Starting phenix.real_space_refine on Wed Feb 4 09:03:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rx0_24721/02_2026/7rx0_24721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rx0_24721/02_2026/7rx0_24721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rx0_24721/02_2026/7rx0_24721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rx0_24721/02_2026/7rx0_24721.map" model { file = "/net/cci-nas-00/data/ceres_data/7rx0_24721/02_2026/7rx0_24721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rx0_24721/02_2026/7rx0_24721.cif" } resolution = 3.89 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= 0.002 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 55 5.16 5 C 6047 2.51 5 N 1679 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9673 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2482 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "G" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 395 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'TRANS': 78} Chain breaks: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'UNK:plan-1': 79} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3349 Classifications: {'peptide': 428} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N VAL C 47 " occ=0.71 ... (5 atoms not shown) pdb=" CG2 VAL C 47 " occ=0.71 residue: pdb=" N PHE C 86 " occ=0.51 ... (9 atoms not shown) pdb=" CZ PHE C 86 " occ=0.51 residue: pdb=" N PHE C 91 " occ=0.63 ... (9 atoms not shown) pdb=" CZ PHE C 91 " occ=0.63 residue: pdb=" N LEU C 168 " occ=0.62 ... (6 atoms not shown) pdb=" CD2 LEU C 168 " occ=0.62 residue: pdb=" N SER C 304 " occ=0.51 ... (4 atoms not shown) pdb=" OG SER C 304 " occ=0.51 Time building chain proxies: 2.18, per 1000 atoms: 0.23 Number of scatterers: 9673 At special positions: 0 Unit cell: (81.9, 111.8, 118.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 9 15.00 Mg 1 11.99 O 1882 8.00 N 1679 7.00 C 6047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 492.4 milliseconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 50.6% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'C' and resid 26 through 31 Processing helix chain 'C' and resid 66 through 82 removed outlier: 4.949A pdb=" N GLN C 76 " --> pdb=" O GLN C 72 " (cutoff:3.500A) Proline residue: C 77 - end of helix Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 118 through 132 Processing helix chain 'C' and resid 188 through 201 Processing helix chain 'C' and resid 266 through 288 removed outlier: 3.934A pdb=" N GLN C 274 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 312 removed outlier: 4.367A pdb=" N ASP C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 345 removed outlier: 3.549A pdb=" N ARG C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 26 Processing helix chain 'G' and resid 50 through 62 Processing helix chain 'G' and resid 80 through 92 Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.665A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 87 removed outlier: 4.374A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 87 " --> pdb=" O ARG A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 147 through 161 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.880A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.655A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.922A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.537A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 6.171A pdb=" N ALA A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.786A pdb=" N ARG A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 402 removed outlier: 3.810A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.983A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 48 removed outlier: 4.537A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 71 through 81 removed outlier: 4.122A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.855A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 removed outlier: 3.625A pdb=" N GLY B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 4.176A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 223 through 241 removed outlier: 3.718A pdb=" N LEU B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.559A pdb=" N ASP B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.980A pdb=" N VAL B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 384 through 400 removed outlier: 3.736A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.958A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 437 removed outlier: 3.896A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 20 through 22 removed outlier: 3.666A pdb=" N VAL C 326 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N THR C 89 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE C 323 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE C 91 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N CYS C 325 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR C 93 " --> pdb=" O CYS C 325 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS C 249 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 90 " --> pdb=" O HIS C 249 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 251 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER C 246 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 225 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 22 removed outlier: 3.666A pdb=" N VAL C 326 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N THR C 89 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE C 323 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE C 91 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N CYS C 325 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR C 93 " --> pdb=" O CYS C 325 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS C 249 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 90 " --> pdb=" O HIS C 249 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 251 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER C 246 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 225 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL C 184 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 41 Processing sheet with id=AA4, first strand: chain 'C' and resid 167 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.203A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 168 " --> pdb=" O CYS A 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.203A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'A' and resid 246 through 248 removed outlier: 6.492A pdb=" N ILE A 355 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.194A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 204 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 56 467 hydrogen bonds defined for protein. 