Starting phenix.real_space_refine on Mon Jul 28 01:04:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rx0_24721/07_2025/7rx0_24721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rx0_24721/07_2025/7rx0_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_2025/7rx0_24721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rx0_24721/07_2025/7rx0_24721.map" model { file = "/net/cci-nas-00/data/ceres_data/7rx0_24721/07_2025/7rx0_24721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rx0_24721/07_2025/7rx0_24721.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.010 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'GLU:plan': 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: 6.59, per 1000 atoms: 0.68 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: 2.84 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.19 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: 3.12 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3265 1.34 - 1.46: 2174 1.46 - 1.58: 4324 1.58 - 1.70: 13 1.70 - 1.81: 89 Bond restraints: 9865 Sorted by residual: bond pdb=" O3B G2P B 501 " pdb=" PG G2P B 501 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" O1A G2P B 501 " pdb=" PA G2P B 501 " ideal model delta sigma weight residual 1.507 1.611 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" O1B G2P B 501 " pdb=" PB G2P B 501 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C5 GTP A 501 " pdb=" C6 GTP A 501 " ideal model delta sigma weight residual 1.390 1.481 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O3A ANP C1401 " pdb=" PB ANP C1401 " ideal model delta sigma weight residual 1.700 1.610 0.090 2.00e-02 2.50e+03 2.03e+01 ... (remaining 9860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 13215 2.74 - 5.49: 160 5.49 - 8.23: 21 8.23 - 10.97: 9 10.97 - 13.71: 2 Bond angle restraints: 13407 Sorted by residual: angle pdb=" C THR C 205 " pdb=" CA THR C 205 " pdb=" CB THR C 205 " ideal model delta sigma weight residual 110.42 124.13 -13.71 1.99e+00 2.53e-01 4.75e+01 angle pdb=" C HIS C 204 " pdb=" N THR C 205 " pdb=" CA THR C 205 " ideal model delta sigma weight residual 121.54 111.50 10.04 1.91e+00 2.74e-01 2.76e+01 angle pdb=" N SER C 215 " pdb=" CA SER C 215 " pdb=" C SER C 215 " ideal model delta sigma weight residual 110.91 115.77 -4.86 1.17e+00 7.31e-01 1.73e+01 angle pdb=" PA G2P B 501 " pdb=" C3A G2P B 501 " pdb=" PB G2P B 501 " ideal model delta sigma weight residual 120.83 109.51 11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" N THR C 208 " pdb=" CA THR C 208 " pdb=" C THR C 208 " ideal model delta sigma weight residual 108.96 103.00 5.96 1.59e+00 3.96e-01 1.41e+01 ... (remaining 13402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 5774 33.70 - 67.39: 119 67.39 - 101.08: 13 101.08 - 134.78: 2 134.78 - 168.47: 4 Dihedral angle restraints: 5912 sinusoidal: 2282 harmonic: 3630 Sorted by residual: dihedral pdb=" C THR C 205 " pdb=" N THR C 205 " pdb=" CA THR C 205 " pdb=" CB THR C 205 " ideal model delta harmonic sigma weight residual -122.00 -147.69 25.69 0 2.50e+00 1.60e-01 1.06e+02 dihedral pdb=" N THR C 205 " pdb=" C THR C 205 " pdb=" CA THR C 205 " pdb=" CB THR C 205 " ideal model delta harmonic sigma weight residual 123.40 142.70 -19.30 0 2.50e+00 1.60e-01 5.96e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.26 -168.47 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 5909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 1503 0.199 - 0.398: 1 0.398 - 0.597: 0 0.597 - 0.796: 0 0.796 - 0.995: 1 Chirality restraints: 1505 Sorted by residual: chirality pdb=" CA THR C 205 " pdb=" N THR C 205 " pdb=" C THR C 205 " pdb=" CB THR C 205 " both_signs ideal model delta sigma weight residual False 2.53 1.53 0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CA HIS C 204 " pdb=" N HIS C 204 " pdb=" C HIS C 204 " pdb=" CB HIS C 204 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C3' ANP C1401 " pdb=" C2' ANP C1401 " pdb=" C4' ANP C1401 " pdb=" O3' ANP C1401 " both_signs ideal model delta sigma weight residual False -2.36 -2.54 0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 1502 not shown) Planarity restraints: 1749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 202 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C ALA C 202 " 0.031 2.00e-02 2.50e+03 pdb=" O ALA C 202 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG C 203 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 269 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO B 270 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 31 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 32 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.021 5.00e-02 4.00e+02 ... (remaining 1746 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 60 2.31 - 2.96: 5377 2.96 - 3.61: 15666 3.61 - 4.25: 22884 4.25 - 4.90: 36308 Nonbonded interactions: 80295 Sorted by model distance: nonbonded pdb=" O ARG C 203 " pdb=" O GLY C 206 " model vdw 1.666 3.040 nonbonded pdb=" O2A G2P B 501 " pdb="MG MG B 502 " model vdw 1.777 2.170 nonbonded pdb=" O2G G2P B 501 " pdb="MG MG B 502 " model vdw 1.923 2.170 nonbonded pdb=" OH TYR C 145 " pdb=" NH2 ARG C 203 " model vdw 1.968 3.120 nonbonded pdb=" OD1 ASN C 200 " pdb=" NH2 ARG C 203 " model vdw 1.996 3.120 ... (remaining 80290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.960 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.895 9870 Z= 1.627 Angle : 0.854 13.713 13407 Z= 0.458 Chirality : 0.051 0.995 1505 Planarity : 0.004 0.045 1749 Dihedral : 15.605 168.471 3576 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 29.17 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.002 TRP A 346 HIS 0.008 0.002 HIS C 298 PHE 0.016 0.002 PHE C 248 TYR 0.013 0.002 TYR B 432 ARG 0.006 0.000 ARG C 258 Details of bonding type