Starting phenix.real_space_refine on Thu Jul 2 19:14:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rx0_24721/07_2026/7rx0_24721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rx0_24721/07_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_24721/07_2026/7rx0_24721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rx0_24721/07_2026/7rx0_24721.map" model { file = "/net/cci-nas-00/data/ceres_data/7rx0_24721/07_2026/7rx0_24721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rx0_24721/07_2026/7rx0_24721.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rx0_24721/07_2026/7rx0_24721.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rx0_24721/07_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-dev-6108/lib/python3.11/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: 1.70, per 1000 atoms: 0.18 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: 0.76 Conformation dependent library (CDL) restraints added in 209.3 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: 0.16 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: 1.29 Time building geometry restraints manager: 0.92 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: 5741 33.70 - 67.39: 97 67.39 - 101.08: 12 101.08 - 134.78: 2 134.78 - 168.47: 4 Dihedral angle restraints: 5856 sinusoidal: 2226 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 5853 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: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.620 Find NCS groups from input model: 0.040 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 : 15.164 168.471 3520 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/Z covalent geometry : bond 0.00620 / 0.32 ( 9865) covalent geometry : angle 0.85406 / 0.46 (13407) hydrogen bonds : bond 0.14830 / 10.29 ( 450) hydrogen bonds : angle 7.13003 / 4.99 ( 1341) Misc. bond : bond 0.70893 / 40.61 ( 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 : 0.208 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: 0.0851 time to fit residues: 34.3591 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 : 0.232 ------------------------------------------------------------------------------- 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... ** 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 = 0.3727 r_free = 0.3727 target = 0.084878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.066507 restraints weight = 34660.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.068808 restraints weight = 18056.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.070367 restraints weight = 11286.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.071401 restraints weight = 7929.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.072068 restraints weight = 6094.079| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 14 (20 function evaluations) r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9870 Z= 0.181 Angle : 0.746 9.427 13407 Z= 0.372 Chirality : 0.045 0.217 1505 Planarity : 0.005 0.083 1749 Dihedral : 10.235 153.030 1379 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.73 % Allowed : 16.46 % Favored : 80.81 % 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: -1.17 (0.24), residues: 1172 helix: 0.12 (0.23), residues: 481 sheet: -0.96 (0.34), residues: 194 loop : -1.51 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 154 TYR 0.041 0.002 TYR C 71 PHE 0.019 0.002 PHE B 262 TRP 0.016 0.002 TRP A 21 HIS 0.007 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 9865) covalent geometry : angle 0.74591 / 0.37 (13407) hydrogen bonds : bond 0.04663 / 3.20 ( 450) hydrogen bonds : angle 5.64742 / 3.95 ( 1341) Misc. bond : bond 0.00159 / 0.08 ( 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 275 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.8772 (t80) cc_final: 0.8306 (t80) REVERT: C 119 ILE cc_start: 0.8586 (mt) cc_final: 0.8329 (mm) REVERT: C 151 GLU cc_start: 0.9048 (mp0) cc_final: 0.8338 (mp0) REVERT: C 205 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7100 (t) REVERT: C 218 HIS cc_start: 0.8454 (m-70) cc_final: 0.7829 (m-70) REVERT: C 274 GLN cc_start: 0.9164 (mt0) cc_final: 0.8545 (pp30) REVERT: C 301 TYR cc_start: 0.9215 (m-80) cc_final: 0.8671 (m-80) REVERT: C 305 LYS cc_start: 0.9265 (mttp) cc_final: 0.8982 (mtpt) REVERT: A 86 LEU cc_start: 0.9359 (mt) cc_final: 0.8927 (mt) REVERT: A 127 ASP cc_start: 0.8771 (m-30) cc_final: 0.8512 (m-30) REVERT: A 196 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8314 (mm-30) REVERT: A 216 ASN cc_start: 0.8985 (m-40) cc_final: 0.8718 (m110) REVERT: A 272 TYR cc_start: 0.8458 (t80) cc_final: 0.8094 (t80) REVERT: A 302 MET cc_start: 0.8335 (mtt) cc_final: 0.8030 (mtt) REVERT: A 363 VAL cc_start: 0.9271 (t) cc_final: 0.8954 (p) REVERT: A 372 GLN cc_start: 0.8893 (mp10) cc_final: 0.8653 (mm-40) REVERT: A 398 MET cc_start: 0.9131 (mpp) cc_final: 0.8807 (mmp) REVERT: A 413 MET cc_start: 0.9181 (mmm) cc_final: 0.8943 (mmm) REVERT: A 430 LYS cc_start: 0.9520 (tptt) cc_final: 0.9140 (tppt) REVERT: A 433 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8713 (tm-30) REVERT: A 434 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8516 (mt-10) REVERT: B 37 HIS cc_start: 0.8642 (m-70) cc_final: 0.8083 (m90) REVERT: B 107 HIS cc_start: 0.8432 (t70) cc_final: 0.7767 (t70) REVERT: B 108 TYR cc_start: 0.8485 (t80) cc_final: 0.8128 (t80) REVERT: B 124 LYS cc_start: 0.9514 (tttp) cc_final: 0.9296 (ttmt) REVERT: B 156 LYS cc_start: 0.9511 (mttt) cc_final: 0.9248 (mmtm) REVERT: B 166 MET cc_start: 