1341 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: 1.20 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3265 1.34 - 1.46: 2174 1.46 - 1.58: 4324 1.58 - 1.70: 13 1.70 - 1.81: 89 Bond restraints: 9865 Sorted by residual: bond pdb=" O3B G2P B 501 " pdb=" PG G2P B 501 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" O1A G2P B 501 " pdb=" PA G2P B 501 " ideal model delta sigma weight residual 1.507 1.611 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" O1B G2P B 501 " pdb=" PB G2P B 501 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C5 GTP A 501 " pdb=" C6 GTP A 501 " ideal model delta sigma weight residual 1.390 1.481 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O3A ANP C1401 " pdb=" PB ANP C1401 " ideal model delta sigma weight residual 1.700 1.610 0.090 2.00e-02 2.50e+03 2.03e+01 ... (remaining 9860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 13215 2.74 - 5.49: 160 5.49 - 8.23: 21 8.23 - 10.97: 9 10.97 - 13.71: 2 Bond angle restraints: 13407 Sorted by residual: angle pdb=" C THR C 205 " pdb=" CA THR C 205 " pdb=" CB THR C 205 " ideal model delta sigma weight residual 110.42 124.13 -13.71 1.99e+00 2.53e-01 4.75e+01 angle pdb=" C HIS C 204 " pdb=" N THR C 205 " pdb=" CA THR C 205 " ideal model delta sigma weight residual 121.54 111.50 10.04 1.91e+00 2.74e-01 2.76e+01 angle pdb=" N SER C 215 " pdb=" CA SER C 215 " pdb=" C SER C 215 " ideal model delta sigma weight residual 110.91 115.77 -4.86 1.17e+00 7.31e-01 1.73e+01 angle pdb=" PA G2P B 501 " pdb=" C3A G2P B 501 " pdb=" PB G2P B 501 " ideal model delta sigma weight residual 120.83 109.51 11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" N THR C 208 " pdb=" CA THR C 208 " pdb=" C THR C 208 " ideal model delta sigma weight residual 108.96 103.00 5.96 1.59e+00 3.96e-01 1.41e+01 ... (remaining 13402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 5774 33.70 - 67.39: 119 67.39 - 101.08: 13 101.08 - 134.78: 2 134.78 - 168.47: 4 Dihedral angle restraints: 5912 sinusoidal: 2282 harmonic: 3630 Sorted by residual: dihedral pdb=" C THR C 205 " pdb=" N THR C 205 " pdb=" CA THR C 205 " pdb=" CB THR C 205 " ideal model delta harmonic sigma weight residual -122.00 -147.69 25.69 0 2.50e+00 1.60e-01 1.06e+02 dihedral pdb=" N THR C 205 " pdb=" C THR C 205 " pdb=" CA THR C 205 " pdb=" CB THR C 205 " ideal model delta harmonic sigma weight residual 123.40 142.70 -19.30 0 2.50e+00 1.60e-01 5.96e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.26 -168.47 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 5909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 1503 0.199 - 0.398: 1 0.398 - 0.597: 0 0.597 - 0.796: 0 0.796 - 0.995: 1 Chirality restraints: 1505 Sorted by residual: chirality pdb=" CA THR C 205 " pdb=" N THR C 205 " pdb=" C THR C 205 " pdb=" CB THR C 205 " both_signs ideal model delta sigma weight residual False 2.53 1.53 0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CA HIS C 204 " pdb=" N HIS C 204 " pdb=" C HIS C 204 " pdb=" CB HIS C 204 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C3' ANP C1401 " pdb=" C2' ANP C1401 " pdb=" C4' ANP C1401 " pdb=" O3' ANP C1401 " both_signs ideal model delta sigma weight residual False -2.36 -2.54 0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 1502 not shown) Planarity restraints: 1749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 202 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C ALA C 202 " 0.031 2.00e-02 2.50e+03 pdb=" O ALA C 202 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG C 203 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 269 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO B 270 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 31 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 32 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.021 5.00e-02 4.00e+02 ... (remaining 1746 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 60 2.31 - 2.96: 5377 2.96 - 3.61: 15666 3.61 - 4.25: 22884 4.25 - 4.90: 36308 Nonbonded interactions: 80295 Sorted by model distance: nonbonded pdb=" O ARG C 203 " pdb=" O GLY C 206 " model vdw 1.666 3.040 nonbonded pdb=" O2A G2P B 501 " pdb="MG MG B 502 " model vdw 1.777 2.170 nonbonded pdb=" O2G G2P B 501 " pdb="MG MG B 502 " model vdw 1.923 2.170 nonbonded pdb=" OH TYR C 145 " pdb=" NH2 ARG C 203 " model vdw 1.968 3.120 nonbonded pdb=" OD1 ASN C 200 " pdb=" NH2 ARG C 203 " model vdw 1.996 3.120 ... (remaining 80290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 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: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.230 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 : 0.017 0.895 9870 Z= 1.627 Angle : 0.854 13.713 13407 Z= 0.458 Chirality : 0.051 0.995 1505 Planarity : 0.004 0.045 1749 Dihedral : 15.605 168.471 3576 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 29.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.22), residues: 1172 helix: -1.24 (0.20), residues: 491 sheet: -1.23 (0.31), residues: 198 loop : -2.37 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 258 TYR 0.013 0.002 TYR B 432 PHE 0.016 0.002 PHE C 248 TRP 0.018 0.002 TRP A 346 HIS 0.008 0.002 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00620 ( 9865) covalent geometry : angle 0.85406 (13407) hydrogen bonds : bond 0.14830 ( 450) hydrogen bonds : angle 7.13003 ( 1341) Misc. bond : bond 0.70893 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 ILE cc_start: 0.8786 (mt) cc_final: 0.8345 (mm) REVERT: C 149 TYR cc_start: 0.8704 (t80) cc_final: 0.8442 (t80) REVERT: C 151 GLU cc_start: 0.9099 (mp0) cc_final: 0.8634 (mp0) REVERT: C 182 LYS cc_start: 0.8830 (tttp) cc_final: 0.8427 (ttmt) REVERT: C 218 HIS cc_start: 0.8399 (m-70) cc_final: 0.7744 (m-70) REVERT: C 225 LEU cc_start: 0.8888 (tp) cc_final: 0.8623 (tp) REVERT: C 274 GLN cc_start: 0.9144 (mt0) cc_final: 0.8111 (pt0) REVERT: C 301 TYR cc_start: 0.9198 (m-80) cc_final: 0.8717 (m-80) REVERT: A 18 ASN cc_start: 0.8886 (m-40) cc_final: 0.8559 (t0) REVERT: A 116 ASP cc_start: 0.9437 (m-30) cc_final: 0.8869 (p0) REVERT: A 118 VAL cc_start: 0.9722 (m) cc_final: 0.9413 (p) REVERT: A 127 ASP cc_start: 0.8830 (m-30) cc_final: 0.8551 (m-30) REVERT: A 155 GLU cc_start: 0.9357 (tp30) cc_final: 0.8858 (tp30) REVERT: A 196 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8413 (mm-30) REVERT: A 216 ASN cc_start: 0.9193 (m-40) cc_final: 0.8719 (m110) REVERT: A 363 VAL cc_start: 0.9237 (t) cc_final: 0.8895 (p) REVERT: A 401 LYS cc_start: 0.9489 (tppt) cc_final: 0.9274 (tppt) REVERT: A 430 LYS cc_start: 0.9453 (tptt) cc_final: 0.8912 (tppt) REVERT: A 433 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8424 (tm-30) REVERT: B 26 ASP cc_start: 0.9318 (t0) cc_final: 0.9078 (t70) REVERT: B 37 HIS cc_start: 0.8802 (m-70) cc_final: 0.8292 (m90) REVERT: B 108 TYR cc_start: 0.8551 (t80) cc_final: 0.8322 (t80) REVERT: B 156 LYS cc_start: 0.9458 (mttt) cc_final: 0.9101 (mmpt) REVERT: B 166 MET cc_start: 0.7478 (mmm) cc_final: 0.7047 (mtm) REVERT: B 199 ASP cc_start: 0.8421 (m-30) cc_final: 0.7889 (m-30) REVERT: B 214 PHE cc_start: 0.8809 (t80) cc_final: 0.8581 (t80) REVERT: B 219 LEU cc_start: 0.8663 (mt) cc_final: 0.8311 (mt) REVERT: B 306 ASP cc_start: 0.9007 (m-30) cc_final: 0.8696 (t70) REVERT: B 309 HIS cc_start: 0.9000 (m170) cc_final: 0.8352 (m-70) REVERT: B 332 MET cc_start: 0.9291 (mmt) cc_final: 0.8944 (mmm) REVERT: B 373 MET cc_start: 0.8298 (ptp) cc_final: 0.7957 (mtp) REVERT: B 394 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8677 (tp40) REVERT: B 413 MET cc_start: 0.9131 (mmm) cc_final: 0.8697 (mmm) REVERT: B 416 MET cc_start: 0.9093 (mmm) cc_final: 0.8126 (tpt) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.0933 time to fit residues: 37.5433 Evaluate side-chains 212 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 40.0000 chunk 33 optimal weight: 50.0000 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN A 18 ASN A 28 HIS A 31 GLN A 35 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN B 14 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.085108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.066683 restraints weight = 34804.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.068975 restraints weight = 17986.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.070512 restraints weight = 11250.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.071524 restraints weight = 7907.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.072189 restraints weight = 6104.549| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9870 Z= 0.179 Angle : 0.751 9.623 13407 Z= 0.375 Chirality : 0.045 0.212 1505 Planarity : 0.005 0.086 1749 Dihedral : 11.228 152.612 1435 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.73 % Allowed : 16.57 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.24), residues: 1172 helix: 0.11 (0.23), residues: 481 sheet: -0.94 (0.33), residues: 202 loop : -1.52 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 203 TYR 0.047 0.002 TYR C 71 PHE 0.018 0.002 PHE B 262 TRP 0.017 0.002 TRP B 346 HIS 0.007 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9865) covalent geometry : angle 0.75056 (13407) hydrogen bonds : bond 0.04660 ( 450) hydrogen bonds : angle 5.66886 ( 1341) Misc. bond : bond 0.00238 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 245 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.8771 (t80) cc_final: 0.8287 (t80) REVERT: C 119 ILE cc_start: 0.8577 (mt) cc_final: 0.8318 (mm) REVERT: C 151 GLU cc_start: 0.9034 (mp0) cc_final: 0.8341 (mp0) REVERT: C 205 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7080 (t) REVERT: C 218 HIS cc_start: 0.8460 (m-70) cc_final: 0.7839 (m-70) REVERT: C 274 GLN cc_start: 0.9161 (mt0) cc_final: 0.8548 (pp30) REVERT: C 301 TYR cc_start: 0.9211 (m-80) cc_final: 0.8663 (m-80) REVERT: C 305 LYS cc_start: 0.9263 (mttp) cc_final: 0.8980 (mtpt) REVERT: A 86 LEU cc_start: 0.9316 (mt) cc_final: 0.8885 (mt) REVERT: A 127 ASP cc_start: 0.8770 (m-30) cc_final: 0.8511 (m-30) REVERT: A 196 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8231 (mm-30) REVERT: A 216 ASN cc_start: 0.8979 (m-40) cc_final: 0.8715 (m110) REVERT: A 272 TYR cc_start: 0.8413 (t80) cc_final: 0.8051 (t80) REVERT: A 302 MET cc_start: 0.8328 (mtt) cc_final: 0.8016 (mtt) REVERT: A 363 VAL cc_start: 0.9273 (t) cc_final: 0.8955 (p) REVERT: A 372 GLN cc_start: 0.8886 (mp10) cc_final: 0.8646 (mm-40) REVERT: A 398 MET cc_start: 0.9093 (mpp) cc_final: 0.8854 (mmp) REVERT: A 413 MET cc_start: 0.9185 (mmm) cc_final: 0.8962 (mmm) REVERT: A 430 LYS cc_start: 0.9518 (tptt) cc_final: 0.9140 (tppt) REVERT: A 433 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8711 (tm-30) REVERT: A 434 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8518 (mt-10) REVERT: B 37 HIS cc_start: 0.8639 (m-70) cc_final: 0.8084 (m90) REVERT: B 108 TYR cc_start: 0.8484 (t80) cc_final: 0.8185 (t80) REVERT: B 156 LYS cc_start: 0.9511 (mttt) cc_final: 0.9249 (mmtm) REVERT: B 166 MET cc_start: 0.7498 (mmm) cc_final: 0.7269 (mtm) REVERT: B 199 ASP cc_start: 0.8594 (m-30) cc_final: 0.8026 (m-30) REVERT: B 211 ASP cc_start: 0.9125 (OUTLIER) cc_final: 0.8402 (t0) REVERT: B 219 LEU cc_start: 0.8620 (mt) cc_final: 0.8239 (mt) REVERT: B 302 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8387 (mtt) REVERT: B 306 ASP cc_start: 0.8955 (m-30) cc_final: 0.8607 (t0) REVERT: B 309 HIS cc_start: 0.8821 (m170) cc_final: 0.8027 (m-70) REVERT: B 332 MET cc_start: 0.9240 (mmt) cc_final: 0.8884 (mmm) REVERT: B 391 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9256 (mp) REVERT: B 413 MET cc_start: 0.9143 (mmm) cc_final: 0.8311 (mmm) outliers start: 27 outliers final: 12 residues processed: 257 average time/residue: 0.0806 time to fit residues: 28.9662 Evaluate side-chains 223 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 50.0000 chunk 33 optimal weight: 60.0000 chunk 6 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 77 optimal weight: 30.0000 chunk 105 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 68 optimal weight: 30.0000 chunk 72 optimal weight: 0.0050 chunk 112 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 overall best weight: 14.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN C 76 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 ASN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS A 329 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN B 406 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.081043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.063328 restraints weight = 35861.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.065502 restraints weight = 18610.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.066963 restraints weight = 11614.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.067946 restraints weight = 8148.