Starting phenix.real_space_refine on Tue Jun 17 22:54:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kfh_9973/06_2025/6kfh_9973.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kfh_9973/06_2025/6kfh_9973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kfh_9973/06_2025/6kfh_9973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kfh_9973/06_2025/6kfh_9973.map" model { file = "/net/cci-nas-00/data/ceres_data/6kfh_9973/06_2025/6kfh_9973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kfh_9973/06_2025/6kfh_9973.cif" } resolution = 3.6 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= 0.000 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 13832 2.51 5 N 3344 2.21 5 O 3568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20840 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Restraints were copied for chains: C, B, E, D, G, F, H Time building chain proxies: 6.97, per 1000 atoms: 0.33 Number of scatterers: 20840 At special positions: 0 Unit cell: (124.432, 124.432, 108.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3568 8.00 N 3344 7.00 C 13832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 58 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 58 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 58 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 58 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS H 58 " - pdb=" SG CYS H 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 76 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 76 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS H 76 " - pdb=" SG CYS H 248 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 2.7 seconds 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4880 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 8 sheets defined 71.1% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 30 through 53 removed outlier: 3.596A pdb=" N VAL A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 79 removed outlier: 4.455A pdb=" N GLN A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 136 through 152 removed outlier: 3.865A pdb=" N ALA A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE A 158 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS A 159 " --> pdb=" O ASP A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 159' Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.575A pdb=" N PHE A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.516A pdb=" N TYR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 212 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 269 through 274 removed outlier: 4.039A pdb=" N GLU A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 337 through 350 removed outlier: 3.804A pdb=" N ASP A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 removed outlier: 3.523A pdb=" N TYR A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 53 removed outlier: 3.595A pdb=" N VAL B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 removed outlier: 4.456A pdb=" N GLN B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.864A pdb=" N ALA B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE B 158 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 159' Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.576A pdb=" N PHE B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 212 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 269 through 274 removed outlier: 4.039A pdb=" N GLU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 326 through 334 Processing helix chain 'B' and resid 337 through 350 removed outlier: 3.803A pdb=" N ASP B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR B 356 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 53 removed outlier: 3.595A pdb=" N VAL C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 removed outlier: 4.455A pdb=" N GLN C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 136 through 152 removed outlier: 3.865A pdb=" N ALA C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE C 158 " --> pdb=" O ASP C 155 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 159' Processing helix chain 'C' and resid 160 through 168 removed outlier: 3.576A pdb=" N PHE C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 212 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 269 through 274 removed outlier: 4.040A pdb=" N GLU C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 326 through 334 Processing helix chain 'C' and resid 337 through 350 removed outlier: 3.802A pdb=" N ASP C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 53 removed outlier: 3.596A pdb=" N VAL D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 79 removed outlier: 4.456A pdb=" N GLN D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) Proline