0.7537 (mmm) cc_final: 0.7276 (mtm) REVERT: B 199 ASP cc_start: 0.8607 (m-30) cc_final: 0.8033 (m-30) REVERT: B 211 ASP cc_start: 0.9132 (OUTLIER) cc_final: 0.8402 (t0) REVERT: B 219 LEU cc_start: 0.8619 (mt) cc_final: 0.8238 (mt) REVERT: B 302 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8374 (mtt) REVERT: B 306 ASP cc_start: 0.8964 (m-30) cc_final: 0.8612 (t0) REVERT: B 309 HIS cc_start: 0.8817 (m170) cc_final: 0.8032 (m-70) REVERT: B 323 MET cc_start: 0.8061 (mpp) cc_final: 0.6421 (mpp) REVERT: B 332 MET cc_start: 0.9248 (mmt) cc_final: 0.8886 (mmm) REVERT: B 373 MET cc_start: 0.8608 (ptp) cc_final: 0.8165 (mtp) REVERT: B 391 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9257 (mp) REVERT: B 413 MET cc_start: 0.9144 (mmm) cc_final: 0.8314 (mmm) outliers start: 27 outliers final: 13 residues processed: 260 average time/residue: 0.0793 time to fit residues: 28.6552 Evaluate side-chains 224 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 C residue 338 ASN 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: 40.0000 chunk 33 optimal weight: 60.0000 chunk 6 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 77 optimal weight: 30.0000 chunk 105 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 30.0000 chunk 72 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 overall best weight: 11.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.082045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.064169 restraints weight = 35575.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.066374 restraints weight = 18506.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.067832 restraints weight = 11583.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.068835 restraints weight = 8145.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.069471 restraints weight = 6249.963| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9870 Z= 0.218 Angle : 0.753 11.780 13407 Z= 0.379 Chirality : 0.045 0.162 1505 Planarity : 0.010 0.382 1749 Dihedral : 10.293 162.989 1379 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.24 % Allowed : 18.69 % Favored : 77.07 % 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: -0.90 (0.24), residues: 1172 helix: 0.42 (0.23), residues: 479 sheet: -0.85 (0.32), residues: 204 loop : -1.45 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG C 203 TYR 0.028 0.002 TYR C 71 PHE 0.014 0.002 PHE B 262 TRP 0.025 0.002 TRP B 346 HIS 0.007 0.002 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.22 ( 9865) covalent geometry : angle 0.75324 / 0.38 (13407) hydrogen bonds : bond 0.04407 / 3.05 ( 450) hydrogen bonds : angle 5.49373 / 3.86 ( 1341) Misc. bond : bond 0.00285 / 0.14 ( 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 258 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 0.348 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: 0.8910 (t80) cc_final: 0.8423 (t80) REVERT: C 119 ILE cc_start: 0.8658 (mt) cc_final: 0.8419 (mm) REVERT: C 145 TYR cc_start: 0.8607 (t80) cc_final: 0.8287 (t80) REVERT: C 151 GLU cc_start: 0.8952 (mp0) cc_final: 0.8186 (mp0) REVERT: C 218 HIS cc_start: 0.8514 (m-70) cc_final: 0.7844 (m-70) REVERT: C 274 GLN cc_start: 0.9084 (mt0) cc_final: 0.8458 (pp30) REVERT: C 301 TYR cc_start: 0.9273 (m-80) cc_final: 0.8749 (m-80) REVERT: C 305 LYS cc_start: 0.9290 (mttp) cc_final: 0.9004 (mtpt) REVERT: A 86 LEU cc_start: 0.9356 (mt) cc_final: 0.9034 (mt) REVERT: A 127 ASP cc_start: 0.8835 (m-30) cc_final: 0.8597 (m-30) REVERT: A 196 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8212 (mm-30) REVERT: A 272 TYR cc_start: 0.8544 (t80) cc_final: 0.8251 (t80) REVERT: A 302 MET cc_start: 0.8357 (mtt) cc_final: 0.7989 (mtt) REVERT: A 363 VAL cc_start: 0.9259 (t) cc_final: 0.8961 (p) REVERT: A 372 GLN cc_start: 0.8980 (mp10) cc_final: 0.8706 (mm-40) REVERT: B 107 HIS cc_start: 0.8342 (t70) cc_final: 0.7704 (t70) REVERT: B 156 LYS cc_start: 0.9554 (mttt) cc_final: 0.9221 (mmpt) REVERT: B 166 MET cc_start: 0.7947 (mmm) cc_final: 0.7584 (mtm) REVERT: B 199 ASP cc_start: 0.8719 (m-30) cc_final: 0.7809 (m-30) REVERT: B 219 LEU cc_start: 0.8637 (mt) cc_final: 0.8272 (mt) REVERT: B 302 MET cc_start: 0.9068 (mmm) cc_final: 0.8355 (mtt) REVERT: B 306 ASP cc_start: 0.8903 (m-30) cc_final: 0.8637 (m-30) REVERT: B 309 HIS cc_start: 0.8752 (m170) cc_final: 0.8268 (m90) REVERT: B 323 MET cc_start: 0.7983 (mpp) cc_final: 0.6585 (mpp) REVERT: B 332 MET cc_start: 0.9287 (mmt) cc_final: 0.8957 (mmm) REVERT: B 373 MET cc_start: 0.8603 (ptp) cc_final: 0.8111 (mtp) REVERT: B 416 MET cc_start: 0.8657 (ptp) cc_final: 0.8061 (tpt) REVERT: B 419 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.8441 (p) REVERT: B 422 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8708 (pp20) outliers start: 42 outliers final: 23 residues processed: 239 average time/residue: 0.0769 time to fit residues: 26.0044 Evaluate side-chains 218 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 269 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 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 68 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: 9.9990 chunk 52 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 2 optimal weight: 50.0000 chunk 74 optimal weight: 50.0000 chunk 14 optimal weight: 9.9990 chunk 100 optimal weight: 30.0000 chunk 68 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 72 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN A 15 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.082635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.064454 restraints weight = 35284.