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.068626 restraints weight = 6267.140| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9870 Z= 0.246 Angle : 0.781 12.273 13407 Z= 0.393 Chirality : 0.045 0.162 1505 Planarity : 0.011 0.408 1749 Dihedral : 11.182 165.952 1435 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.14 % Allowed : 19.09 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.24), residues: 1172 helix: 0.35 (0.22), residues: 486 sheet: -0.90 (0.32), residues: 206 loop : -1.49 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG C 203 TYR 0.029 0.002 TYR C 71 PHE 0.014 0.002 PHE C 248 TRP 0.020 0.002 TRP B 346 HIS 0.007 0.002 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 9865) covalent geometry : angle 0.78063 (13407) hydrogen bonds : bond 0.04526 ( 450) hydrogen bonds : angle 5.58230 ( 1341) Misc. bond : bond 0.00236 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.8963 (t80) cc_final: 0.8511 (t80) REVERT: C 119 ILE cc_start: 0.8715 (mt) cc_final: 0.8497 (mm) REVERT: C 145 TYR cc_start: 0.8550 (t80) cc_final: 0.8333 (t80) REVERT: C 151 GLU cc_start: 0.8958 (mp0) cc_final: 0.8205 (mp0) REVERT: C 218 HIS cc_start: 0.8546 (m-70) cc_final: 0.7843 (m-70) REVERT: C 274 GLN cc_start: 0.9078 (mt0) cc_final: 0.8461 (pp30) REVERT: C 301 TYR cc_start: 0.9269 (m-80) cc_final: 0.8737 (m-80) REVERT: C 305 LYS cc_start: 0.9278 (mttp) cc_final: 0.8995 (mtpt) REVERT: A 86 LEU cc_start: 0.9354 (mt) cc_final: 0.9012 (mt) REVERT: A 127 ASP cc_start: 0.8818 (m-30) cc_final: 0.8579 (m-30) REVERT: A 196 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8312 (mm-30) REVERT: A 272 TYR cc_start: 0.8568 (t80) cc_final: 0.8233 (t80) REVERT: A 302 MET cc_start: 0.8393 (mtt) cc_final: 0.7918 (mtt) REVERT: A 363 VAL cc_start: 0.9263 (t) cc_final: 0.8936 (p) REVERT: A 372 GLN cc_start: 0.8972 (mp10) cc_final: 0.8668 (mm-40) REVERT: A 433 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8621 (tm-30) REVERT: B 68 VAL cc_start: 0.9292 (p) cc_final: 0.9078 (m) REVERT: B 107 HIS cc_start: 0.8326 (t70) cc_final: 0.7714 (t70) REVERT: B 156 LYS cc_start: 0.9560 (mttt) cc_final: 0.9251 (mmpt) REVERT: B 166 MET cc_start: 0.7970 (mmm) cc_final: 0.7587 (mtm) REVERT: B 199 ASP cc_start: 0.8769 (m-30) cc_final: 0.7930 (m-30) REVERT: B 219 LEU cc_start: 0.8712 (mt) cc_final: 0.8339 (mt) REVERT: B 302 MET cc_start: 0.9088 (mmm) cc_final: 0.8406 (mtt) REVERT: B 306 ASP cc_start: 0.8908 (m-30) cc_final: 0.8662 (m-30) REVERT: B 309 HIS cc_start: 0.8764 (m170) cc_final: 0.8291 (m90) REVERT: B 323 MET cc_start: 0.7878 (mpp) cc_final: 0.6127 (mpp) REVERT: B 332 MET cc_start: 0.9277 (mmt) cc_final: 0.8957 (mmm) REVERT: B 346 TRP cc_start: 0.7913 (m100) cc_final: 0.7676 (m100) REVERT: B 373 MET cc_start: 0.8634 (ptp) cc_final: 0.8181 (mtp) REVERT: B 416 MET cc_start: 0.8697 (ptp) cc_final: 0.8027 (tpt) REVERT: B 419 THR cc_start: 0.9333 (OUTLIER) cc_final: 0.8418 (p) REVERT: B 422 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8725 (pp20) outliers start: 41 outliers final: 24 residues processed: 235 average time/residue: 0.0775 time to fit residues: 25.9530 Evaluate side-chains 218 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 422 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 44 optimal weight: 30.0000 chunk 50 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 2 optimal weight: 50.0000 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 30.0000 chunk 100 optimal weight: 30.0000 chunk 68 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN A 139 HIS A 226 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.083434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.065280 restraints weight = 35094.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.067501 restraints weight = 18130.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.068961 restraints weight = 11326.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.069959 restraints weight = 7984.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.070645 restraints weight = 6145.128| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9870 Z= 0.151 Angle : 0.726 13.348 13407 Z= 0.357 Chirality : 0.045 0.275 1505 Planarity : 0.009 0.348 1749 Dihedral : 10.864 167.642 1435 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.14 % Allowed : 20.61 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.24), residues: 1172 helix: 0.78 (0.23), residues: 481 sheet: -0.66 (0.34), residues: 192 loop : -1.32 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG C 203 TYR 0.022 0.002 TYR A 224 PHE 0.015 0.001 PHE C 333 TRP 0.012 0.001 TRP A 21 HIS 0.006 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9865) covalent geometry : angle 0.72637 (13407) hydrogen bonds : bond 0.04183 ( 450) hydrogen bonds : angle 5.19247 ( 1341) Misc. bond : bond 0.00511 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.8931 (t80) cc_final: 0.8483 (t80) REVERT: C 119 ILE cc_start: 0.8664 (mt) cc_final: 0.8318 (mm) REVERT: C 124 MET cc_start: 0.8995 (mmm) cc_final: 0.8664 (mmm) REVERT: C 151 GLU cc_start: 0.9034 (mp0) cc_final: 0.8316 (mp0) REVERT: C 166 ILE cc_start: 0.9256 (pp) cc_final: 0.8693 (mt) REVERT: C 182 LYS cc_start: 0.8818 (tptp) cc_final: 0.8591 (tptp) REVERT: C 218 HIS cc_start: 0.8552 (m-70) cc_final: 0.7864 (m-70) REVERT: C 252 ASP cc_start: 0.8640 (t0) cc_final: 0.8143 (t0) REVERT: C 274 GLN cc_start: 0.9046 (mt0) cc_final: 0.8412 (pp30) REVERT: C 301 TYR cc_start: 0.9293 (m-80) cc_final: 0.8771 (m-80) REVERT: C 305 LYS cc_start: 0.9270 (mttp) cc_final: 0.8945 (mtpt) REVERT: C 338 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8712 (t0) REVERT: A 21 TRP cc_start: 0.9233 (m100) cc_final: 0.8917 (m100) REVERT: A 36 MET cc_start: 0.9025 (tmm) cc_final: 0.8809 (tmm) REVERT: A 86 LEU cc_start: 0.9333 (mt) cc_final: 0.8985 (mt) REVERT: A 116 ASP cc_start: 0.9152 (p0) cc_final: 0.8701 (p0) REVERT: A 127 ASP cc_start: 0.8848 (m-30) cc_final: 0.8599 (m-30) REVERT: A 196 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8399 (mm-30) REVERT: A 272 TYR cc_start: 0.8520 (t80) cc_final: 0.8169 (t80) REVERT: A 285 GLN cc_start: 0.2979 (OUTLIER) cc_final: 0.2066 (mt0) REVERT: A 302 MET cc_start: 0.8502 (mtt) cc_final: 0.8118 (mtt) REVERT: A 363 VAL cc_start: 0.9250 (t) cc_final: 0.8927 (p) REVERT: A 372 GLN cc_start: 0.9088 (mp10) cc_final: 0.8831 (mm-40) REVERT: A 375 VAL cc_start: 0.9441 (t) cc_final: 0.9179 (p) REVERT: A 401 LYS cc_start: 0.8913 (pttt) cc_final: 0.7763 (pttt) REVERT: B 68 VAL cc_start: 0.9300 (p) cc_final: 0.8965 (m) REVERT: B 107 HIS cc_start: 0.8462 (t70) cc_final: 0.7816 (t70) REVERT: B 156 LYS cc_start: 0.9555 (mttt) cc_final: 0.9167 (mmtm) REVERT: B 159 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7870 (mt-10) REVERT: B 166 MET cc_start: 0.7901 (mmm) cc_final: 0.7628 (mtm) REVERT: B 211 ASP cc_start: 0.9205 (OUTLIER) cc_final: 0.8905 (t0) REVERT: B 219 LEU cc_start: 0.8685 (mt) cc_final: 0.8319 (mt) REVERT: B 269 MET cc_start: 0.8215 (pmm) cc_final: 0.7960 (pmm) REVERT: B 302 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8453 (mtt) REVERT: B 306 ASP cc_start: 0.8905 (m-30) cc_final: 0.8667 (t0) REVERT: B 309 HIS cc_start: 0.8701 (m170) cc_final: 0.7877 (m-70) REVERT: B 323 MET cc_start: 0.7970 (mpp) cc_final: 0.6706 (mpp) REVERT: B 332 MET cc_start: 0.9334 (mmt) cc_final: 0.8958 (mmm) REVERT: B 373 MET cc_start: 0.8642 (ptp) cc_final: 0.8293 (mtm) REVERT: B 391 ILE cc_start: 0.9322 (mp) cc_final: 0.9032 (tt) REVERT: B 416 MET cc_start: 0.8612 (ptp) cc_final: 0.8298 (ptp) outliers start: 41 outliers final: 19 residues processed: 246 average time/residue: 0.0711 time to fit residues: 24.5815 Evaluate side-chains 219 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 377 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 44 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 108 optimal weight: 50.0000 chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 116 optimal weight: 40.0000 chunk 110 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 35 optimal weight: 50.0000 chunk 64 optimal weight: 6.9990 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.083613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.065446 restraints weight = 34744.