rmsd hydrogen bonds : bond 0.14830 ( 450) hydrogen bonds : angle 7.13003 ( 1341) covalent geometry : bond 0.00620 ( 9865) covalent geometry : angle 0.85406 (13407) Misc. bond : bond 0.70893 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.067 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: 0.8550 (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: 0.8297 (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: 0.2473 time to fit residues: 99.0785 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 : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 31 optimal weight: 50.0000 chunk 62 optimal weight: 0.0980 chunk 49 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 37 optimal weight: 50.0000 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN A 18 ASN A 28 HIS A 31 GLN A 35 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 426 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.085828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.067413 restraints weight = 34016.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.069754 restraints weight = 17663.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.071312 restraints weight = 10995.782| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2275 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= 0.165 Angle : 0.739 9.275 13407 Z= 0.368 Chirality : 0.045 0.208 1505 Planarity : 0.005 0.082 1749 Dihedral : 11.062 151.202 1435 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.63 % Allowed : 15.86 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.24), residues: 1172 helix: 0.19 (0.23), residues: 481 sheet: -0.83 (0.34), residues: 190 loop : -1.49 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 21 HIS 0.007 0.001 HIS C 204 PHE 0.019 0.002 PHE B 262 TYR 0.044 0.002 TYR C 71 ARG 0.013 0.001 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.04610 ( 450) hydrogen bonds : angle 5.57095 ( 1341) covalent geometry : bond 0.00363 ( 9865) covalent geometry : angle 0.73932 (13407) Misc. bond : bond 0.00259 ( 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 283 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 257 time to evaluate : 1.187 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: C 151 GLU cc_start: 0.9082 (mp0) cc_final: 0.8390 (mp0) REVERT: C 196 LEU cc_start: 0.9183 (mt) cc_final: 0.8980 (mt) REVERT: C 205 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7479 (t) REVERT: C 218 HIS cc_start: 0.8448 (m-70) cc_final: 0.7806 (m-70) REVERT: C 274 GLN cc_start: 0.9174 (mt0) cc_final: 0.8563 (pp30) REVERT: C 301 TYR cc_start: 0.9209 (m-80) cc_final: 0.8646 (m-80) REVERT: C 305 LYS cc_start: 0.9241 (mttp) cc_final: 0.9018 (mtpt) REVERT: A 86 LEU cc_start: 0.9324 (mt) cc_final: 0.8894 (mt) REVERT: A 196 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8387 (mm-30) REVERT: A 216 ASN cc_start: 0.8954 (m-40) cc_final: 0.8697 (m110) REVERT: A 272 TYR cc_start: 0.8433 (t80) cc_final: 0.8063 (t80) REVERT: A 302 MET cc_start: 0.8345 (mtt) cc_final: 0.8034 (mtt) REVERT: A 363 VAL cc_start: 0.9267 (t) cc_final: 0.8942 (p) REVERT: A 372 GLN cc_start: 0.8928 (mp10) cc_final: 0.8688 (mm-40) REVERT: A 398 MET cc_start: 0.9112 (mpp) cc_final: 0.8849 (mmp) REVERT: A 413 MET cc_start: 0.9179 (mmm) cc_final: 0.8951 (mmm) REVERT: A 430 LYS cc_start: 0.9531 (tptt) cc_final: 0.9137 (tppt) REVERT: A 433 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8704 (tm-30) REVERT: A 434 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8458 (mt-10) REVERT: B 26 ASP cc_start: 0.9237 (t0) cc_final: 0.9017 (t70) REVERT: B 37 HIS cc_start: 0.8677 (m-70) cc_final: 0.8077 (m90) REVERT: B 68 VAL cc_start: 0.9333 (p) cc_final: 0.8997 (m) REVERT: B 69 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.7037 (t70) REVERT: B 107 HIS cc_start: 0.8420 (t70) cc_final: 0.7714 (t70) REVERT: B 124 LYS cc_start: 0.9489 (tttp) cc_final: 0.9273 (ttmt) REVERT: B 156 LYS cc_start: 0.9493 (mttt) cc_final: 0.9235 (mmtm) REVERT: B 166 MET cc_start: 0.7589 (mmm) cc_final: 0.7315 (mtm) REVERT: B 211 ASP cc_start: 0.9188 (OUTLIER) cc_final: 0.8927 (t0) REVERT: B 219 LEU cc_start: 0.8619 (mt) cc_final: 0.8246 (mt) REVERT: B 302 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8368 (mtt) REVERT: B 306 ASP cc_start: 0.8963 (m-30) cc_final: 0.8626 (t0) REVERT: B 309 HIS cc_start: 0.8795 (m170) cc_final: 0.8026 (m-70) REVERT: B 323 MET cc_start: 0.8058 (mpp) cc_final: 0.6399 (mpp) REVERT: B 332 MET cc_start: 0.9248 (mmt) cc_final: 0.8882 (mmm) REVERT: B 373 MET cc_start: 0.8601 (ptp) cc_final: 0.8225 (mtp) REVERT: B 391 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9242 (mp) REVERT: B 417 GLU cc_start: 0.8482 (mp0) cc_final: 0.7882 (mp0) outliers start: 26 outliers final: 10 residues processed: 268 average time/residue: 0.2235 time to fit residues: 83.3204 Evaluate side-chains 221 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 69 ASP 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 32 optimal weight: 50.0000 chunk 108 optimal weight: 40.0000 chunk 35 optimal weight: 50.0000 chunk 73 optimal weight: 0.0060 chunk 82 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 77 optimal weight: 30.0000 chunk 49 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 7 optimal weight: 50.0000 chunk 54 optimal weight: 30.0000 overall best weight: 11.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN C 76 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 ASN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN A 342 GLN ** 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 B 426 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.082277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.064489 restraints weight = 34987.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066711 restraints weight = 18228.