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066656 restraints weight = 18394.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.068118 restraints weight = 11522.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.069099 restraints weight = 8129.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.069782 restraints weight = 6304.371| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9870 Z= 0.179 Angle : 0.737 12.079 13407 Z= 0.365 Chirality : 0.044 0.176 1505 Planarity : 0.004 0.043 1749 Dihedral : 10.085 167.498 1379 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.14 % Allowed : 20.91 % Favored : 74.95 % 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: -0.58 (0.24), residues: 1172 helix: 0.73 (0.23), residues: 481 sheet: -0.68 (0.33), residues: 198 loop : -1.34 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 203 TYR 0.023 0.002 TYR A 224 PHE 0.015 0.002 PHE C 333 TRP 0.028 0.002 TRP B 346 HIS 0.007 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 ( 9865) covalent geometry : angle 0.73702 / 0.36 (13407) hydrogen bonds : bond 0.04228 / 2.93 ( 450) hydrogen bonds : angle 5.29999 / 3.71 ( 1341) Misc. bond : bond 0.00553 / 0.28 ( 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 255 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 0.305 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: 0.8912 (t80) cc_final: 0.8545 (t80) REVERT: C 119 ILE cc_start: 0.8667 (mt) cc_final: 0.8352 (mm) REVERT: C 124 MET cc_start: 0.9016 (mmm) cc_final: 0.8679 (mmm) REVERT: C 151 GLU cc_start: 0.8965 (mp0) cc_final: 0.8182 (mp0) REVERT: C 166 ILE cc_start: 0.9280 (pp) cc_final: 0.8981 (tt) REVERT: C 182 LYS cc_start: 0.8784 (tptp) cc_final: 0.8559 (tptp) REVERT: C 205 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7731 (t) REVERT: C 218 HIS cc_start: 0.8556 (m-70) cc_final: 0.7850 (m-70) REVERT: C 274 GLN cc_start: 0.9040 (mt0) cc_final: 0.8425 (pp30) REVERT: C 301 TYR cc_start: 0.9299 (m-80) cc_final: 0.8780 (m-80) REVERT: C 305 LYS cc_start: 0.9281 (mttp) cc_final: 0.8968 (mtpt) REVERT: C 338 ASN cc_start: 0.9088 (OUTLIER) cc_final: 0.8689 (t0) REVERT: A 86 LEU cc_start: 0.9311 (mt) cc_final: 0.8952 (mt) REVERT: A 127 ASP cc_start: 0.8842 (m-30) cc_final: 0.8596 (m-30) REVERT: A 196 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8383 (mm-30) REVERT: A 272 TYR cc_start: 0.8511 (t80) cc_final: 0.8173 (t80) REVERT: A 285 GLN cc_start: 0.3036 (OUTLIER) cc_final: 0.1947 (mt0) REVERT: A 302 MET cc_start: 0.8475 (mtt) cc_final: 0.8060 (mtt) REVERT: A 363 VAL cc_start: 0.9254 (t) cc_final: 0.8939 (p) REVERT: A 372 GLN cc_start: 0.9076 (mp10) cc_final: 0.8822 (mm-40) REVERT: B 107 HIS cc_start: 0.8381 (t70) cc_final: 0.7747 (t70) REVERT: B 156 LYS cc_start: 0.9557 (mttt) cc_final: 0.9151 (mmtm) REVERT: B 159 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7820 (mt-10) REVERT: B 166 MET cc_start: 0.7914 (mmm) cc_final: 0.7623 (mtm) REVERT: B 219 LEU cc_start: 0.8692 (mt) cc_final: 0.8333 (mt) REVERT: B 269 MET cc_start: 0.8157 (pmm) cc_final: 0.7939 (pmm) REVERT: B 302 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8464 (mtt) REVERT: B 306 ASP cc_start: 0.8908 (m-30) cc_final: 0.8665 (t0) REVERT: B 309 HIS cc_start: 0.8717 (m170) cc_final: 0.7905 (m-70) REVERT: B 323 MET cc_start: 0.8004 (mpp) cc_final: 0.6603 (mpp) REVERT: B 332 MET cc_start: 0.9316 (mmt) cc_final: 0.8957 (mmm) REVERT: B 373 MET cc_start: 0.8608 (ptp) cc_final: 0.8143 (mtp) REVERT: B 391 ILE cc_start: 0.9327 (mp) cc_final: 0.9052 (tt) outliers start: 41 outliers final: 26 residues processed: 242 average time/residue: 0.0698 time to fit residues: 24.0772 Evaluate side-chains 226 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 205 THR 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 75 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 290 GLU 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 68 VAL 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 376 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 44 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 108 optimal weight: 0.0770 chunk 80 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 35 optimal weight: 50.0000 chunk 64 optimal weight: 3.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.084393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.065870 restraints weight = 34741.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.068114 restraints weight = 18247.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.069594 restraints weight = 11541.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.070617 restraints weight = 8226.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.071279 restraints weight = 6352.303| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9870 Z= 0.140 Angle : 0.720 14.213 13407 Z= 0.355 Chirality : 0.044 0.183 1505 Planarity : 0.004 0.040 1749 Dihedral : 9.925 165.476 1379 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.94 % Allowed : 21.01 % 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: -0.45 (0.24), residues: 1172 helix: 0.79 (0.23), residues: 480 sheet: -0.59 (0.34), residues: 197 loop : -1.22 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 203 TYR 0.017 0.001 TYR A 224 PHE 0.021 0.001 PHE B 262 TRP 0.032 0.002 TRP B 346 HIS 0.009 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 9865) covalent geometry : angle 0.71977 / 0.35 (13407) hydrogen bonds : bond 0.04011 / 2.74 ( 450) hydrogen bonds : angle 5.09011 / 