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.067687 restraints weight = 18358.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.069173 restraints weight = 11578.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.070212 restraints weight = 8212.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.070876 restraints weight = 6329.746| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9870 Z= 0.151 Angle : 0.732 13.861 13407 Z= 0.356 Chirality : 0.044 0.192 1505 Planarity : 0.005 0.117 1749 Dihedral : 10.722 169.187 1435 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.54 % Allowed : 21.41 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.24), residues: 1172 helix: 0.82 (0.23), residues: 480 sheet: -0.56 (0.33), residues: 203 loop : -1.22 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 203 TYR 0.020 0.002 TYR A 224 PHE 0.022 0.001 PHE B 262 TRP 0.039 0.003 TRP B 346 HIS 0.006 0.001 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9865) covalent geometry : angle 0.73231 (13407) hydrogen bonds : bond 0.04060 ( 450) hydrogen bonds : angle 5.12032 ( 1341) Misc. bond : bond 0.00189 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.8986 (t80) cc_final: 0.8523 (t80) REVERT: C 124 MET cc_start: 0.8925 (mmm) cc_final: 0.8607 (mmm) REVERT: C 146 LEU cc_start: 0.8815 (pt) cc_final: 0.8419 (tt) REVERT: C 151 GLU cc_start: 0.9031 (mp0) cc_final: 0.8522 (mp0) REVERT: C 166 ILE cc_start: 0.9277 (pp) cc_final: 0.9030 (tt) REVERT: C 210 LEU cc_start: 0.4163 (OUTLIER) cc_final: 0.3090 (tt) REVERT: C 218 HIS cc_start: 0.8586 (m-70) cc_final: 0.7913 (m-70) REVERT: C 274 GLN cc_start: 0.8993 (mt0) cc_final: 0.8445 (pm20) REVERT: C 301 TYR cc_start: 0.9290 (m-80) cc_final: 0.8764 (m-80) REVERT: C 305 LYS cc_start: 0.9252 (mttp) cc_final: 0.8931 (mtpt) REVERT: C 338 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8735 (t0) REVERT: A 21 TRP cc_start: 0.9247 (m100) cc_final: 0.8875 (m100) REVERT: A 86 LEU cc_start: 0.9355 (mt) cc_final: 0.8983 (mt) REVERT: A 127 ASP cc_start: 0.8828 (m-30) cc_final: 0.8574 (m-30) REVERT: A 196 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8344 (mm-30) REVERT: A 272 TYR cc_start: 0.8550 (t80) cc_final: 0.8158 (t80) REVERT: A 276 ILE cc_start: 0.9520 (tp) cc_final: 0.9278 (tp) REVERT: A 285 GLN cc_start: 0.3070 (OUTLIER) cc_final: 0.1973 (mt0) REVERT: A 302 MET cc_start: 0.8381 (mtt) cc_final: 0.8110 (mtt) REVERT: A 363 VAL cc_start: 0.9263 (t) cc_final: 0.8708 (p) REVERT: A 372 GLN cc_start: 0.9088 (mp10) cc_final: 0.8749 (mm-40) REVERT: A 375 VAL cc_start: 0.9422 (t) cc_final: 0.9159 (p) REVERT: A 401 LYS cc_start: 0.8667 (pttt) cc_final: 0.7778 (pttt) REVERT: A 413 MET cc_start: 0.9066 (mmm) cc_final: 0.8687 (mmp) REVERT: B 68 VAL cc_start: 0.9408 (p) cc_final: 0.9118 (m) REVERT: B 107 HIS cc_start: 0.8490 (t70) cc_final: 0.7875 (t70) REVERT: B 156 LYS cc_start: 0.9553 (mttt) cc_final: 0.9167 (mmtm) REVERT: B 159 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7921 (mt-10) REVERT: B 166 MET cc_start: 0.7860 (mmm) cc_final: 0.7617 (mtm) REVERT: B 302 MET cc_start: 0.8979 (mmm) cc_final: 0.8595 (mtt) REVERT: B 309 HIS cc_start: 0.8669 (m170) cc_final: 0.8295 (m90) REVERT: B 323 MET cc_start: 0.7974 (mpp) cc_final: 0.6418 (mpp) REVERT: B 332 MET cc_start: 0.9342 (mmt) cc_final: 0.8995 (mmm) REVERT: B 373 MET cc_start: 0.8541 (ptp) cc_final: 0.8257 (mtp) REVERT: B 413 MET cc_start: 0.8898 (mmt) cc_final: 0.8226 (mmt) REVERT: B 416 MET cc_start: 0.8730 (ptp) cc_final: 0.7947 (tpt) outliers start: 35 outliers final: 23 residues processed: 234 average time/residue: 0.0767 time to fit residues: 25.5652 Evaluate side-chains 221 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 80.0000 chunk 107 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 12 optimal weight: 50.0000 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 26 optimal weight: 10.0000 chunk 9 optimal weight: 50.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN A 380 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.096378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.075846 restraints weight = 34958.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.078111 restraints weight = 16544.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.079580 restraints weight = 9782.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.080571 restraints weight = 6612.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.081185 restraints weight = 4939.995| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9870 Z= 0.200 Angle : 0.775 14.881 13407 Z= 0.377 Chirality : 0.045 0.216 1505 Planarity : 0.007 0.240 1749 Dihedral : 10.948 176.267 1435 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.65 % Allowed : 21.92 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.24), residues: 1172 helix: 0.75 (0.23), residues: 480 sheet: -0.61 (0.33), residues: 195 loop : -1.28 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG C 203 TYR 0.018 0.002 TYR C 149 PHE 0.017 0.002 PHE B 262 TRP 0.048 0.002 TRP B 346 HIS 0.006 0.001 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 9865) covalent geometry : angle 0.77471 (13407) hydrogen bonds : bond 0.04114 ( 450) hydrogen bonds : angle 5.15120 ( 1341) Misc. bond : bond 0.00242 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.8946 (t80) cc_final: 0.8538 (t80) REVERT: C 151 GLU cc_start: 0.9087 (mp0) cc_final: 0.8592 (mp0) REVERT: C 173 ARG cc_start: 0.9039 (mmm160) cc_final: 0.8820 (tpp-160) REVERT: C 210 LEU cc_start: 0.4155 (OUTLIER) cc_final: 0.3185 (tt) REVERT: C 218 HIS cc_start: 0.8550 (m-70) cc_final: 0.7838 (m-70) REVERT: C 252 ASP cc_start: 0.8633 (t0) cc_final: 0.8134 (t0) REVERT: C 274 GLN cc_start: 0.8983 (mt0) cc_final: 0.8462 (pm20) REVERT: C 301 TYR cc_start: 0.9272 (m-80) cc_final: 0.8869 (m-80) REVERT: C 305 LYS cc_start: 0.9246 (mttp) cc_final: 0.8938 (mtpt) REVERT: C 338 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8702 (t0) REVERT: A 86 LEU cc_start: 0.9433 (mt) cc_final: 0.9022 (mt) REVERT: A 121 ARG cc_start: 0.9239 (mmp80) cc_final: 0.9000 (mmp80) REVERT: A 127 ASP cc_start: 0.8894 (m-30) cc_final: 0.8638 (m-30) REVERT: A 196 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8308 (mm-30) REVERT: A 224 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: A 272 TYR cc_start: 0.8656 (t80) cc_final: 0.8293 (t80) REVERT: A 276 ILE cc_start: 0.9475 (tp) cc_final: 0.9243 (tp) REVERT: A 285 GLN cc_start: 0.2356 (OUTLIER) cc_final: 0.1607 (mt0) REVERT: A 302 MET cc_start: 0.8504 (mtt) cc_final: 0.8113 (mtt) REVERT: A 363 VAL cc_start: 0.8904 (t) cc_final: 0.8658 (p) REVERT: A 372 GLN cc_start: 0.9172 (mp10) cc_final: 0.8785 (mm-40) REVERT: A 375 VAL cc_start: 0.9448 (t) cc_final: 0.9170 (p) REVERT: A 413 MET cc_start: 0.9213 (mmm) cc_final: 0.8810 (mmm) REVERT: A 422 ARG cc_start: 0.8847 (ttp80) cc_final: 0.8568 (tmm-80) REVERT: B 156 LYS cc_start: 0.9558 (mttt) cc_final: 0.9177 (mmpt) REVERT: B 159 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7917 (mt-10) REVERT: B 166 MET cc_start: 0.8287 (mmm) cc_final: 0.7705 (mtm) REVERT: B 302 MET cc_start: 0.9097 (mmm) cc_final: 0.8460 (mtt) REVERT: B 309 HIS cc_start: 0.8839 (m170) cc_final: 0.8490 (m90) REVERT: B 323 MET cc_start: 0.7875 (mpp) cc_final: 0.6075 (mpp) REVERT: B 332 MET cc_start: 0.9481 (mmt) cc_final: 0.9116 (mmm) REVERT: B 345 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8353 (pp20) REVERT: B 373 MET cc_start: 0.8721 (ptp) cc_final: 0.8288 (mtp) REVERT: B 400 ARG cc_start: 0.7958 (ttm110) cc_final: 0.7491 (mtm110) outliers start: 46 outliers final: 30 residues processed: 229 average time/residue: 0.0765 time to fit residues: 24.7437 Evaluate side-chains 224 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 50 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 3 optimal weight: 50.0000 chunk 88 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.083355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.063992 restraints weight = 35152.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.066325 restraints weight = 18013.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.067891 restraints weight = 11313.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.068916 restraints weight = 8019.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.069686 restraints weight = 6240.810| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9870 Z= 0.150 Angle : 0.771 17.189 13407 Z= 0.369 Chirality : 0.046 0.238 1505 Planarity : 0.007 0.233 1749 Dihedral : 10.846 174.498 1435 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.74 % Allowed : 24.44 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.24), residues: 1172 helix: 0.85 (0.23), residues: 481 sheet: -0.54 (0.34), residues: 194 loop : -1.20 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG C 203 TYR 0.019 0.001 TYR B 224 PHE 0.018 0.001 PHE B 272 TRP 0.029 0.002 TRP B 346 HIS 0.006 0.001 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9865) covalent geometry : angle 0.77143 (13407) hydrogen bonds : bond 0.03923 ( 450) hydrogen bonds : angle 5.05677 ( 1341) Misc. bond : bond 0.00368 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.8860 (t80) cc_final: 0.8514 (t80) REVERT: C 119 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7944 (tp) REVERT: C 149 TYR cc_start: 0.8801 (t80) cc_final: 0.8414 (t80) REVERT: C 151 GLU cc_start: 0.9062 (mp0) cc_final: 0.8456 (mp0) REVERT: C 173 ARG cc_start: 0.9027 (mmm160) cc_final: 0.8778 (tpp-160) REVERT: C 210 LEU cc_start: 0.4509 (OUTLIER) cc_final: 0.3673 (tt) REVERT: C 218 HIS cc_start: 0.8471 (m-70) cc_final: 0.7816 (m-70) REVERT: C 274 GLN cc_start: 0.8969 (mt0) cc_final: 0.8438 (pp30) REVERT: C 301 TYR cc_start: 0.9185 (m-80) cc_final: 0.8875 (m-80) REVERT: C 305 LYS cc_start: 0.9257 (mttp) cc_final: 0.8943 (mtpt) REVERT: C 338 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8735 (t0) REVERT: A 86 LEU cc_start: 0.9451 (mt) cc_final: 0.9043 (mt) REVERT: A 127 ASP cc_start: 0.8895 (m-30) cc_final: 0.8625 (m-30) REVERT: A 196 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8305 (mm-30) REVERT: A 272 TYR cc_start: 0.8549 (t80) cc_final: 0.8153 (t80) REVERT: A 276 ILE cc_start: 0.9412 (tp) cc_final: 0.9189 (tp) REVERT: A 302 MET cc_start: 0.8581 (mtt) cc_final: 0.8125 (mtt) REVERT: A 363 VAL cc_start: 0.8842 (t) cc_final: 0.8568 (p) REVERT: A 372 GLN cc_start: 0.9148 (mp10) cc_final: 0.8814 (mm-40) REVERT: A 375 VAL cc_start: 0.9391 (t) cc_final: 0.9021 (p) REVERT: A 413 MET cc_start: 0.9244 (mmm) cc_final: 0.8870 (mmm) REVERT: A 422 ARG cc_start: 0.8927 (ttp80) cc_final: 0.8708 (tmm-80) REVERT: B 8 GLN cc_start: 0.8900 (mt0) cc_final: 0.8226 (mt0) REVERT: B 68 VAL cc_start: 0.9398 (p) cc_final: 0.9112 (m) REVERT: B 107 HIS cc_start: 0.8688 (t70) cc_final: 0.7893 (t70) REVERT: B 156 LYS cc_start: 0.9528 (mttt) cc_final: 0.9290 (mmtm) REVERT: B 159 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8015 (mt-10) REVERT: B 166 MET cc_start: 0.8357 (mmm) cc_final: 0.7863 (mtm) REVERT: B 199 ASP cc_start: 0.8687 (m-30) cc_final: 0.8217 (m-30) REVERT: B 302 MET cc_start: 0.9112 (mmm) cc_final: 0.8293 (mtt) REVERT: B 309 HIS cc_start: 0.8843 (m170) cc_final: 0.8492 (m90) REVERT: B 323 MET cc_start: 0.7934 (mpp) cc_final: 0.6190 (mpp) REVERT: B 325 MET cc_start: 0.8927 (mpp) cc_final: 0.8704 (mtm) REVERT: B 332 MET cc_start: 0.9557 (mmt) cc_final: 0.9174 (mmm) REVERT: B 345 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8150 (pp20) REVERT: B 416 MET cc_start: 0.8758 (ptp) cc_final: 0.8522 (ppp) outliers start: 37 outliers final: 23 residues processed: 229 average time/residue: 0.0780 time to fit residues: 25.6163 Evaluate side-chains 227 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 398 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 3 optimal weight: 50.0000 chunk 56 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 108 optimal weight: 30.0000 chunk 102 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 20 optimal weight: 50.0000 chunk 84 optimal weight: 30.0000 chunk 38 optimal weight: 60.0000 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.084434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064949 restraints weight = 34955.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.067295 restraints weight = 17942.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.068884 restraints weight = 11273.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.069942 restraints weight = 7975.