start: 0.9141 (OUTLIER) cc_final: 0.8728 (t) REVERT: B 157 ILE cc_start: 0.9097 (tt) cc_final: 0.8789 (tt) REVERT: B 191 SER cc_start: 0.8534 (m) cc_final: 0.8065 (m) REVERT: B 220 GLN cc_start: 0.8376 (mp-120) cc_final: 0.8001 (mp10) REVERT: B 226 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7471 (mp0) REVERT: B 234 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8688 (m-80) REVERT: B 258 ASP cc_start: 0.7790 (t0) cc_final: 0.7187 (t0) REVERT: B 259 GLN cc_start: 0.7704 (pt0) cc_final: 0.7367 (pt0) REVERT: C 13 ARG cc_start: 0.8636 (ttm-80) cc_final: 0.8353 (ptp-110) REVERT: C 25 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8615 (mp) REVERT: D 6 ARG cc_start: 0.8587 (ttp-170) cc_final: 0.8373 (ptm160) REVERT: D 13 TYR cc_start: 0.7866 (t80) cc_final: 0.7334 (t80) REVERT: E 47 ARG cc_start: 0.6803 (mtt-85) cc_final: 0.6525 (ttm110) REVERT: R 55 TYR cc_start: 0.8137 (m-80) cc_final: 0.7558 (m-80) REVERT: R 96 LEU cc_start: 0.9001 (mp) cc_final: 0.8761 (mp) REVERT: R 126 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8139 (ttpp) REVERT: R 127 GLU cc_start: 0.8599 (tp30) cc_final: 0.7980 (tp30) REVERT: R 163 LYS cc_start: 0.8055 (mppt) cc_final: 0.7630 (mmtm) REVERT: R 224 LEU cc_start: 0.8643 (tp) cc_final: 0.8346 (tp) REVERT: R 227 MET cc_start: 0.7907 (mtp) cc_final: 0.7625 (ttm) REVERT: R 228 LEU cc_start: 0.9016 (mm) cc_final: 0.8733 (mm) REVERT: R 229 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7368 (m-10) REVERT: R 246 LYS cc_start: 0.8609 (ptmm) cc_final: 0.8120 (ptpp) REVERT: R 287 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7714 (pp20) REVERT: R 304 ILE cc_start: 0.8992 (tp) cc_final: 0.8749 (tp) REVERT: R 306 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7216 (t70) REVERT: R 323 HIS cc_start: 0.8138 (m90) cc_final: 0.7870 (m-70) REVERT: S 109 ASP cc_start: 0.8241 (p0) cc_final: 0.8035 (p0) REVERT: S 128 MET cc_start: 0.8775 (mmm) cc_final: 0.7983 (mmm) outliers start: 49 outliers final: 36 residues processed: 314 average time/residue: 0.1055 time to fit residues: 46.4216 Evaluate side-chains 319 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 8 optimal weight: 0.4980 chunk 105 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 75 GLN B 175 GLN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.144350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.112389 restraints weight = 17032.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.114809 restraints weight = 8915.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116094 restraints weight = 5543.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117046 restraints weight = 4510.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.117327 restraints weight = 4070.636| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10398 Z= 0.178 Angle : 0.688 11.086 14095 Z= 0.346 Chirality : 0.044 0.172 1621 Planarity : 0.004 0.072 1768 Dihedral : 5.026 36.188 1474 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.01 % Allowed : 24.98 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.96 (0.23), residues: 1284 helix: 0.03 (0.26), residues: 424 sheet: -1.98 (0.30), residues: 280 loop : -1.89 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 27 TYR 0.030 0.002 TYR A 302 PHE 0.018 0.002 PHE S 200 TRP 0.039 0.002 TRP R 112 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00410 (10390) covalent geometry : angle 0.68726 (14079) SS BOND : bond 0.00218 ( 8) SS BOND : angle 1.07320 ( 16) hydrogen bonds : bond 0.02980 ( 363) hydrogen bonds : angle 4.72512 ( 1023) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7972 (mp0) REVERT: A 26 ASP cc_start: 0.8924 (t70) cc_final: 0.8444 (t0) REVERT: A 243 MET cc_start: 0.8634 (mmm) cc_final: 0.8017 (mmm) REVERT: A 255 ASN cc_start: 0.8586 (m-40) cc_final: 0.8299 (m110) REVERT: A 305 CYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8035 (m) REVERT: A 341 ASP cc_start: 