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.068198 restraints weight = 11431.835| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9870 Z= 0.208 Angle : 0.754 12.183 13407 Z= 0.375 Chirality : 0.045 0.203 1505 Planarity : 0.005 0.077 1749 Dihedral : 10.767 161.048 1435 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.94 % Allowed : 18.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.24), residues: 1172 helix: 0.44 (0.23), residues: 478 sheet: -0.81 (0.32), residues: 201 loop : -1.40 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 346 HIS 0.010 0.002 HIS A 28 PHE 0.014 0.002 PHE B 262 TYR 0.027 0.002 TYR C 71 ARG 0.007 0.001 ARG B 215 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 450) hydrogen bonds : angle 5.43233 ( 1341) covalent geometry : bond 0.00444 ( 9865) covalent geometry : angle 0.75367 (13407) Misc. bond : bond 0.00430 ( 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 255 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 1.134 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: C 71 TYR cc_start: 0.8843 (t80) cc_final: 0.8327 (t80) REVERT: C 119 ILE cc_start: 0.8108 (mm) cc_final: 0.7871 (mm) REVERT: C 145 TYR cc_start: 0.8557 (t80) cc_final: 0.7876 (t80) REVERT: C 151 GLU cc_start: 0.9011 (mp0) cc_final: 0.8179 (mp0) REVERT: C 182 LYS cc_start: 0.8935 (tttp) cc_final: 0.8586 (ttmt) REVERT: C 218 HIS cc_start: 0.8532 (m-70) cc_final: 0.7896 (m-70) REVERT: C 274 GLN cc_start: 0.9083 (mt0) cc_final: 0.8429 (pp30) REVERT: C 301 TYR cc_start: 0.9284 (m-80) cc_final: 0.8761 (m-80) REVERT: C 305 LYS cc_start: 0.9259 (mttp) cc_final: 0.8985 (mtpt) REVERT: A 86 LEU cc_start: 0.9343 (mt) cc_final: 0.9018 (mt) REVERT: A 127 ASP cc_start: 0.8875 (m-30) cc_final: 0.8629 (m-30) REVERT: A 196 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8252 (mm-30) REVERT: A 272 TYR cc_start: 0.8569 (t80) cc_final: 0.8272 (t80) REVERT: A 302 MET cc_start: 0.8402 (mtt) cc_final: 0.8011 (mtt) REVERT: A 363 VAL cc_start: 0.9255 (t) cc_final: 0.8950 (p) REVERT: A 372 GLN cc_start: 0.9000 (mp10) cc_final: 0.8719 (mm-40) REVERT: A 401 LYS cc_start: 0.8833 (pttt) cc_final: 0.8161 (pttt) REVERT: B 26 ASP cc_start: 0.9336 (t0) cc_final: 0.9107 (t70) REVERT: B 107 HIS cc_start: 0.8368 (t70) cc_final: 0.7715 (t70) REVERT: B 156 LYS cc_start: 0.9548 (mttt) cc_final: 0.9216 (mmpt) REVERT: B 166 MET cc_start: 0.7968 (mmm) cc_final: 0.7598 (mtm) REVERT: B 219 LEU cc_start: 0.8645 (mt) cc_final: 0.8297 (mt) REVERT: B 302 MET cc_start: 0.9109 (mmm) cc_final: 0.8405 (mtt) REVERT: B 306 ASP cc_start: 0.8955 (m-30) cc_final: 0.8720 (t0) REVERT: B 309 HIS cc_start: 0.8754 (m170) cc_final: 0.8049 (m-70) REVERT: B 323 MET cc_start: 0.7994 (mpp) cc_final: 0.6641 (mpp) REVERT: B 332 MET cc_start: 0.9316 (mmt) cc_final: 0.8985 (mmm) REVERT: B 346 TRP cc_start: 0.7804 (m100) cc_final: 0.7603 (m100) REVERT: B 373 MET cc_start: 0.8584 (ptp) cc_final: 0.8103 (mtp) outliers start: 39 outliers final: 23 residues processed: 239 average time/residue: 0.2230 time to fit residues: 73.8017 Evaluate side-chains 217 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 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 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 90 ASP 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 353 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 61 optimal weight: 0.0670 chunk 64 optimal weight: 9.9990 chunk 18 optimal weight: 30.0000 chunk 111 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 67 optimal weight: 5.9990 chunk 81 optimal weight: 30.0000 chunk 93 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 116 optimal weight: 40.0000 overall best weight: 5.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS A 226 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.083770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.065644 restraints weight = 34093.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.067896 restraints weight = 17893.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.069403 restraints weight = 11217.927| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 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 = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9870 Z= 0.146 Angle : 0.722 11.972 13407 Z= 0.354 Chirality : 0.044 0.262 1505 Planarity : 0.004 0.051 1749 Dihedral : 10.509 160.501 1435 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.64 % Allowed : 19.70 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1172 helix: 0.77 (0.23), residues: 480 sheet: -0.57 (0.34), residues: 195 loop : -1.26 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.005 0.001 HIS A 28 PHE 0.015 0.001 PHE C 333 TYR 0.022 0.001 TYR A 224 ARG 0.008 0.001 ARG C 203 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 450) hydrogen bonds : angle 5.13442 ( 1341) covalent geometry : bond 0.00320 ( 9865) covalent geometry : angle 0.72229 (13407) Misc. bond : bond 0.00409 ( 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 253 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 1.108 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: 0.8981 (t80) cc_final: 0.8511 (t80) REVERT: C 119 ILE cc_start: 0.8261 (mm) cc_final: 0.7830 (mm) REVERT: C 124 MET cc_start: 0.9010 (mmm) cc_final: 0.8665 (mmm) REVERT: C 151 GLU cc_start: 0.9029 (mp0) cc_final: 0.8303 (mp0) REVERT: C 166 ILE cc_start: 0.9267 (pp) cc_final: 0.8725 (mt) REVERT: C 205 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7370 (t) REVERT: C 218 HIS cc_start: 0.8515 (m-70) cc_final: 0.7832 (m-70) REVERT: C 274 GLN cc_start: 0.9049 (mt0) cc_final: 0.8451 (pp30) REVERT: C 301 TYR cc_start: 0.9287 (m-80) cc_final: 0.8755 (m-80) REVERT: C 305 LYS cc_start: 0.9229 (mttp) cc_final: 0.8880 (mtpt) REVERT: C 338 ASN cc_start: 0.9106 (OUTLIER) cc_final: 