residue: D 122 - end of helix Processing helix chain 'D' and resid 136 through 152 removed outlier: 3.864A pdb=" N ALA D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE D 158 " --> pdb=" O ASP D 155 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 155 through 159' Processing helix chain 'D' and resid 160 through 168 removed outlier: 3.575A pdb=" N PHE D 165 " --> pdb=" O ARG D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 181 removed outlier: 3.518A pdb=" N TYR D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 212 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 269 through 274 removed outlier: 4.039A pdb=" N GLU D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 326 through 334 Processing helix chain 'D' and resid 337 through 350 removed outlier: 3.803A pdb=" N ASP D 343 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR D 356 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU D 357 " --> pdb=" O PRO D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 53 removed outlier: 3.595A pdb=" N VAL E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 79 removed outlier: 4.455A pdb=" N GLN E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) Proline residue: E 122 - end of helix Processing helix chain 'E' and resid 136 through 152 removed outlier: 3.864A pdb=" N ALA E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE E 158 " --> pdb=" O ASP E 155 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 155 through 159' Processing helix chain 'E' and resid 160 through 168 removed outlier: 3.576A pdb=" N PHE E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 212 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 269 through 274 removed outlier: 4.038A pdb=" N GLU E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 316 Processing helix chain 'E' and resid 326 through 334 Processing helix chain 'E' and resid 337 through 350 removed outlier: 3.803A pdb=" N ASP E 343 " --> pdb=" O LEU E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR E 356 " --> pdb=" O ILE E 352 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU E 357 " --> pdb=" O PRO E 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 53 removed outlier: 3.596A pdb=" N VAL F 34 " --> pdb=" O LEU F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 79 removed outlier: 4.456A pdb=" N GLN F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 133 removed outlier: 4.549A pdb=" N ALA F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) Proline residue: F 122 - end of helix Processing helix chain 'F' and resid 136 through 152 removed outlier: 3.864A pdb=" N ALA F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 159 removed outlier: 3.603A pdb=" N PHE F 158 " --> pdb=" O ASP F 155 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 155 through 159' Processing helix chain 'F' and resid 160 through 168 removed outlier: 3.575A pdb=" N PHE F 165 " --> pdb=" O ARG F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 212 Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 269 through 274 removed outlier: 4.039A pdb=" N GLU F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE F 282 " --> pdb=" O ILE F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 326 through 334 Processing helix chain 'F' and resid 337 through 350 removed outlier: 3.802A pdb=" N ASP F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 364 removed outlier: 3.523A pdb=" N TYR F 356 " --> pdb=" O ILE F 352 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU F 357 " --> pdb=" O PRO F 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 53 removed outlier: 3.596A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 79 removed outlier: 4.456A pdb=" N GLN G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Proline residue: G 122 - end of helix Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.864A pdb=" N ALA G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE G 158 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 155 through 159' Processing helix chain 'G' and resid 160 through 168 removed outlier: 3.576A pdb=" N PHE G 165 " --> pdb=" O ARG G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR G 172 " --> pdb=" O ARG G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 212 Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 269 through 274 removed outlier: 4.039A pdb=" N GLU G 274 " --> pdb=" O ASN G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE G 282 " --> pdb=" O ILE G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 326 through 334 Processing helix chain 'G' and resid 337 through 350 removed outlier: 3.803A pdb=" N ASP G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR G 356 " --> pdb=" O ILE G 352 