3.57 ( 1341) Misc. bond : bond 0.00414 / 0.21 ( 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 259 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 0.286 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 71 TYR cc_start: 0.8984 (t80) cc_final: 0.8646 (t80) REVERT: C 119 ILE cc_start: 0.8714 (mt) cc_final: 0.8289 (mm) REVERT: C 124 MET cc_start: 0.8956 (mmm) cc_final: 0.8616 (mmm) REVERT: C 146 LEU cc_start: 0.9080 (pt) cc_final: 0.8667 (tt) REVERT: C 151 GLU cc_start: 0.9027 (mp0) cc_final: 0.8527 (mp0) REVERT: C 166 ILE cc_start: 0.9297 (pp) cc_final: 0.9034 (tt) REVERT: C 205 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7260 (t) REVERT: C 218 HIS cc_start: 0.8570 (m-70) cc_final: 0.7846 (m-70) REVERT: C 274 GLN cc_start: 0.9037 (mt0) cc_final: 0.8456 (pm20) REVERT: C 301 TYR cc_start: 0.9289 (m-80) cc_final: 0.8783 (m-80) REVERT: C 305 LYS cc_start: 0.9289 (mttp) cc_final: 0.8968 (mtpt) REVERT: C 338 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8717 (t0) REVERT: A 21 TRP cc_start: 0.9218 (m100) cc_final: 0.8841 (m100) REVERT: A 22 GLU cc_start: 0.8866 (pt0) cc_final: 0.8429 (pt0) REVERT: A 86 LEU cc_start: 0.9358 (mt) cc_final: 0.9021 (mt) REVERT: A 127 ASP cc_start: 0.8832 (m-30) cc_final: 0.8582 (m-30) REVERT: A 196 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8327 (mm-30) REVERT: A 272 TYR cc_start: 0.8528 (t80) cc_final: 0.8167 (t80) REVERT: A 276 ILE cc_start: 0.9510 (tp) cc_final: 0.9264 (tp) REVERT: A 302 MET cc_start: 0.8387 (mtt) cc_final: 0.8118 (mtt) REVERT: A 313 MET cc_start: 0.6470 (tpt) cc_final: 0.6004 (tpt) REVERT: A 363 VAL cc_start: 0.9257 (t) cc_final: 0.8941 (p) REVERT: A 372 GLN cc_start: 0.9044 (mp10) cc_final: 0.8742 (mm-40) REVERT: A 375 VAL cc_start: 0.9390 (t) cc_final: 0.9123 (p) REVERT: A 377 MET cc_start: 0.8460 (tmm) cc_final: 0.8030 (tmm) REVERT: A 413 MET cc_start: 0.9065 (mmm) cc_final: 0.8663 (mmm) REVERT: B 8 GLN cc_start: 0.8588 (mt0) cc_final: 0.8087 (mt0) REVERT: B 107 HIS cc_start: 0.8462 (t70) cc_final: 0.7736 (t70) REVERT: B 156 LYS cc_start: 0.9545 (mttt) cc_final: 0.9198 (mmtm) REVERT: B 159 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7943 (mt-10) REVERT: B 211 ASP cc_start: 0.9207 (OUTLIER) cc_final: 0.8999 (t0) REVERT: B 302 MET cc_start: 0.8987 (mmm) cc_final: 0.8502 (mtt) REVERT: B 309 HIS cc_start: 0.8678 (m170) cc_final: 0.8295 (m90) REVERT: B 323 MET cc_start: 0.7970 (mpp) cc_final: 0.6455 (mpp) REVERT: B 332 MET cc_start: 0.9329 (mmt) cc_final: 0.8977 (mmm) REVERT: B 373 MET cc_start: 0.8559 (ptp) cc_final: 0.8231 (mtp) REVERT: B 416 MET cc_start: 0.8602 (ptp) cc_final: 0.8136 (tpt) outliers start: 39 outliers final: 24 residues processed: 244 average time/residue: 0.0740 time to fit residues: 25.6199 Evaluate side-chains 233 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 205 THR Chi-restraints excluded: chain C residue 210 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 75 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 205 ASP 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 33 THR Chi-restraints excluded: chain B residue 68 VAL 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 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: 6.9990 chunk 41 optimal weight: 9.9990 chunk 12 optimal weight: 40.0000 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 26 optimal weight: 30.0000 chunk 9 optimal weight: 50.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 72 GLN ** C 117 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** B 59 ASN ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.083578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.065297 restraints weight = 35002.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.067510 restraints weight = 18479.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.068981 restraints weight = 11732.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.069955 restraints weight = 8350.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.070682 restraints weight = 6498.941| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9870 Z= 0.163 Angle : 0.768 14.471 13407 Z= 0.375 Chirality : 0.045 0.225 1505 Planarity : 0.010 0.402 1749 Dihedral : 10.480 169.474 1379 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.84 % Allowed : 23.13 % Favored : 73.03 % 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: -0.41 (0.24), residues: 1172 helix: 0.81 (0.23), residues: 481 sheet: -0.55 (0.33), residues: 198 loop : -1.18 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 203 TYR 0.018 0.001 TYR C 149 PHE 0.017 0.001 PHE B 262 TRP 0.034 0.002 TRP B 346 HIS 0.006 0.001 HIS C 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 9865) covalent geometry : angle 0.76847 / 0.38 (13407) hydrogen bonds : bond 0.04029 / 2.79 ( 450) hydrogen bonds : angle 5.09960 / 3.57 ( 1341) Misc. bond : bond 0.00363 / 0.18 ( 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 242 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.233 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: 0.9022 (t80) cc_final: 0.8572 (t80) REVERT: C 151 GLU cc_start: 0.9072 (mp0) cc_final: 0.8569 (mp0) REVERT: C 166 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9112 (tt) REVERT: C 173 ARG cc_start: 0.9015 (mmm160) cc_final: 0.8791 (tpp-160) REVERT: C 205 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.6994 (t) REVERT: C 218 HIS cc_start: 0.8586 (m-70) cc_final: 0.7905 (m-70) REVERT: C 252 ASP cc_start: 0.8757 (t0) cc_final: 0.8300 (t0) REVERT: C 274 GLN