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.070653 restraints weight = 6185.716| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9870 Z= 0.142 Angle : 0.795 14.664 13407 Z= 0.382 Chirality : 0.047 0.324 1505 Planarity : 0.008 0.274 1749 Dihedral : 10.791 171.303 1435 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.74 % Allowed : 24.85 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.24), residues: 1172 helix: 0.86 (0.23), residues: 481 sheet: -0.54 (0.34), residues: 194 loop : -1.22 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.001 ARG C 203 TYR 0.013 0.001 TYR B 224 PHE 0.017 0.001 PHE B 272 TRP 0.011 0.002 TRP A 21 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9865) covalent geometry : angle 0.79518 (13407) hydrogen bonds : bond 0.03843 ( 450) hydrogen bonds : angle 4.98396 ( 1341) Misc. bond : bond 0.00436 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.8656 (t80) cc_final: 0.8442 (t80) REVERT: C 119 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7966 (tp) REVERT: C 149 TYR cc_start: 0.8778 (t80) cc_final: 0.8381 (t80) REVERT: C 151 GLU cc_start: 0.9054 (mp0) cc_final: 0.8452 (mp0) REVERT: C 173 ARG cc_start: 0.9012 (mmm160) cc_final: 0.8784 (tpp-160) REVERT: C 182 LYS cc_start: 0.8969 (tptp) cc_final: 0.8746 (tptp) REVERT: C 210 LEU cc_start: 0.4122 (OUTLIER) cc_final: 0.3314 (tt) REVERT: C 218 HIS cc_start: 0.8465 (m-70) cc_final: 0.7921 (m-70) REVERT: C 274 GLN cc_start: 0.8965 (mt0) cc_final: 0.8417 (pp30) REVERT: C 301 TYR cc_start: 0.9216 (m-80) cc_final: 0.8888 (m-80) REVERT: C 305 LYS cc_start: 0.9229 (mttp) cc_final: 0.8909 (mtpt) REVERT: C 338 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8719 (t0) REVERT: A 86 LEU cc_start: 0.9443 (mt) cc_final: 0.9035 (mt) REVERT: A 124 LYS cc_start: 0.9567 (ttpt) cc_final: 0.9351 (ttpt) REVERT: A 127 ASP cc_start: 0.8897 (m-30) cc_final: 0.8629 (m-30) REVERT: A 196 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8317 (mm-30) REVERT: A 224 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: A 272 TYR cc_start: 0.8540 (t80) cc_final: 0.8106 (t80) REVERT: A 276 ILE cc_start: 0.9438 (tp) cc_final: 0.9198 (tp) REVERT: A 302 MET cc_start: 0.8550 (mtt) cc_final: 0.8112 (mtt) REVERT: A 304 LYS cc_start: 0.9068 (tttm) cc_final: 0.8752 (tttt) REVERT: A 363 VAL cc_start: 0.8896 (t) cc_final: 0.8617 (p) REVERT: A 372 GLN cc_start: 0.9145 (mp10) cc_final: 0.8797 (mm-40) REVERT: A 375 VAL cc_start: 0.9396 (t) cc_final: 0.9028 (p) REVERT: A 380 ASN cc_start: 0.8580 (t0) cc_final: 0.8328 (m-40) REVERT: A 413 MET cc_start: 0.9197 (mmm) cc_final: 0.8805 (mmm) REVERT: A 422 ARG cc_start: 0.8900 (ttp80) cc_final: 0.8679 (tmm-80) REVERT: B 8 GLN cc_start: 0.8754 (mt0) cc_final: 0.8245 (mt0) REVERT: B 68 VAL cc_start: 0.9407 (p) cc_final: 0.9129 (m) REVERT: B 107 HIS cc_start: 0.8657 (t70) cc_final: 0.7918 (t70) REVERT: B 156 LYS cc_start: 0.9542 (mttt) cc_final: 0.9333 (mmtm) REVERT: B 159 GLU cc_start: 0.8245 (mt-10) cc_final: 0.8038 (mt-10) REVERT: B 166 MET cc_start: 0.8349 (mmm) cc_final: 0.7893 (mtm) REVERT: B 202 TYR cc_start: 0.9098 (m-80) cc_final: 0.8423 (m-80) REVERT: B 302 MET cc_start: 0.9025 (mmm) cc_final: 0.8089 (mtp) REVERT: B 309 HIS cc_start: 0.8718 (m170) cc_final: 0.8429 (m-70) REVERT: B 323 MET cc_start: 0.8413 (mpp) cc_final: 0.7480 (mpp) REVERT: B 325 MET cc_start: 0.8939 (mpp) cc_final: 0.8687 (mpp) REVERT: B 332 MET cc_start: 0.9523 (mmt) cc_final: 0.9212 (mmm) outliers start: 37 outliers final: 23 residues processed: 239 average time/residue: 0.0875 time to fit residues: 29.1482 Evaluate side-chains 232 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 63 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 37 optimal weight: 50.0000 chunk 56 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 30.0000 chunk 48 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.085005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.065184 restraints weight = 34936.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.067575 restraints weight = 18267.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.069164 restraints weight = 11475.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.070223 restraints weight = 8124.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.070977 restraints weight = 6322.891| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9870 Z= 0.147 Angle : 0.830 22.281 13407 Z= 0.404 Chirality : 0.046 0.273 1505 Planarity : 0.010 0.390 1749 Dihedral : 11.091 170.181 1435 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.35 % Favored : 95.56 % Rotamer: Outliers : 3.13 % Allowed : 25.76 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.24), residues: 1172 helix: 0.80 (0.23), residues: 483 sheet: -0.47 (0.34), residues: 195 loop : -1.18 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 278 TYR 0.013 0.001 TYR C 93 PHE 0.017 0.001 PHE B 272 TRP 0.011 0.001 TRP A 21 HIS 0.007 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9865) covalent geometry : angle 0.83030 (13407) hydrogen bonds : bond 0.03790 ( 450) hydrogen bonds : angle 4.99803 ( 1341) Misc. bond : bond 0.00512 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 219 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7817 (tp) REVERT: C 149 TYR cc_start: 0.8739 (t80) cc_final: 0.8322 (t80) REVERT: C 151 GLU cc_start: 0.9048 (mp0) cc_final: 0.8495 (mp0) REVERT: C 173 ARG cc_start: 0.9034 (mmm160) cc_final: 0.8778 (tpp-160) REVERT: C 210 LEU cc_start: 0.4406 (OUTLIER) cc_final: 0.3612 (tt) REVERT: C 218 HIS cc_start: 0.8523 (m-70) cc_final: 0.8014 (m-70) REVERT: C 274 GLN cc_start: 0.8975 (mt0) cc_final: 0.8414 (pp30) REVERT: C 301 TYR cc_start: 0.9234 (m-80) cc_final: 0.8911 (m-80) REVERT: C 305 LYS cc_start: 0.9175 (mttp) cc_final: 0.8860 (mtpt) REVERT: C 338 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8660 (t0) REVERT: A 86 LEU cc_start: 0.9354 (mt) cc_final: 0.8859 (mt) REVERT: A 127 ASP cc_start: 0.8895 (m-30) cc_final: 0.8617 (m-30) REVERT: A 154 MET cc_start: 0.9232 (ttt) cc_final: 0.8749 (tmm) REVERT: A 196 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8476 (mm-30) REVERT: A 224 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8233 (m-80) REVERT: A 272 TYR cc_start: 0.8597 (t80) cc_final: 0.8182 (t80) REVERT: A 276 ILE cc_start: 0.9393 (tp) cc_final: 0.9168 (tp) REVERT: A 302 MET cc_start: 0.8538 (mtt) cc_final: 0.8111 (mtt) REVERT: A 304 LYS cc_start: 0.9019 (tttm) cc_final: 0.8706 (tttt) REVERT: A 363 VAL cc_start: 0.8947 (t) cc_final: 0.8661 (p) REVERT: A 372 GLN cc_start: 0.9170 (mp10) cc_final: 0.8766 (mm-40) REVERT: A 375 VAL cc_start: 0.9390 (t) cc_final: 0.9023 (p) REVERT: A 380 ASN cc_start: 0.8570 (t0) cc_final: 0.8169 (m-40) REVERT: A 413 MET cc_start: 0.9107 (mmm) cc_final: 0.8749 (mmm) REVERT: A 422 ARG cc_start: 0.8863 (ttp80) cc_final: 0.8629 (tmm-80) REVERT: B 8 GLN cc_start: 0.8726 (mt0) cc_final: 0.8207 (mt0) REVERT: B 68 VAL cc_start: 0.9413 (p) cc_final: 0.9140 (m) REVERT: B 119 LEU cc_start: 0.9810 (tt) cc_final: 0.9376 (tt) REVERT: B 156 LYS cc_start: 0.9544 (mttt) cc_final: 0.9286 (mmtm) REVERT: B 159 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8000 (mt-10) REVERT: B 166 MET cc_start: 0.8194 (mmm) cc_final: 0.7774 (mtm) REVERT: B 218 LYS cc_start: 0.9371 (mptt) cc_final: 0.9109 (mmtm) REVERT: B 302 MET cc_start: 0.8987 (mmm) cc_final: 0.8295 (mtt) REVERT: B 309 HIS cc_start: 0.8801 (m170) cc_final: 0.8544 (m-70) REVERT: B 323 MET cc_start: 0.8048 (mpp) cc_final: 0.7373 (mpp) REVERT: B 325 MET cc_start: 0.8847 (mpp) cc_final: 0.8526 (mpp) REVERT: B 332 MET cc_start: 0.9486 (mmt) cc_final: 0.9267 (mmm) outliers start: 31 outliers final: 24 residues processed: 237 average time/residue: 0.0819 time to fit residues: 27.6138 Evaluate side-chains 229 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 377 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 76 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 10 optimal weight: 40.0000 chunk 13 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 7 optimal weight: 50.0000 chunk 18 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.083176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.064042 restraints weight = 35261.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.066361 restraints weight = 18444.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.067921 restraints weight = 11590.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.068993 restraints weight = 8183.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.069741 restraints weight = 6320.474| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9870 Z= 0.193 Angle : 0.888 20.358 13407 Z= 0.432 Chirality : 0.048 0.376 1505 Planarity : 0.009 0.296 1749 Dihedral : 11.424 176.340 1435 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.13 % Allowed : 26.16 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.24), residues: 1172 helix: 0.67 (0.23), residues: 487 sheet: -0.42 (0.33), residues: 196 loop : -1.15 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 203 TYR 0.017 0.002 TYR C 71 PHE 0.028 0.002 PHE A 149 TRP 0.065 0.003 TRP B 346 HIS 0.010 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 9865) covalent geometry : angle 0.88786 (13407) hydrogen bonds : bond 0.04087 ( 450) hydrogen bonds : angle 5.18175 ( 1341) Misc. bond : bond 0.00535 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: 0.8847 (mmm) cc_final: 0.8355 (tpt) REVERT: C 149 TYR cc_start: 0.8754 (t80) cc_final: 0.8385 (t80) REVERT: C 151 GLU cc_start: 0.9117 (mp0) cc_final: 0.8650 (mp0) REVERT: C 210 LEU cc_start: 0.4773 (OUTLIER) cc_final: 0.3849 (tt) REVERT: C 218 HIS cc_start: 0.8538 (m-70) cc_final: 0.8029 (m-70) REVERT: C 274 GLN cc_start: 0.8994 (mt0) cc_final: 0.8546 (pm20) REVERT: C 301 TYR cc_start: 0.9239 (m-80) cc_final: 0.8960 (m-80) REVERT: C 305 LYS cc_start: 0.9136 (mttp) cc_final: 0.8841 (mtpt) REVERT: C 338 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8709 (t0) REVERT: A 86 LEU cc_start: 0.9412 (mt) cc_final: 0.9114 (mt) REVERT: A 127 ASP cc_start: 0.8871 (m-30) cc_final: 0.8602 (m-30) REVERT: A 154 MET cc_start: 0.9265 (ttt) cc_final: 0.8801 (tmm) REVERT: A 224 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: A 272 TYR cc_start: 0.8605 (t80) cc_final: 0.8270 (t80) REVERT: A 276 ILE cc_start: 0.9382 (tp) cc_final: 0.9178 (tp) REVERT: A 302 MET cc_start: 0.8508 (mtt) cc_final: 0.8218 (mtt) REVERT: A 363 VAL cc_start: 0.9010 (t) cc_final: 0.8702 (p) REVERT: A 372 GLN cc_start: 0.9216 (mp10) cc_final: 0.8793 (mm-40) REVERT: A 375 VAL cc_start: 0.9420 (t) cc_final: 0.9126 (p) REVERT: A 380 ASN cc_start: 0.8640 (t0) cc_final: 0.8406 (t0) REVERT: A 413 MET cc_start: 0.9135 (mmm) cc_final: 0.8770 (mmm) REVERT: A 422 ARG cc_start: 0.8869 (ttp80) cc_final: 0.8659 (tmm-80) REVERT: A 434 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8667 (pm20) REVERT: B 8 GLN cc_start: 0.8794 (mt0) cc_final: 0.8303 (mt0) REVERT: B 156 LYS cc_start: 0.9605 (mttt) cc_final: 0.9361 (mmtm) REVERT: B 159 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7978 (mt-10) REVERT: B 166 MET cc_start: 0.8339 (mmm) cc_final: 0.7709 (mtt) REVERT: B 202 TYR cc_start: 0.9004 (m-80) cc_final: 0.8238 (m-80) REVERT: B 302 MET cc_start: 0.9054 (mmm) cc_final: 0.8138 (mtp) REVERT: B 309 HIS cc_start: 0.8898 (m170) cc_final: 0.8546 (m90) REVERT: B 325 MET cc_start: 0.8913 (mpp) cc_final: 0.8535 (mpp) REVERT: B 332 MET cc_start: 0.9527 (mmt) cc_final: 0.9275 (mmm) REVERT: B 342 TYR cc_start: 0.8905 (m-80) cc_final: 0.8446 (m-80) outliers start: 31 outliers final: 26 residues processed: 218 average time/residue: 0.0788 time to fit residues: 24.4265 Evaluate side-chains 223 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 422 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 114 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 50 optimal weight: 30.0000 chunk 12 optimal weight: 0.0670 chunk 113 optimal weight: 6.9990 chunk 18 optimal weight: 30.0000 chunk 5 optimal weight: 0.0670 overall best weight: 4.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.085455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.065554 restraints weight = 35265.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.067902 restraints weight = 18382.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.069465 restraints weight = 11605.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.070556 restraints weight = 8245.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.071296 restraints weight = 6399.657| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9870 Z= 0.148 Angle : 0.879 19.343 13407 Z= 0.419 Chirality : 0.048 0.342 1505 Planarity : 0.008 0.302 1749 Dihedral : 11.262 172.191 1435 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.63 % Allowed : 26.77 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.24), residues: 1172 helix: 0.70 (0.23), residues: 486 sheet: -0.37 (0.35), residues: 185 loop : -1.13 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 400 TYR 0.014 0.001 TYR C 71 PHE 0.026 0.001 PHE A 149 TRP 0.044 0.002 TRP B 346 HIS 0.012 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9865) covalent geometry : angle 0.87856 (13407) hydrogen bonds : bond 0.03973 ( 450) hydrogen bonds : angle 5.05922 ( 1341) Misc. bond : bond 0.00422 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1441.05 seconds wall clock time: 25 minutes 44.76 seconds (1544.76 seconds total)