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU G 357 " --> pdb=" O PRO G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 53 removed outlier: 3.596A pdb=" N VAL H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 79 removed outlier: 4.456A pdb=" N GLN H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA H 113 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Proline residue: H 122 - end of helix Processing helix chain 'H' and resid 136 through 152 removed outlier: 3.865A pdb=" N ALA H 140 " --> pdb=" O ASP H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE H 158 " --> pdb=" O ASP H 155 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 155 through 159' Processing helix chain 'H' and resid 160 through 168 removed outlier: 3.575A pdb=" N PHE H 165 " --> pdb=" O ARG H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR H 172 " --> pdb=" O ARG H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 212 Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 269 through 274 removed outlier: 4.039A pdb=" N GLU H 274 " --> pdb=" O ASN H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE H 282 " --> pdb=" O ILE H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 326 through 334 Processing helix chain 'H' and resid 337 through 350 removed outlier: 3.803A pdb=" N ASP H 343 " --> pdb=" O LEU H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR H 356 " --> pdb=" O ILE H 352 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU H 357 " --> pdb=" O PRO H 353 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA2, first strand: chain 'B' and resid 245 through 246 Processing sheet with id=AA3, first strand: chain 'C' and resid 245 through 246 Processing sheet with id=AA4, first strand: chain 'D' and resid 245 through 246 Processing sheet with id=AA5, first strand: chain 'E' and resid 245 through 246 Processing sheet with id=AA6, first strand: chain 'F' and resid 245 through 246 Processing sheet with id=AA7, first strand: chain 'G' and resid 245 through 246 Processing sheet with id=AA8, first strand: chain 'H' and resid 245 through 246 1224 hydrogen bonds defined for protein. 3648 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: 5.88 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6232 1.34 - 1.46: 5580 1.46 - 1.58: 9524 1.58 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 21472 Sorted by residual: bond pdb=" CA ILE G 56 " pdb=" CB ILE G 56 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.94e+00 bond pdb=" CA ILE F 56 " pdb=" CB ILE F 56 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.85e+00 bond pdb=" CA ILE E 56 " pdb=" CB ILE E 56 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.71e+00 bond pdb=" CA ILE C 56 " pdb=" CB ILE C 56 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.63e+00 bond pdb=" CA ILE A 56 " pdb=" CB ILE A 56 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.59e+00 ... (remaining 21467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 28835 2.33 - 4.66: 368 4.66 - 6.99: 61 6.99 - 9.32: 0 9.32 - 11.65: 8 Bond angle restraints: 29272 Sorted by residual: angle pdb=" C TRP C 59 " pdb=" N THR C 60 " pdb=" CA THR C 60 " ideal model delta sigma weight residual 121.95 110.30 11.65 3.74e+00 7.15e-02 9.70e+00 angle pdb=" C TRP F 59 " pdb=" N THR F 60 " pdb=" CA THR F 60 " ideal model delta sigma weight residual 121.95 110.35 11.60 3.74e+00 7.15e-02 9.63e+00 angle pdb=" C TRP H 59 " pdb=" N THR H 60 " pdb=" CA THR H 60 " ideal model delta sigma weight residual 121.95 110.36 11.59 3.74e+00 7.15e-02 9.61e+00 angle pdb=" C TRP B 59 " pdb=" N THR B 60 " pdb=" CA THR B 60 " ideal model delta sigma weight residual 121.95 110.37 11.58 3.74e+00 7.15e-02 9.59e+00 angle pdb=" C TRP A 59 " pdb=" N THR A 60 " pdb=" CA THR A 60 " ideal model delta sigma weight residual 121.95 110.37 11.58 3.74e+00 7.15e-02 9.58e+00 ... (remaining 29267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 10564 15.88 - 31.77: 1284 31.77 - 47.65: 360 47.65 - 63.53: 8 63.53 - 79.41: 24 Dihedral angle restraints: 12240 sinusoidal: 4704 harmonic: 7536 Sorted by residual: dihedral pdb=" CA ASP F 28 " pdb=" C ASP F 28 " pdb=" N ARG F 29 " pdb=" CA ARG F 29 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ASP C 28 " pdb=" C ASP C 28 " pdb=" N ARG C 29 " pdb=" CA ARG C 29 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ASP D 28 " pdb=" C ASP D 28 " pdb=" N ARG D 29 " pdb=" CA ARG D 29 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 12237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1979 0.036 - 0.071: 907 0.071 - 0.107: 237 0.107 - 0.143: 86 0.143 - 0.178: 23 Chirality restraints: 3232 Sorted by residual: chirality pdb=" CA GLU G 274 " pdb=" N GLU G 274 " pdb=" C GLU G 274 " pdb=" CB GLU G 274 