cc_start: 0.8995 (mt0) cc_final: 0.8453 (pm20) REVERT: C 301 TYR cc_start: 0.9265 (m-80) cc_final: 0.8829 (m-80) REVERT: C 305 LYS cc_start: 0.9265 (mttp) cc_final: 0.8953 (mtpt) REVERT: C 338 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8725 (t0) REVERT: A 86 LEU cc_start: 0.9355 (mt) cc_final: 0.8987 (mt) REVERT: A 127 ASP cc_start: 0.8828 (m-30) cc_final: 0.8600 (m-30) REVERT: A 196 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8336 (mm-30) REVERT: A 203 MET cc_start: 0.7807 (ttt) cc_final: 0.7053 (tpt) REVERT: A 272 TYR cc_start: 0.8543 (t80) cc_final: 0.8221 (t80) REVERT: A 276 ILE cc_start: 0.9514 (tp) cc_final: 0.9296 (tp) REVERT: A 285 GLN cc_start: 0.3108 (OUTLIER) cc_final: 0.1922 (mt0) REVERT: A 302 MET cc_start: 0.8401 (mtt) cc_final: 0.8157 (mtt) REVERT: A 363 VAL cc_start: 0.9282 (t) cc_final: 0.8770 (p) REVERT: A 372 GLN cc_start: 0.9079 (mp10) cc_final: 0.8759 (mm-40) REVERT: A 375 VAL cc_start: 0.9415 (t) cc_final: 0.9151 (p) REVERT: A 413 MET cc_start: 0.9201 (mmm) cc_final: 0.8829 (mmm) REVERT: B 8 GLN cc_start: 0.8532 (mt0) cc_final: 0.8140 (mt0) REVERT: B 107 HIS cc_start: 0.8506 (t70) cc_final: 0.7906 (t70) REVERT: B 156 LYS cc_start: 0.9571 (mttt) cc_final: 0.9146 (mmtm) REVERT: B 159 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7945 (mt-10) REVERT: B 302 MET cc_start: 0.8980 (mmm) cc_final: 0.8483 (mtt) REVERT: B 309 HIS cc_start: 0.8655 (m170) cc_final: 0.8287 (m90) REVERT: B 323 MET cc_start: 0.7857 (mpp) cc_final: 0.7320 (mpp) REVERT: B 332 MET cc_start: 0.9353 (mmt) cc_final: 0.8996 (mmm) REVERT: B 391 ILE cc_start: 0.9374 (mp) cc_final: 0.8992 (tt) REVERT: B 416 MET cc_start: 0.8618 (ptp) cc_final: 0.8082 (tpt) outliers start: 38 outliers final: 29 residues processed: 228 average time/residue: 0.0711 time to fit residues: 22.9797 Evaluate side-chains 226 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 166 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 THR 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 62 VAL 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 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 A residue 434 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 68 VAL 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 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: 6.9990 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 30.0000 chunk 50 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 15 optimal weight: 50.0000 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 40.0000 chunk 88 optimal weight: 6.9990 chunk 121 optimal weight: 30.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 72 GLN ** B 6 HIS ** 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 = 0.3694 r_free = 0.3694 target = 0.083292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.064816 restraints weight = 34967.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.066999 restraints weight = 18849.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.068489 restraints weight = 12053.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.069452 restraints weight = 8615.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.070158 restraints weight = 6744.148| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9870 Z= 0.173 Angle : 0.787 18.188 13407 Z= 0.381 Chirality : 0.045 0.193 1505 Planarity : 0.010 0.375 1749 Dihedral : 10.681 173.750 1379 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.44 % Allowed : 23.94 % Favored : 71.62 % 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: 0.81 (0.23), residues: 482 sheet: -0.54 (0.33), residues: 198 loop : -1.17 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 203 TYR 0.017 0.001 TYR C 149 PHE 0.019 0.002 PHE B 262 TRP 0.032 0.002 TRP B 346 HIS 0.011 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 9865) covalent geometry : angle 0.78655 / 0.38 (13407) hydrogen bonds : bond 0.03962 / 2.73 ( 450) hydrogen bonds : angle 5.12891 / 3.58 ( 1341) Misc. bond : bond 0.00334 / 0.17 ( 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 244 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 0.204 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: 0.8850 (t80) cc_final: 0.8641 (t80) REVERT: C 151 GLU cc_start: 0.9153 (mp0) cc_final: 0.8659 (mp0) REVERT: C 173 ARG cc_start: 0.9021 (mmm160) cc_final: 0.8820 (tpp-160) REVERT: C 205 THR cc_start: 0.7685 (OUTLIER) cc_final: 0.7106 (t) REVERT: C 218 HIS cc_start: 0.8584 (m-70) cc_final: 0.7903 (m-70) REVERT: C 274 GLN cc_start: 0.8985 (mt0) cc_final: 0.8446 (pm20) REVERT: C 301 TYR cc_start: 0.9233 (m-80) cc_final: 0.8805 (m-80) REVERT: C 305 LYS cc_start: 0.9260 (mttp) cc_final: 0.8969 (mtpt) REVERT: C 338 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8762 (t0) REVERT: A 86 LEU cc_start: 0.9390 (mt) cc_final: 0.9003 (mt) REVERT: A 127 ASP cc_start: 0.8827 (m-30) cc_final: 0.8588 (m-30) REVERT: A 203 MET cc_start: 0.7868 (ttt) cc_final: 0.7264 (tpt) REVERT: A 224 TYR cc_start: 0.9218 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: A 272 TYR cc_start: 0.8564 (t80) cc_final: 0.8205 (t80) REVERT: A 302 MET cc_start: 0.8332 (mtt) cc_final: 0.8077 (mtt) REVERT: A 363 VAL cc_start: 0.8985 (t) cc_final: 0.8756 (p) REVERT: A 372 GLN cc_start: 0.9089 (mp10) cc_final: 0.8760 (mm-40) REVERT: A 375 VAL cc_start: 0.9410 (t) cc_final: 0.9153 (p) REVERT: A 377 MET cc_start: 0.8368 (tmm) cc_final: 0.7980 (tmm) REVERT: A 380 ASN cc_start: 0.7778 (m-40) cc_final: 0.7551 (m-40) REVERT: A 398 MET cc_start: 0.9078 (mpp) cc_final: 0.8709 (mmp) REVERT: A 413 MET cc_start: 0.9226 (mmm) cc_final: 0.8884 (mmm) REVERT: B 8 GLN cc_start: 0.8536 (mt0) cc_final: 0.8247 (mt0) REVERT: B 302 MET cc_start: 0.8975 (mmm) cc_final: 0.8563 (mtt) REVERT: B 309 HIS cc_start: 0.8653 (m170) cc_final: 0.8389 (m-70) REVERT: B 323 MET cc_start: 0.8151 (mpp) cc_final: 0.6700 (mpp) REVERT: B 325 MET cc_start: 0.8543 (mpp) cc_final: 0.8003 (mpp) REVERT: B 332 MET cc_start: 0.9364 (mmt) cc_final: 0.9002 (mmm) REVERT: B 400 ARG cc_start: 0.7841 (ttm110) cc_final: 0.7437 (mtm110) REVERT: B 416 MET cc_start: 0.8608 (ptp) cc_final: 0.8062 (tpt) outliers start: 44 outliers final: 27 residues processed: 224 average time/residue: 0.0682 time to fit residues: 22.0537 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 : 0.291 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain C residue 205 THR 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 5 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 68 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 3 optimal weight: 50.0000 chunk 56 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 102 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 20 optimal weight: 50.0000 chunk 84 optimal weight: 4.9990 chunk 38 optimal weight: 60.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 72 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** B 6 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.083511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.063954 restraints weight = 35086.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.066281 restraints weight = 18170.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.067851 restraints weight = 11441.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.068939 restraints weight = 8109.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.069649 restraints weight = 6262.200| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9870 Z= 0.158 Angle : 0.803 19.465 13407 Z= 0.388 Chirality : 0.046 0.272 1505 Planarity : 0.010 0.365 1749 Dihedral : 10.692 172.746 1379 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.54 % Allowed : 24.85 % Favored : 71.62 % 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: -0.36 (0.24), residues: 1172 helix: 0.80 (0.23), residues: 483 sheet: -0.51 (0.34), residues: 197 loop : -1.10 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 278 TYR 0.018 0.001 TYR B 224 PHE 0.018 0.001 PHE B 262 TRP 0.026 0.002 TRP B 346 HIS 0.012 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 9865) covalent geometry : angle 0.80282 / 0.39 (13407) hydrogen bonds : bond 0.03951 / 2.73 ( 450) hydrogen bonds : angle 5.10106 / 3.56 ( 1341) Misc. bond : bond 0.00423 / 0.21 ( 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 238 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.268 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 102 TYR cc_start: 0.7298 (t80) cc_final: 0.7056 (t80) REVERT: C 149 TYR cc_start: 0.8806 (t80) cc_final: 0.8489 (t80) REVERT: C 151 GLU cc_start: 0.9082 (mp0) cc_final: 0.8506 (mp0) REVERT: C 173 ARG cc_start: 0.9053 (mmm160) cc_final: 0.8827 (tpp-160) REVERT: C 193 LEU cc_start: 0.9077 (tp) cc_final: 0.8872 (pp) REVERT: C 218 HIS cc_start: 0.8458 (m-70) cc_final: 0.7816 (m-70) REVERT: C 274 GLN cc_start: 0.8977 (mt0) cc_final: 0.8427 (pp30) REVERT: C 301 TYR cc_start: 0.9213 (m-80) cc_final: 0.8902 (m-80) REVERT: C 305 LYS cc_start: 0.9254 (mttp) cc_final: 0.8935 (mtpt) REVERT: C 338 ASN cc_start: 0.9085 (OUTLIER) cc_final: 0.8752 (t0) REVERT: A 86 LEU cc_start: 0.9433 (mt) cc_final: 0.9004 (mt) REVERT: A 127 ASP cc_start: 0.8895 (m-30) cc_final: 0.8628 (m-30) REVERT: A 203 MET cc_start: 0.7754 (ttt) cc_final: 0.7072 (tpt) REVERT: A 224 TYR cc_start: 0.9173 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: A 272 TYR cc_start: 0.8556 (t80) cc_final: 0.8198 (t80) REVERT: A 302 MET cc_start: 0.8495 (mtt) cc_final: 0.8077 (mtt) REVERT: A 304 LYS cc_start: 0.9078 (tttm) cc_final: 0.8750 (tttt) REVERT: A 363 VAL cc_start: 0.8908 (t) cc_final: 0.8640 (p) REVERT: A 372 GLN cc_start: 0.9155 (mp10) cc_final: 0.8815 (mm-40) REVERT: A 375 VAL cc_start: 0.9429 (t) cc_final: 0.9134 (p) REVERT: A 377 MET cc_start: 0.8517 (tmm) cc_final: 0.8071 (tmm) REVERT: A 380 ASN cc_start: 0.7685 (m-40) cc_final: 0.7445 (m-40) REVERT: A 398 MET cc_start: 0.9166 (mpp) cc_final: 0.8769 (mmp) REVERT: A 413 MET cc_start: 0.9245 (mmm) cc_final: 0.8900 (mmm) REVERT: A 422 ARG cc_start: 0.8920 (ttp80) cc_final: 0.8719 (tmm-80) REVERT: B 8 GLN cc_start: 0.8762 (mt0) cc_final: 0.8211 (mt0) REVERT: B 156 LYS cc_start: 0.9557 (mttt) cc_final: 0.9264 (tppt) REVERT: B 265 LEU cc_start: 0.8998 (mt) cc_final: 0.8794 (mp) REVERT: B 302 MET cc_start: 0.9194 (mmm) cc_final: 0.8433 (mtt) REVERT: B 309 HIS cc_start: 0.8808 (m170) cc_final: 0.8560 (m-70) REVERT: B 323 MET cc_start: 0.8123 (mpp) cc_final: 0.7493 (mpp) REVERT: B 325 MET cc_start: 0.8664 (mpp) cc_final: 0.8362 (mpp) REVERT: B 332 MET cc_start: 0.9503 (mmt) cc_final: 0.9139 (mmm) REVERT: B 400 ARG cc_start: 0.8029 (ttm110) cc_final: 0.7811 (mtt180) REVERT: B 416 MET cc_start: 0.8734 (ptp) cc_final: 0.8086 (tpt) outliers start: 35 outliers final: 27 residues processed: 223 average time/residue: 0.0720 time to fit residues: 22.8780 Evaluate side-chains 223 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 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 5 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 68 VAL 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 376 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 398 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 63 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 37 optimal weight: 50.0000 chunk 56 optimal weight: 20.0000 chunk 100 optimal weight: 0.0980 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 29 optimal weight: 50.0000 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** B 300 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 = 0.3675 r_free = 0.3675 target = 0.084081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.064649 restraints weight = 34654.