0.8728 (t0) REVERT: A 21 TRP cc_start: 0.9277 (m100) cc_final: 0.8949 (m100) REVERT: A 86 LEU cc_start: 0.9327 (mt) cc_final: 0.8988 (mt) REVERT: A 127 ASP cc_start: 0.8864 (m-30) cc_final: 0.8605 (m-30) REVERT: A 196 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8409 (mm-30) REVERT: A 221 ARG cc_start: 0.8656 (mmt180) cc_final: 0.8445 (mmt90) REVERT: A 272 TYR cc_start: 0.8504 (t80) cc_final: 0.8106 (t80) REVERT: A 302 MET cc_start: 0.8477 (mtt) cc_final: 0.8034 (mtt) REVERT: A 363 VAL cc_start: 0.9251 (t) cc_final: 0.8919 (p) REVERT: A 372 GLN cc_start: 0.9028 (mp10) cc_final: 0.8800 (mm-40) REVERT: A 375 VAL cc_start: 0.9389 (t) cc_final: 0.9130 (p) REVERT: A 398 MET cc_start: 0.9158 (mpp) cc_final: 0.8765 (mmp) REVERT: A 401 LYS cc_start: 0.8854 (pttt) cc_final: 0.8101 (pttt) REVERT: B 26 ASP cc_start: 0.9301 (t0) cc_final: 0.9025 (t70) REVERT: B 37 HIS cc_start: 0.8683 (m-70) cc_final: 0.8062 (m90) REVERT: B 107 HIS cc_start: 0.8439 (t70) cc_final: 0.7816 (t70) REVERT: B 156 LYS cc_start: 0.9542 (mttt) cc_final: 0.9176 (mmtm) REVERT: B 159 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7900 (mt-10) REVERT: B 166 MET cc_start: 0.7893 (mmm) cc_final: 0.7562 (mtm) REVERT: B 199 ASP cc_start: 0.8603 (m-30) cc_final: 0.7619 (m-30) REVERT: B 269 MET cc_start: 0.8146 (pmm) cc_final: 0.7906 (pmm) REVERT: B 302 MET cc_start: 0.9104 (mmm) cc_final: 0.8480 (mtt) REVERT: B 306 ASP cc_start: 0.8902 (m-30) cc_final: 0.8654 (t0) REVERT: B 309 HIS cc_start: 0.8706 (m170) cc_final: 0.7893 (m-70) REVERT: B 323 MET cc_start: 0.7975 (mpp) cc_final: 0.6494 (mpp) REVERT: B 332 MET cc_start: 0.9351 (mmt) cc_final: 0.8954 (mmm) REVERT: B 373 MET cc_start: 0.8589 (ptp) cc_final: 0.8246 (mtp) REVERT: B 391 ILE cc_start: 0.9313 (mp) cc_final: 0.9038 (tt) REVERT: B 413 MET cc_start: 0.8072 (mmt) cc_final: 0.7766 (mmt) REVERT: B 416 MET cc_start: 0.8787 (ptp) cc_final: 0.8251 (ppp) outliers start: 36 outliers final: 20 residues processed: 236 average time/residue: 0.2172 time to fit residues: 71.6299 Evaluate side-chains 222 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 96 THR 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 23 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 309 HIS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 353 THR 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 61 optimal weight: 6.9990 chunk 98 optimal weight: 50.0000 chunk 48 optimal weight: 8.9990 chunk 33 optimal weight: 60.0000 chunk 45 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 58 optimal weight: 30.0000 overall best weight: 12.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B 294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.081783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.063889 restraints weight = 35114.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.066012 restraints weight = 18729.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.067413 restraints weight = 11936.359| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3533 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= 0.225 Angle : 0.781 16.510 13407 Z= 0.387 Chirality : 0.045 0.225 1505 Planarity : 0.009 0.309 1749 Dihedral : 11.425 172.006 1435 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.95 % Allowed : 20.30 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1172 helix: 0.69 (0.23), residues: 479 sheet: -0.56 (0.33), residues: 197 loop : -1.37 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 346 HIS 0.007 0.002 HIS A 28 PHE 0.020 0.002 PHE B 262 TYR 0.024 0.002 TYR A 224 ARG 0.008 0.001 ARG C 203 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 450) hydrogen bonds : angle 5.27831 ( 1341) covalent geometry : bond 0.00481 ( 9865) covalent geometry : angle 0.78057 (13407) Misc. bond : bond 0.00273 ( 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 249 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 1.601 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: C 71 TYR cc_start: 0.9000 (t80) cc_final: 0.8565 (t80) REVERT: C 151 GLU cc_start: 0.9020 (mp0) cc_final: 0.8198 (mp0) REVERT: C 166 ILE cc_start: 0.9304 (pp) cc_final: 0.9087 (tt) REVERT: C 218 HIS cc_start: 0.8583 (m-70) cc_final: 0.7882 (m-70) REVERT: C 252 ASP cc_start: 0.8730 (t0) cc_final: 0.8209 (t0) REVERT: C 274 GLN cc_start: 0.9068 (mt0) cc_final: 0.8438 (pp30) REVERT: C 301 TYR cc_start: 0.9251 (m-80) cc_final: 0.8782 (m-80) REVERT: C 305 LYS cc_start: 0.9236 (mttp) cc_final: 0.8898 (mtpt) REVERT: C 338 ASN cc_start: 0.9106 (OUTLIER) cc_final: 0.8731 (t0) REVERT: A 22 GLU cc_start: 0.8881 (pt0) cc_final: 0.8629 (pm20) REVERT: A 86 LEU cc_start: 0.9393 (mt) cc_final: 0.9020 (mt) REVERT: A 127 ASP cc_start: 0.8870 (m-30) cc_final: 0.8621 (m-30) REVERT: A 221 ARG cc_start: 0.8655 (mmt180) cc_final: 0.8426 (mmt90) REVERT: A 272 TYR cc_start: 0.8609 (t80) cc_final: 0.8277 (t80) REVERT: A 276 ILE cc_start: 0.9563 (tp) cc_final: 0.9358 (tp) REVERT: A 285 GLN cc_start: 0.3223 (OUTLIER) cc_final: 0.2165 (mt0) REVERT: A 302 MET cc_start: 0.8325 (mtt) cc_final: 0.7855 (mtt) REVERT: A 363 VAL cc_start: 0.9258 (t) cc_final: 0.8942 (p) REVERT: A 372 GLN cc_start: 0.9154 (mp10) cc_final: 0.8886 (mm-40) REVERT: A 377 MET cc_start: 0.8323 (tmm) cc_final: 0.7947 (tmm) REVERT: A 380 ASN cc_start: 0.8582 (t0) cc_final: 0.8335 (m-40) REVERT: A 401 LYS cc_start: 0.8877 (pttt) cc_final: 0.8307 (pttt) REVERT: A 413 MET cc_start: 0.9208 (mmm) cc_final: 0.8889 (mmm) REVERT: B 26 ASP cc_start: 0.9344 (t0) cc_final: 0.9084 (t70) REVERT: B 107 HIS cc_start: 0.8395 (t70) cc_final: 0.7775 (t70) REVERT: B 156 LYS cc_start: 0.9567 (mttt) cc_final: 0.9176 (mmpt) REVERT: B 159 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7818 (mt-10) REVERT: B 166 MET cc_start: 0.7957 (mmm) cc_final: 0.7632 (mtm) REVERT: B 