0.8615 (t0) cc_final: 0.8362 (t0) REVERT: B 13 GLN cc_start: 0.8801 (mm110) cc_final: 0.7584 (tm-30) REVERT: B 19 ARG cc_start: 0.7964 (ttp-170) cc_final: 0.7690 (mtm180) REVERT: B 79 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8856 (tt) REVERT: B 82 TRP cc_start: 0.8770 (m100) cc_final: 0.8080 (m100) REVERT: B 147 SER cc_start: 0.9157 (OUTLIER) cc_final: 0.8913 (t) REVERT: B 157 ILE cc_start: 0.9105 (tt) cc_final: 0.8769 (tt) REVERT: B 188 MET cc_start: 0.8383 (mmm) cc_final: 0.7913 (mmm) REVERT: B 220 GLN cc_start: 0.8418 (mp-120) cc_final: 0.8022 (mp10) REVERT: B 226 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7523 (mp0) REVERT: B 234 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8805 (m-80) REVERT: B 258 ASP cc_start: 0.7703 (t0) cc_final: 0.7130 (t0) REVERT: B 259 GLN cc_start: 0.7905 (pt0) cc_final: 0.7510 (pt0) REVERT: C 13 ARG cc_start: 0.8607 (ttm-80) cc_final: 0.8323 (ptp-110) REVERT: C 25 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8508 (mp) REVERT: D 6 ARG cc_start: 0.8714 (ttp-170) cc_final: 0.8210 (ptm160) REVERT: D 13 TYR cc_start: 0.7875 (t80) cc_final: 0.7363 (t80) REVERT: E 47 ARG cc_start: 0.6742 (mtt-85) cc_final: 0.6531 (ttm110) REVERT: R 55 TYR cc_start: 0.8245 (m-80) cc_final: 0.7611 (m-80) REVERT: R 96 LEU cc_start: 0.8988 (mp) cc_final: 0.8770 (mp) REVERT: R 127 GLU cc_start: 0.8597 (tp30) cc_final: 0.7957 (tp30) REVERT: R 163 LYS cc_start: 0.8079 (mppt) cc_final: 0.7627 (mmtm) REVERT: R 224 LEU cc_start: 0.8777 (tp) cc_final: 0.8481 (tp) REVERT: R 227 MET cc_start: 0.7952 (mtp) cc_final: 0.7679 (ttm) REVERT: R 228 LEU cc_start: 0.9081 (mm) cc_final: 0.8820 (mm) REVERT: R 229 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7403 (m-10) REVERT: R 287 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7694 (pp20) REVERT: R 304 ILE cc_start: 0.9073 (tp) cc_final: 0.8844 (tp) REVERT: R 306 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7302 (t70) REVERT: R 323 HIS cc_start: 0.8152 (m90) cc_final: 0.7868 (m-70) REVERT: S 109 ASP cc_start: 0.8244 (p0) cc_final: 0.8014 (p0) REVERT: S 128 MET cc_start: 0.8778 (mmm) cc_final: 0.7981 (mmm) outliers start: 44 outliers final: 30 residues processed: 301 average time/residue: 0.1029 time to fit residues: 43.2480 Evaluate side-chains 303 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 86 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 0.0870 chunk 95 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN R 129 ASN R 150 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.148688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.116127 restraints weight = 17064.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119786 restraints weight = 8814.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.120870 restraints weight = 5168.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121521 restraints weight = 4238.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.121786 restraints weight = 3868.484| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10398 Z= 0.127 Angle : 0.678 9.960 14095 Z= 0.336 Chirality : 0.043 0.158 1621 Planarity : 0.004 0.071 1768 Dihedral : 4.875 36.321 1474 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.10 % Allowed : 25.62 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.83 (0.23), residues: 1284 helix: 0.11 (0.26), residues: 431 sheet: -1.92 (0.30), residues: 278 loop : -1.82 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 62 TYR 0.028 0.001 TYR B 59 PHE 0.017 0.001 PHE S 200 TRP 0.025 0.001 TRP R 112 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00294 (10390) covalent geometry : angle 0.67730 (14079) SS BOND : bond 0.00211 ( 8) SS BOND : angle 0.94989 ( 16) hydrogen bonds : bond 0.02851 ( 363) hydrogen bonds : angle 4.67024 ( 1023) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2007.32 seconds wall clock time: 35 minutes 28.55 seconds (2128.55 seconds total)