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.067000 restraints weight = 17951.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.068585 restraints weight = 11284.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.069640 restraints weight = 7982.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.070415 restraints weight = 6174.747| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 9870 Z= 0.164 Angle : 0.868 18.925 13407 Z= 0.422 Chirality : 0.048 0.386 1505 Planarity : 0.004 0.043 1749 Dihedral : 10.180 171.563 1379 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 2.93 % Allowed : 25.86 % Favored : 71.21 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.30 (0.25), residues: 1172 helix: 0.82 (0.23), residues: 487 sheet: -0.42 (0.34), residues: 197 loop : -1.08 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG C 203 TYR 0.031 0.002 TYR C 71 PHE 0.018 0.002 PHE B 272 TRP 0.024 0.002 TRP B 346 HIS 0.014 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 9865) covalent geometry : angle 0.86762 / 0.42 (13407) hydrogen bonds : bond 0.04057 / 2.82 ( 450) hydrogen bonds : angle 5.09849 / 3.53 ( 1341) Misc. bond : bond 0.00920 / 0.46 ( 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 236 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.221 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 102 TYR cc_start: 0.7300 (t80) cc_final: 0.7034 (t80) REVERT: C 149 TYR cc_start: 0.8797 (t80) cc_final: 0.8405 (t80) REVERT: C 151 GLU cc_start: 0.9070 (mp0) cc_final: 0.8627 (mp0) REVERT: C 173 ARG cc_start: 0.9037 (mmm160) cc_final: 0.8792 (tpp-160) REVERT: C 190 ASP cc_start: 0.9345 (t0) cc_final: 0.9137 (t0) REVERT: C 193 LEU cc_start: 0.9170 (tp) cc_final: 0.8934 (pp) REVERT: C 218 HIS cc_start: 0.8466 (m-70) cc_final: 0.7817 (m-70) REVERT: C 274 GLN cc_start: 0.8972 (mt0) cc_final: 0.8519 (pm20) REVERT: C 301 TYR cc_start: 0.9195 (m-80) cc_final: 0.8903 (m-80) REVERT: C 305 LYS cc_start: 0.9270 (mttp) cc_final: 0.8953 (mtpt) REVERT: C 338 ASN cc_start: 0.9036 (OUTLIER) cc_final: 0.8677 (t0) REVERT: A 86 LEU cc_start: 0.9454 (mt) cc_final: 0.9048 (mt) REVERT: A 124 LYS cc_start: 0.9604 (ttpt) cc_final: 0.9325 (ttpp) REVERT: A 127 ASP cc_start: 0.8902 (m-30) cc_final: 0.8635 (m-30) REVERT: A 203 MET cc_start: 0.7734 (ttt) cc_final: 0.7053 (tpt) REVERT: A 224 TYR cc_start: 0.9145 (OUTLIER) cc_final: 0.7780 (m-80) REVERT: A 272 TYR cc_start: 0.8544 (t80) cc_final: 0.8178 (t80) REVERT: A 302 MET cc_start: 0.8487 (mtt) cc_final: 0.8072 (mtt) REVERT: A 304 LYS cc_start: 0.9088 (tttm) cc_final: 0.8771 (tttt) REVERT: A 363 VAL cc_start: 0.8920 (t) cc_final: 0.8640 (p) REVERT: A 372 GLN cc_start: 0.9169 (mp10) cc_final: 0.8821 (mm-40) REVERT: A 375 VAL cc_start: 0.9403 (t) cc_final: 0.9037 (p) REVERT: A 377 MET cc_start: 0.8501 (tmm) cc_final: 0.8038 (tmm) REVERT: A 380 ASN cc_start: 0.7644 (m-40) cc_final: 0.7434 (m-40) REVERT: A 398 MET cc_start: 0.9170 (mpp) cc_final: 0.8768 (mmp) REVERT: A 413 MET cc_start: 0.9198 (mmm) cc_final: 0.8826 (mmm) REVERT: A 422 ARG cc_start: 0.8885 (ttp80) cc_final: 0.8649 (tmm-80) REVERT: B 8 GLN cc_start: 0.8766 (mt0) cc_final: 0.8273 (mt0) REVERT: B 68 VAL cc_start: 0.9420 (OUTLIER) cc_final: 0.9145 (m) REVERT: B 119 LEU cc_start: 0.9812 (tt) cc_final: 0.9507 (tt) REVERT: B 156 LYS cc_start: 0.9553 (mttt) cc_final: 0.9246 (tppt) REVERT: B 302 MET cc_start: 0.9200 (mmm) cc_final: 0.8425 (mtt) REVERT: B 309 HIS cc_start: 0.8720 (m170) cc_final: 0.8425 (m-70) REVERT: B 325 MET cc_start: 0.8639 (mpp) cc_final: 0.8328 (mpp) REVERT: B 332 MET cc_start: 0.9486 (mmt) cc_final: 0.9233 (mmm) REVERT: B 373 MET cc_start: 0.8207 (mmt) cc_final: 0.7994 (mmm) REVERT: B 416 MET cc_start: 0.8704 (ptp) cc_final: 0.8053 (tpt) outliers start: 29 outliers final: 22 residues processed: 222 average time/residue: 0.0741 time to fit residues: 23.3815 Evaluate side-chains 220 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 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 68 VAL 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 377 PHE Chi-restraints excluded: chain B residue 398 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 76 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 chunk 97 optimal weight: 30.0000 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 50.0000 chunk 18 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 72 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** B 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.084852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.065260 restraints weight = 34898.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.067615 restraints weight = 18243.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.069211 restraints weight = 11547.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.070305 restraints weight = 8192.