199 ASP cc_start: 0.8690 (m-30) cc_final: 0.7877 (m-30) REVERT: B 302 MET cc_start: 0.9097 (mmm) cc_final: 0.8594 (mtt) REVERT: B 306 ASP cc_start: 0.8884 (m-30) cc_final: 0.8598 (m-30) REVERT: B 309 HIS cc_start: 0.8742 (m170) cc_final: 0.8200 (m90) REVERT: B 323 MET cc_start: 0.7937 (mpp) cc_final: 0.6101 (mpp) REVERT: B 332 MET cc_start: 0.9352 (mmt) cc_final: 0.9024 (mmm) REVERT: B 373 MET cc_start: 0.8547 (ptp) cc_final: 0.8314 (mtp) REVERT: B 416 MET cc_start: 0.8680 (ptp) cc_final: 0.7926 (tpt) outliers start: 49 outliers final: 34 residues processed: 232 average time/residue: 0.2807 time to fit residues: 92.1236 Evaluate side-chains 224 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 119 LEU 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 285 GLN 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 62 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 181 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 415 GLU 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 52 optimal weight: 0.0000 chunk 101 optimal weight: 40.0000 chunk 81 optimal weight: 30.0000 chunk 14 optimal weight: 50.0000 chunk 72 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 overall best weight: 5.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN ** A 15 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 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 = 0.3709 r_free = 0.3709 target = 0.083931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.065243 restraints weight = 34886.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.067441 restraints weight = 18433.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.068931 restraints weight = 11720.615| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 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 = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9870 Z= 0.141 Angle : 0.733 13.266 13407 Z= 0.356 Chirality : 0.044 0.183 1505 Planarity : 0.011 0.407 1749 Dihedral : 11.114 168.132 1435 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.74 % Allowed : 22.73 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.24), residues: 1172 helix: 0.86 (0.23), residues: 480 sheet: -0.60 (0.33), residues: 199 loop : -1.19 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 346 HIS 0.005 0.001 HIS A 28 PHE 0.017 0.001 PHE C 333 TYR 0.029 0.002 TYR A 172 ARG 0.006 0.001 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 450) hydrogen bonds : angle 4.98068 ( 1341) covalent geometry : bond 0.00318 ( 9865) covalent geometry : angle 0.73304 (13407) Misc. bond : bond 0.00185 ( 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 252 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.992 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: 0.8872 (t80) cc_final: 0.8581 (t80) REVERT: C 149 TYR cc_start: 0.8625 (t80) cc_final: 0.8299 (t80) REVERT: C 151 GLU cc_start: 0.9023 (mp0) cc_final: 0.8394 (mp0) REVERT: C 173 ARG cc_start: 0.9034 (mmm160) cc_final: 0.8773 (tpp-160) REVERT: C 182 LYS cc_start: 0.8969 (tttp) cc_final: 0.8618 (tttp) REVERT: C 210 LEU cc_start: 0.4184 (OUTLIER) cc_final: 0.3128 (tt) REVERT: C 218 HIS cc_start: 0.8561 (m-70) cc_final: 0.7845 (m-70) REVERT: C 274 GLN cc_start: 0.8979 (mt0) cc_final: 0.8435 (pp30) REVERT: C 301 TYR cc_start: 0.9200 (m-80) cc_final: 0.8755 (m-80) REVERT: C 305 LYS cc_start: 0.9277 (mttp) cc_final: 0.8972 (mtpt) REVERT: C 338 ASN cc_start: 0.9100 (OUTLIER) cc_final: 0.8719 (t0) REVERT: A 21 TRP cc_start: 0.9296 (m100) cc_final: 0.8899 (m100) REVERT: A 86 LEU cc_start: 0.9343 (mt) cc_final: 0.8964 (mt) REVERT: A 127 ASP cc_start: 0.8874 (m-30) cc_final: 0.8632 (m-30) REVERT: A 196 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8320 (mm-30) REVERT: A 221 ARG cc_start: 0.8644 (mmt180) cc_final: 0.8281 (mmt90) REVERT: A 224 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: A 272 TYR cc_start: 0.8592 (t80) cc_final: 0.8229 (t80) REVERT: A 276 ILE cc_start: 0.9523 (tp) cc_final: 0.9300 (tp) REVERT: A 302 MET cc_start: 0.8441 (mtt) cc_final: 0.8092 (mtt) REVERT: A 363 VAL cc_start: 0.9261 (t) cc_final: 0.8731 (p) REVERT: A 372 GLN cc_start: 0.9102 (mp10) cc_final: 0.8774 (mm-40) REVERT: A 375 VAL cc_start: 0.9397 (t) cc_final: 0.9119 (p) REVERT: A 398 MET cc_start: 0.9238 (mpp) cc_final: 0.8925 (mmp) REVERT: A 413 MET cc_start: 0.9264 (mmm) cc_final: 0.8885 (mmm) REVERT: A 434 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8815 (mp0) REVERT: B 26 ASP cc_start: 0.9284 (t0) cc_final: 0.9005 (t70) REVERT: B 107 HIS cc_start: 0.8526 (t70) cc_final: 0.7837 (t70) REVERT: B 159 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7933 (mt-10) REVERT: B 302 MET cc_start: 0.9025 (mmm) cc_final: 0.8534 (mtt) REVERT: B 309 HIS cc_start: 0.8689 (m170) cc_final: 0.8305 (m90) REVERT: B 332 MET cc_start: 0.9400 (mmt) cc_final: 0.9011 (mmm) outliers start: 37 outliers final: 25 residues processed: 234 average time/residue: 0.2082 time to fit residues: 68.3776 Evaluate side-chains 222 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 415 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 63 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 112 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3657 r_free = 0.3657 target = 0.082852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.063985 restraints weight = 35171.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.066324 restraints weight = 18070.