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.071034 restraints weight = 6310.630| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9870 Z= 0.157 Angle : 0.831 16.002 13407 Z= 0.400 Chirality : 0.047 0.307 1505 Planarity : 0.010 0.351 1749 Dihedral : 10.275 169.867 1379 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.83 % Allowed : 26.06 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.30 (0.25), residues: 1172 helix: 0.75 (0.23), residues: 484 sheet: -0.30 (0.35), residues: 187 loop : -1.05 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.071 0.001 ARG C 203 TYR 0.015 0.001 TYR C 93 PHE 0.019 0.001 PHE B 272 TRP 0.021 0.002 TRP B 346 HIS 0.009 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 9865) covalent geometry : angle 0.83057 / 0.40 (13407) hydrogen bonds : bond 0.04003 / 2.82 ( 450) hydrogen bonds : angle 5.11660 / 3.56 ( 1341) Misc. bond : bond 0.00942 / 0.47 ( 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 246 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.280 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 102 TYR cc_start: 0.7315 (t80) cc_final: 0.7070 (t80) REVERT: C 149 TYR cc_start: 0.8737 (t80) cc_final: 0.8346 (t80) REVERT: C 151 GLU cc_start: 0.9132 (mp0) cc_final: 0.8779 (mp0) REVERT: C 173 ARG cc_start: 0.9022 (mmm160) cc_final: 0.8765 (tpp-160) REVERT: C 218 HIS cc_start: 0.8548 (m-70) cc_final: 0.7933 (m-70) REVERT: C 274 GLN cc_start: 0.8968 (mt0) cc_final: 0.8412 (pp30) REVERT: C 301 TYR cc_start: 0.9190 (m-80) cc_final: 0.8912 (m-80) REVERT: C 305 LYS cc_start: 0.9240 (mttp) cc_final: 0.8925 (mtmt) REVERT: C 338 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8642 (t0) REVERT: A 86 LEU cc_start: 0.9452 (mt) cc_final: 0.9043 (mt) REVERT: A 124 LYS cc_start: 0.9558 (ttpt) cc_final: 0.9342 (ttpt) REVERT: A 127 ASP cc_start: 0.8902 (m-30) cc_final: 0.8622 (m-30) REVERT: A 154 MET cc_start: 0.9218 (ttt) cc_final: 0.8677 (tmm) REVERT: A 203 MET cc_start: 0.7696 (ttt) cc_final: 0.7036 (tpt) REVERT: A 224 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: A 272 TYR cc_start: 0.8562 (t80) cc_final: 0.8176 (t80) REVERT: A 302 MET cc_start: 0.8491 (mtt) cc_final: 0.8079 (mtt) REVERT: A 304 LYS cc_start: 0.9006 (tttm) cc_final: 0.8704 (tttt) REVERT: A 313 MET cc_start: 0.6429 (tpt) cc_final: 0.5982 (tpt) REVERT: A 363 VAL cc_start: 0.8944 (t) cc_final: 0.8671 (p) REVERT: A 372 GLN cc_start: 0.9193 (mp10) cc_final: 0.8772 (mm-40) REVERT: A 375 VAL cc_start: 0.9410 (t) cc_final: 0.9047 (p) REVERT: A 377 MET cc_start: 0.8483 (tmm) cc_final: 0.8036 (tmm) REVERT: A 380 ASN cc_start: 0.7689 (m-40) cc_final: 0.7418 (m-40) REVERT: A 398 MET cc_start: 0.9172 (mpp) cc_final: 0.8760 (mmp) REVERT: A 413 MET cc_start: 0.9153 (mmm) cc_final: 0.8817 (mmm) REVERT: A 422 ARG cc_start: 0.8909 (ttp80) cc_final: 0.8697 (tmm-80) REVERT: B 8 GLN cc_start: 0.8718 (mt0) cc_final: 0.8186 (mt0) REVERT: B 68 VAL cc_start: 0.9417 (OUTLIER) cc_final: 0.9148 (m) REVERT: B 156 LYS cc_start: 0.9573 (mttt) cc_final: 0.9228 (tppt) REVERT: B 159 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8145 (mt-10) REVERT: B 299 LYS cc_start: 0.9615 (tppt) cc_final: 0.8992 (tppt) REVERT: B 302 MET cc_start: 0.9166 (mmm) cc_final: 0.8411 (mtt) REVERT: B 309 HIS cc_start: 0.8720 (m170) cc_final: 0.8400 (m-70) REVERT: B 325 MET cc_start: 0.8518 (mpp) cc_final: 0.8310 (mpp) REVERT: B 332 MET cc_start: 0.9473 (mmt) cc_final: 0.9249 (mmm) outliers start: 28 outliers final: 23 residues processed: 231 average time/residue: 0.0732 time to fit residues: 24.0780 Evaluate side-chains 228 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 A residue 434 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 68 VAL 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 377 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 114 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 108 optimal weight: 40.0000 chunk 120 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 110 optimal weight: 30.0000 chunk 50 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 5 optimal weight: 0.0020 overall best weight: 4.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 72 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.085619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.066394 restraints weight = 34569.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.068740 restraints weight = 18103.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.070333 restraints weight = 11366.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.071400 restraints weight = 8028.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.072148 restraints weight = 6201.759| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9870 Z= 0.159 Angle : 0.894 28.068 13407 Z= 0.427 Chirality : 0.047 0.292 1505 Planarity : 0.011 0.401 1749 Dihedral : 10.204 169.123 1379 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.53 % Allowed : 26.36 % 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: -0.28 (0.25), residues: 1172 helix: 0.74 (0.23), residues: 486 sheet: -0.29 (0.34), residues: 198 loop : -1.02 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.001 ARG C 203 TYR 0.016 0.001 TYR C 93 PHE 0.028 0.002 PHE A 149 TRP 0.020 0.002 TRP B 346 HIS 0.006 0.001 HIS C 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 9865) covalent geometry : angle 0.89367 / 0.43 (13407) hydrogen bonds : bond 0.04001 / 2.84 ( 450) hydrogen bonds : angle 5.13228 / 3.62 ( 1341) Misc. bond : bond 0.00955 / 0.48 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1375.43 seconds wall clock time: 24 minutes 36.49 seconds (1476.49 seconds total)