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.067899 restraints weight = 11299.405| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9870 Z= 0.161 Angle : 0.763 15.771 13407 Z= 0.369 Chirality : 0.045 0.293 1505 Planarity : 0.004 0.038 1749 Dihedral : 10.647 169.139 1435 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.55 % Allowed : 22.53 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.24), residues: 1172 helix: 0.88 (0.23), residues: 480 sheet: -0.57 (0.33), residues: 201 loop : -1.16 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 346 HIS 0.005 0.001 HIS C 298 PHE 0.016 0.001 PHE B 272 TYR 0.014 0.001 TYR C 149 ARG 0.007 0.000 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 450) hydrogen bonds : angle 5.04349 ( 1341) covalent geometry : bond 0.00359 ( 9865) covalent geometry : angle 0.76329 (13407) Misc. bond : bond 0.00695 ( 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 253 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 208 time to evaluate : 1.144 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 102 TYR cc_start: 0.7300 (t80) cc_final: 0.7081 (t80) REVERT: C 151 GLU cc_start: 0.9089 (mp0) cc_final: 0.8713 (mp0) REVERT: C 166 ILE cc_start: 0.9465 (tt) cc_final: 0.9262 (mp) REVERT: C 173 ARG cc_start: 0.9032 (mmm160) cc_final: 0.8805 (tpp-160) REVERT: C 182 LYS cc_start: 0.8957 (tttp) cc_final: 0.8533 (tttp) REVERT: C 210 LEU cc_start: 0.4286 (OUTLIER) cc_final: 0.3435 (tt) REVERT: C 218 HIS cc_start: 0.8468 (m-70) cc_final: 0.7802 (m-70) REVERT: C 274 GLN cc_start: 0.8995 (mt0) cc_final: 0.8472 (pp30) REVERT: C 301 TYR cc_start: 0.9221 (m-80) cc_final: 0.8905 (m-80) REVERT: C 305 LYS cc_start: 0.9243 (mttp) cc_final: 0.8932 (mtmt) REVERT: C 338 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8748 (t0) REVERT: A 86 LEU cc_start: 0.9308 (mt) cc_final: 0.8792 (mt) REVERT: A 127 ASP cc_start: 0.8897 (m-30) cc_final: 0.8640 (m-30) REVERT: A 221 ARG cc_start: 0.8762 (mmt180) cc_final: 0.8421 (mmt90) REVERT: A 224 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.8296 (m-80) REVERT: A 272 TYR cc_start: 0.8538 (t80) cc_final: 0.8163 (t80) REVERT: A 276 ILE cc_start: 0.9455 (tp) cc_final: 0.9216 (tp) REVERT: A 302 MET cc_start: 0.8541 (mtt) cc_final: 0.8008 (mtt) REVERT: A 363 VAL cc_start: 0.8816 (t) cc_final: 0.8551 (p) REVERT: A 372 GLN cc_start: 0.9155 (mp10) cc_final: 0.8822 (mm-40) REVERT: A 375 VAL cc_start: 0.9411 (t) cc_final: 0.9100 (p) REVERT: A 377 MET cc_start: 0.8386 (tmm) cc_final: 0.7951 (tmm) REVERT: A 413 MET cc_start: 0.9251 (mmm) cc_final: 0.8889 (mmm) REVERT: A 434 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8812 (mp0) REVERT: B 8 GLN cc_start: 0.8821 (mt0) cc_final: 0.8148 (mt0) REVERT: B 26 ASP cc_start: 0.9455 (t0) cc_final: 0.9196 (t70) REVERT: B 107 HIS cc_start: 0.8587 (t70) cc_final: 0.7960 (t70) REVERT: B 302 MET cc_start: 0.9135 (mmm) cc_final: 0.8299 (mtt) REVERT: B 309 HIS cc_start: 0.8798 (m170) cc_final: 0.8409 (m90) REVERT: B 323 MET cc_start: 0.7901 (mpp) cc_final: 0.6458 (mpp) REVERT: B 332 MET cc_start: 0.9544 (mmt) cc_final: 0.9196 (mmm) REVERT: B 345 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8301 (pp20) REVERT: B 373 MET cc_start: 0.8733 (ptp) cc_final: 0.8298 (mtp) REVERT: B 400 ARG cc_start: 0.8087 (ttm110) cc_final: 0.7837 (mtt180) REVERT: B 416 MET cc_start: 0.8790 (ptp) cc_final: 0.8436 (ppp) outliers start: 45 outliers final: 31 residues processed: 235 average time/residue: 0.2161 time to fit residues: 71.1996 Evaluate side-chains 231 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 415 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 8 optimal weight: 30.0000 chunk 59 optimal weight: 9.9990 chunk 7 optimal weight: 40.0000 chunk 42 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 91 optimal weight: 30.0000 chunk 46 optimal weight: 0.0470 chunk 83 optimal weight: 30.0000 chunk 35 optimal weight: 50.0000 overall best weight: 5.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3690 r_free = 0.3690 target = 0.084243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.065417 restraints weight = 34901.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.067740 restraints weight = 18152.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.069325 restraints weight = 11386.727| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9870 Z= 0.150 Angle : 0.768 17.727 13407 Z= 0.370 Chirality : 0.044 0.217 1505 Planarity : 0.004 0.039 1749 Dihedral : 10.560 168.378 1435 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.04 % Allowed : 23.84 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1172 helix: 0.85 (0.23), residues: 485 sheet: -0.44 (0.34), residues: 195 loop : -1.09 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 346 HIS 0.007 0.001 HIS C 142 PHE 0.023 0.001 PHE A 149 TYR 0.030 0.002 TYR C 71 ARG 0.011 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 450) hydrogen bonds : angle 4.97893 ( 1341) covalent geometry : bond 0.00344 ( 9865) covalent geometry : angle 0.76832 (13407) Misc. bond : bond 0.00346 ( 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 243 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 1.033 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 149 TYR cc_start: 0.8756 (t80) cc_final: 0.8338 (t80) REVERT: C 151 GLU cc_start: 0.9051 (mp0) cc_final: 0.8457 (mp0) REVERT: C 173 ARG cc_start: 0.9059 (mmm160) cc_final: 0.8840 (tpp-160) REVERT: C 182 LYS cc_start: 0.8991 (tttp) cc_final: 0.8575 (tttp) REVERT: C 210 LEU cc_start: 0.4179 (OUTLIER) cc_final: 0.3386 (tt) REVERT: C 218 HIS cc_start: 0.8527 (m-70) cc_final: 0.7829 (m-70) REVERT: C 274 GLN cc_start: 0.8983 (mt0) cc_final: 0.8450 (pp30) REVERT: C 301 TYR cc_start: 0.9241 (m-80) cc_final: 0.8875 (m-80) REVERT: C 305 LYS cc_start: 0.9193 (mttp) cc_final: 0.8885 (mtpt) REVERT: C 338 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8720 (t0) REVERT: A 86 LEU cc_start: 0.9458 (mt) cc_final: 0.9063 (mt) REVERT: A 127 ASP cc_start: 0.8880 (m-30) cc_final: 0.8627 (m-30) REVERT: A 221 ARG cc_start: 0.8735 (mmt180) cc_final: 0.8371 (mmt90) REVERT: A 224 TYR cc_start: 0.9084 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: A 272 TYR cc_start: 0.8531 (t80) cc_final: 0.8152 (t80) REVERT: A 276 ILE cc_start: 0.9454 (tp) cc_final: 0.9239 (tp) REVERT: A 302 MET cc_start: 0.8486 (mtt) cc_final: 0.8066 (mtt) REVERT: A 313 MET cc_start: 0.6647 (tpt) cc_final: 0.6141 (tpt) REVERT: A 363 VAL cc_start: 0.8928 (t) cc_final: 0.8670 (p) REVERT: A 372 GLN cc_start: 0.9152 (mp10) cc_final: 0.8800 (mm-40) REVERT: A 375 VAL cc_start: 0.9391 (t) cc_final: 0.9038 (p) REVERT: A 377 MET cc_start: 0.8547 (tmm) cc_final: 0.8116 (tmm) REVERT: A 398 MET cc_start: 0.9361 (tpp) cc_final: 0.9027 (mmp) REVERT: A 413 MET cc_start: 0.9218 (mmm) cc_final: 0.8863 (mmm) REVERT: A 434 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8803 (mp0) REVERT: B 8 GLN cc_start: 0.8639 (mt0) cc_final: 0.8246 (mt0) REVERT: B 68 VAL cc_start: 0.9397 (OUTLIER) cc_final: 0.9118 (m) REVERT: B 107 HIS cc_start: 0.8547 (t70) cc_final: 0.7887 (t70) REVERT: B 299 LYS cc_start: 0.9569 (tppt) cc_final: 0.9049 (tppt) REVERT: B 302 MET cc_start: 0.8940 (mmm) cc_final: 0.8302 (mtt) REVERT: B 309 HIS cc_start: 0.8707 (m170) cc_final: 0.8414 (m-70) REVERT: B 323 MET cc_start: 0.7948 (mpp) cc_final: 0.6490 (mpp) REVERT: B 345 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8272 (pp20) REVERT: B 373 MET cc_start: 0.8539 (ptp) cc_final: 0.8236 (mtp) REVERT: B 416 MET cc_start: 0.8768 (ptp) cc_final: 0.8547 (ppp) outliers start: 40 outliers final: 28 residues processed: 226 average time/residue: 0.2579 time to fit residues: 82.7072 Evaluate side-chains 229 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 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 C residue 338 ASN Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 353 THR 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 26 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 21 optimal weight: 30.0000 chunk 18 optimal weight: 30.0000 chunk 41 optimal weight: 0.8980 chunk 22 optimal weight: 30.0000 chunk 7 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 50.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.084247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.064859 restraints weight = 34508.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.067169 restraints weight = 18267.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.068739 restraints weight = 11620.102| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 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 = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9870 Z= 0.154 Angle : 0.779 18.417 13407 Z= 0.375 Chirality : 0.045 0.190 1505 Planarity : 0.004 0.040 1749 Dihedral : 10.563 169.537 1435 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.43 % Allowed : 24.85 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.24), residues: 1172 helix: 0.81 (0.23), residues: 484 sheet: -0.40 (0.33), residues: 196 loop : -1.07 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 346 HIS 0.006 0.001 HIS A 8 PHE 0.017 0.002 PHE B 395 TYR 0.013 0.002 TYR C 93 ARG 0.008 0.001 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 450) hydrogen bonds : angle 4.96400 ( 1341) covalent geometry : bond 0.00349 ( 9865) covalent geometry : angle 0.77856 (13407) Misc. bond : bond 0.00290 ( 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 233 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 1.063 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 149 TYR cc_start: 0.8711 (t80) cc_final: 0.8280 (t80) REVERT: C 151 GLU cc_start: 0.9111 (mp0) cc_final: 0.8465 (mp0) REVERT: C 173 ARG cc_start: 0.9036 (mmm160) cc_final: 0.8811 (tpp-160) REVERT: C 182 LYS cc_start: 0.8972 (tttp) cc_final: 0.8532 (tttp) REVERT: C 210 LEU cc_start: 0.4360 (OUTLIER) cc_final: 0.3714 (tt) REVERT: C 218 HIS cc_start: 0.8547 (m-70) cc_final: 0.8014 (m-70) REVERT: C 252 ASP cc_start: 0.8381 (t0) cc_final: 0.8134 (t0) REVERT: C 274 GLN cc_start: 0.8999 (mt0) cc_final: 0.8470 (pp30) REVERT: C 301 TYR cc_start: 0.9210 (m-80) cc_final: 0.8927 (m-80) REVERT: C 305 LYS cc_start: 0.9283 (mttp) cc_final: 0.8972 (mtpt) REVERT: C 338 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8662 (t0) REVERT: A 86 LEU cc_start: 0.9411 (mt) cc_final: 0.8927 (mt) REVERT: A 127 ASP cc_start: 0.8840 (m-30) cc_final: 0.8568 (m-30) REVERT: A 221 ARG cc_start: 0.8694 (mmt180) cc_final: 0.8357 (mmt90) REVERT: A 224 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.8202 (m-80) REVERT: A 272 TYR cc_start: 0.8568 (t80) cc_final: 0.8153 (t80) REVERT: A 276 ILE cc_start: 0.9422 (tp) cc_final: 0.9205 (tp) REVERT: A 302 MET cc_start: 0.8493 (mtt) cc_final: 0.8073 (mtt) REVERT: A 304 LYS cc_start: 0.9033 (tttm) cc_final: 0.8697 (tttt) REVERT: A 363 VAL cc_start: 0.8919 (t) cc_final: 0.8654 (p) REVERT: A 372 GLN cc_start: 0.9191 (mp10) cc_final: 0.8789 (mm-40) REVERT: A 375 VAL cc_start: 0.9397 (t) cc_final: 0.9027 (p) REVERT: A 377 MET cc_start: 0.8545 (tmm) cc_final: 0.8095 (tmm) REVERT: A 380 ASN cc_start: 0.8685 (t0) cc_final: 0.8294 (m-40) REVERT: A 413 MET cc_start: 0.9177 (mmm) cc_final: 0.8823 (mmm) REVERT: B 8 GLN cc_start: 0.8726 (mt0) cc_final: 0.8216 (mt0) REVERT: B 299 LYS cc_start: 0.9573 (tppt) cc_final: 0.8955 (tptt) REVERT: B 302 MET cc_start: 0.9092 (mmm) cc_final: 0.8282 (mtt) REVERT: B 309 HIS cc_start: 0.8821 (m170) cc_final: 0.8575 (m-70) REVERT: B 323 MET cc_start: 0.7856 (mpp) cc_final: 0.6307 (mpp) REVERT: B 373 MET cc_start: 0.8608 (ptp) cc_final: 0.8330 (mtp) outliers start: 34 outliers final: 29 residues processed: 216 average time/residue: 0.2057 time to fit residues: 62.7692 Evaluate side-chains 226 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 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 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 259 LEU 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 181 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 376 THR 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 82 optimal weight: 20.0000 chunk 112 optimal weight: 40.0000 chunk 90 optimal weight: 40.0000 chunk 54 optimal weight: 30.0000 chunk 59 optimal weight: 20.0000 chunk 70 optimal weight: 0.2980 chunk 44 optimal weight: 6.9990 chunk 48 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 80 optimal weight: 50.0000 overall best weight: 13.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.081460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.062521 restraints weight = 36119.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.064787 restraints weight = 18889.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.066288 restraints weight = 11947.982| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9870 Z= 0.241 Angle : 0.839 18.247 13407 Z= 0.413 Chirality : 0.047 0.217 1505 Planarity : 0.005 0.051 1749 Dihedral : 11.002 177.394 1435 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.43 % Allowed : 25.35 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.24), residues: 1172 helix: 0.54 (0.23), residues: 482 sheet: -0.59 (0.33), residues: 200 loop : -1.21 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 346 HIS 0.009 0.002 HIS A 28 PHE 0.026 0.002 PHE A 149 TYR 0.015 0.002 TYR B 224 ARG 0.009 0.001 ARG B 390 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 450) hydrogen bonds : angle 5.22305 ( 1341) covalent geometry : bond 0.00522 ( 9865) covalent geometry : angle 0.83936 (13407) Misc. bond : bond 0.00300 ( 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 222 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 1.133 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 124 MET cc_start: 0.8467 (mmm) cc_final: 0.7924 (tpt) REVERT: C 149 TYR cc_start: 0.8704 (t80) cc_final: 0.8330 (t80) REVERT: C 151 GLU cc_start: 0.9127 (mp0) cc_final: 0.8420 (mp0) REVERT: C 182 LYS cc_start: 0.8938 (tttp) cc_final: 0.8509 (tttp) REVERT: C 210 LEU cc_start: 0.4584 (OUTLIER) cc_final: 0.3921 (tt) REVERT: C 218 HIS cc_start: 0.8559 (m-70) cc_final: 0.8007 (m-70) REVERT: C 274 GLN cc_start: 0.9022 (mt0) cc_final: 0.8499 (pp30) REVERT: C 301 TYR cc_start: 0.9199 (m-80) cc_final: 0.8863 (m-80) REVERT: C 305 LYS cc_start: 0.9219 (mttp) cc_final: 0.8916 (mtpt) REVERT: C 338 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8719 (t0) REVERT: A 86 LEU cc_start: 0.9440 (mt) cc_final: 0.9118 (mt) REVERT: A 127 ASP cc_start: 0.8841 (m-30) cc_final: 0.8577 (m-30) REVERT: A 221 ARG cc_start: 0.8775 (mmt180) cc_final: 0.8476 (mmt90) REVERT: A 224 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.8446 (m-80) REVERT: A 272 TYR cc_start: 0.8600 (t80) cc_final: 0.8289 (t80) REVERT: A 276 ILE cc_start: 0.9399 (tp) cc_final: 0.9186 (tp) REVERT: A 297 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8276 (tm-30) REVERT: A 302 MET cc_start: 0.8483 (mtt) cc_final: 0.8230 (mtt) REVERT: A 363 VAL cc_start: 0.8950 (t) cc_final: 0.8649 (p) REVERT: A 372 GLN cc_start: 0.9237 (mp10) cc_final: 0.8835 (mm-40) REVERT: A 375 VAL cc_start: 0.9444 (t) cc_final: 0.9159 (p) REVERT: A 377 MET cc_start: 0.8496 (tmm) cc_final: 0.8064 (tmm) REVERT: A 380 ASN cc_start: 0.8641 (t0) cc_final: 0.8211 (m-40) REVERT: A 413 MET cc_start: 0.9283 (mmm) cc_final: 0.8904 (mmm) REVERT: B 204 ILE cc_start: 0.9383 (pt) cc_final: 0.9136 (mp) REVERT: B 302 MET cc_start: 0.9182 (mmm) cc_final: 0.8299 (mtt) REVERT: B 309 HIS cc_start: 0.8976 (m170) cc_final: 0.8625 (m90) REVERT: B 323 MET cc_start: 0.8060 (mpp) cc_final: 0.6552 (mpp) REVERT: B 373 MET cc_start: 0.8674 (ptp) cc_final: 0.8363 (mtp) REVERT: B 416 MET cc_start: 0.8899 (ptp) cc_final: 0.8689 (ppp) outliers start: 34 outliers final: 26 residues processed: 208 average time/residue: 0.2177 time to fit residues: 64.2534 Evaluate side-chains 211 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 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 C residue 338 ASN Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 265 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 353 THR Chi-restraints excluded: chain B residue 376 THR 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 61 optimal weight: 6.9990 chunk 19 optimal weight: 50.0000 chunk 41 optimal weight: 0.0670 chunk 35 optimal weight: 50.0000 chunk 101 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 67 optimal weight: 30.0000 chunk 83 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 chunk 97 optimal weight: 40.0000 chunk 25 optimal weight: 6.9990 overall best weight: 8.8130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.082881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.063327 restraints weight = 35799.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.065636 restraints weight = 18765.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.067148 restraints weight = 11862.327| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9870 Z= 0.178 Angle : 0.824 18.301 13407 Z= 0.400 Chirality : 0.047 0.386 1505 Planarity : 0.004 0.048 1749 Dihedral : 10.984 176.140 1435 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.93 % Allowed : 25.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.24), residues: 1172 helix: 0.59 (0.23), residues: 482 sheet: -0.56 (0.34), residues: 187 loop : -1.16 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 346 HIS 0.008 0.001 HIS A 28 PHE 0.025 0.002 PHE A 149 TYR 0.015 0.002 TYR B 202 ARG 0.009 0.001 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 450) hydrogen bonds : angle 5.12390 ( 1341) covalent geometry : bond 0.00400 ( 9865) covalent geometry : angle 0.82413 (13407) Misc. bond : bond 0.00275 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3555.83 seconds wall clock time: 64 minutes 40.31 seconds (3880.31 seconds total)