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CA GLU D 274 " pdb=" N GLU D 274 " pdb=" C GLU D 274 " pdb=" CB GLU D 274 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA GLU F 274 " pdb=" N GLU F 274 " pdb=" C GLU F 274 " pdb=" CB GLU F 274 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 3229 not shown) Planarity restraints: 3584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 305 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C LYS G 305 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS G 305 " 0.009 2.00e-02 2.50e+03 pdb=" N THR G 306 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 305 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" C LYS H 305 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS H 305 " 0.009 2.00e-02 2.50e+03 pdb=" N THR H 306 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 305 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" C LYS F 305 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS F 305 " 0.009 2.00e-02 2.50e+03 pdb=" N THR F 306 " 0.008 2.00e-02 2.50e+03 ... (remaining 3581 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5610 2.78 - 3.31: 20640 3.31 - 3.84: 33880 3.84 - 4.37: 37027 4.37 - 4.90: 64227 Nonbonded interactions: 161384 Sorted by model distance: nonbonded pdb=" O ASN F 31 " pdb=" OG1 THR F 35 " model vdw 2.255 3.040 nonbonded pdb=" O ASN E 31 " pdb=" OG1 THR E 35 " model vdw 2.255 3.040 nonbonded pdb=" O ASN G 31 " pdb=" OG1 THR G 35 " model vdw 2.255 3.040 nonbonded pdb=" O ASN D 31 " pdb=" OG1 THR D 35 " model vdw 2.255 3.040 nonbonded pdb=" O ASN B 31 " pdb=" OG1 THR B 35 " model vdw 2.255 3.040 ... (remaining 161379 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 43.690 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 : 0.007 0.050 21488 Z= 0.313 Angle : 0.735 11.650 29304 Z= 0.389 Chirality : 0.045 0.178 3232 Planarity : 0.003 0.021 3584 Dihedral : 14.752 79.413 7312 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.15 (0.15), residues: 2480 helix: -0.95 (0.11), residues: 1680 sheet: -5.11 (0.18), residues: 40 loop : -4.48 (0.16), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.004 0.001 HIS G 50 PHE 0.012 0.002 PHE D 119 TYR 0.008 0.001 TYR A 172 ARG 0.003 0.000 ARG E 168 Details of bonding type rmsd hydrogen bonds : bond 0.13705 ( 1224) hydrogen bonds : angle 6.28556 ( 3648) SS BOND : bond 0.00262 ( 16) SS BOND : angle 0.70845 ( 32) covalent geometry : bond 0.00706 (21472) covalent geometry : angle 0.73493 (29272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 772 time to evaluate : 2.248 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: symmetry clash REVERT: A 28 ASP cc_start: 0.8209 (m-30) cc_final: 0.7900 (m-30) REVERT: A 54 ASP cc_start: 0.7573 (p0) cc_final: 0.7340 (p0) REVERT: A 67 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7432 (mm-40) REVERT: A 103 GLN cc_start: 0.7094 (pt0) cc_final: 0.6744 (pt0) REVERT: A 107 TRP cc_start: 0.8173 (m100) cc_final: 0.7858 (m-10) REVERT: A 142 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8959 (mtpp) REVERT: A 145 ASP cc_start: 0.8700 (t70) cc_final: 0.8461 (t0) REVERT: A 198 TRP cc_start: 0.8621 (t-100) cc_final: 0.8241 (t-100) REVERT: A 226 ILE cc_start: 0.7735 (mm) cc_final: 0.7449 (mm) REVERT: A 241 HIS cc_start: 0.8118 (p90) cc_final: 0.7639 (p-80) REVERT: A 313 LYS cc_start: 0.8845 (mtpt) cc_final: 0.8580 (mtmm) REVERT: B 28 ASP cc_start: 0.8118 (m-30) cc_final: 0.7786 (m-30) REVERT: B 103 GLN cc_start: 0.6822 (pt0) cc_final: 0.6601 (pt0) REVERT: B 107 TRP cc_start: 0.7935 (m100) cc_final: 0.7706 (m-10) REVERT: B 145 ASP cc_start: 0.8691 (t70) cc_final: 0.8362 (t0) REVERT: B 313 LYS cc_start: 0.8750 (mtpt) cc_final: 0.8516 (mtmm) REVERT: B 353 PRO cc_start: 0.9454 (Cg_endo) cc_final: 0.9203 (Cg_exo) REVERT: C 45 LEU cc_start: 0.8259 (tp) cc_final: 0.8031 (tp) REVERT: C 49 SER cc_start: 0.9049 (t) cc_final: 0.8744 (m) REVERT: C 103 GLN cc_start: 0.7088 (pt0) cc_final: 0.6714 (pt0) REVERT: C 107 TRP cc_start: 0.8226 (m100) cc_final: 0.7850 (m-10) REVERT: C 154 LYS cc_start: 0.8644 (mttt) cc_final: 0.8442 (mttt) REVERT: C 157 LYS cc_start: 0.7931 (mmtt) cc_final: 0.7716 (mtmm) REVERT: C 198 TRP cc_start: 0.8577 (t-100) cc_final: 0.8150 (t-100) REVERT: C 361 MET cc_start: 0.9464 (mtp) cc_final: 0.9224 (mtm) REVERT: D 23 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7988 (mmtm) REVERT: D 103 GLN cc_start: 0.6794 (pt0) cc_final: 0.6579 (pt0) REVERT: D 107 TRP cc_start: 0.8123 (m100) cc_final: 0.7899 (m-10) REVERT: D 303 CYS cc_start: 0.7983 (t) cc_final: 0.7654 (t) REVERT: D 313 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8378 (mtmm) REVERT: E 59 TRP cc_start: 0.7497 (t-100) cc_final: 0.7278 (t60) REVERT: E 103 GLN cc_start: 0.6976 (pt0) cc_final: 0.6669 (pt0) REVERT: E 107 TRP cc_start: 0.8177 (m100) cc_final: 0.7835 (m-10) REVERT: E 142 LYS cc_start: 0.9192 (mtmm) cc_final: 0.8992 (mtmt) REVERT: E 307 LYS cc_start: 0.8375 (mttt) cc_final: 0.8117 (tmtt) REVERT: E 313 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8517 (mtmm) REVERT: E 361 MET cc_start: 0.9426 (mtp) cc_final: 0.9197 (mtm) REVERT: F 23 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7917 (mmtm) REVERT: F 313 LYS cc_start: 0.8759 (mtpt) cc_final: 0.8485 (mtmm) REVERT: F 353 PRO cc_start: 0.9477 (Cg_endo) cc_final: 0.9263 (Cg_exo) REVERT: G 28 ASP cc_start: 0.8136 (m-30) cc_final: 0.7817 (m-30) REVERT: G 54 ASP cc_start: 0.7497 (p0) cc_final: 0.7260 (p0) REVERT: G 103 GLN cc_start: 0.7069 (pt0) cc_final: 0.6725 (pt0) REVERT: G 107 TRP cc_start: 0.8141 (m100) cc_final: 0.7832 (m-10) REVERT: G 142 LYS cc_start: 0.9201 (mtmm) cc_final: 0.8941 (mtpp) REVERT: G 145 ASP cc_start: 0.8778 (t70) cc_final: 0.8565 (t0) REVERT: G 177 ILE cc_start: 0.9366 (mm) cc_final: 0.9148 (mt) REVERT: G 198 TRP cc_start: 0.8711 (t-100) cc_final: 0.8405 (t-100) REVERT: G 226 ILE cc_start: 0.7693 (mm) cc_final: 0.7408 (mm) REVERT: G 241 HIS cc_start: 0.8117 (p90) cc_final: 0.7640 (p-80) REVERT: G 313 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8493 (mtmm) REVERT: G 361 MET cc_start: 0.9396 (mtp) cc_final: 0.9185 (mtm) REVERT: H 23 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7967 (mmtm) REVERT: H 107 TRP cc_start: 0.8017 (m100) cc_final: 0.7768 (m-10) REVERT: H 145 ASP cc_start: 0.8732 (t70) cc_final: 0.8486 (t0) REVERT: H 313 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8493 (mtmm) REVERT: H 325 ILE cc_start: 0.8524 (mp) cc_final: 0.8319 (mm) outliers start: 0 outliers final: 0 residues processed: 772 average time/residue: 0.3353 time to fit residues: 388.7663 Evaluate side-chains 556 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 225 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN A 232 GLN A 247 HIS A 329 GLN B 199 GLN B 212 GLN B 232 GLN B 247 HIS B 329 GLN C 212 GLN C 232 GLN C 247 HIS C 329 GLN D 199 GLN D 212 GLN D 232 GLN D 247 HIS D 314 ASN D 329 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN E 232 GLN E 247 HIS E 329 GLN F 63 GLN F 212 GLN F 232 GLN F 247 HIS F 329 GLN G 50 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 GLN G 232 GLN G 247 HIS G 329 GLN H 199 GLN H 212 GLN H 232 GLN H 247 HIS H 329 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.130005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.108517 restraints weight = 29823.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112424 restraints weight = 15536.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.115045 restraints weight = 10122.962| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21488 Z= 0.136 Angle : 0.615 6.132 29304 Z= 0.322 Chirality : 0.042 0.164 3232 Planarity : 0.004 0.065 3584 Dihedral : 4.900 20.795 2752 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.54 % Allowed : 19.52 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.49 (0.16), residues: 2480 helix: 0.27 (0.12), residues: 1712 sheet: None (None), residues: 0 loop : -4.02 (0.17), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 68 HIS 0.012 0.001 HIS G 50 PHE 0.014 0.001 PHE G 242 TYR 0.017 0.001 TYR C 301 ARG 0.006 0.000 ARG B 244 Details of bonding type rmsd hydrogen bonds : bond 0.04597 ( 1224) hydrogen bonds : angle 4.60069 ( 3648) SS BOND : bond 0.00068 ( 16) SS BOND : angle 0.87980 ( 32) covalent geometry : bond 0.00291 (21472) covalent geometry : angle 0.61436 (29272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 631 time to evaluate : 2.053 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7854 (p0) cc_final: 0.7585 (p0) REVERT: A 107 TRP cc_start: 0.8314 (m100) cc_final: 0.7636 (m-10) REVERT: A 145 ASP cc_start: 0.8617 (t70) cc_final: 0.8386 (t0) REVERT: A 156 ASP cc_start: 0.8356 (t0) cc_final: 0.8131 (t0) REVERT: A 313 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8599 (mtmm) REVERT: B 107 TRP cc_start: 0.7978 (m100) cc_final: 0.7431 (m-10) REVERT: B 130 ILE cc_start: 0.9029 (tp) cc_final: 0.8521 (tp) REVERT: B 145 ASP cc_start: 0.8577 (t70) cc_final: 0.8326 (t0) REVERT: B 159 LYS cc_start: 0.8031 (mptt) cc_final: 0.7735 (mptt) REVERT: B 313 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8459 (mtmm) REVERT: C 45 LEU cc_start: 0.8133 (tp) cc_final: 0.7907 (tp) REVERT: C 49 SER cc_start: 0.8945 (t) cc_final: 0.8494 (m) REVERT: C 67 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7532 (mp10) REVERT: C 103 GLN cc_start: 0.7108 (pt0) cc_final: 0.6857 (pt0) REVERT: C 107 TRP cc_start: 0.8327 (m100) cc_final: 0.7624 (m-10) REVERT: C 154 LYS cc_start: 0.8716 (mttt) cc_final: 0.8510 (mtmt) REVERT: C 186 ARG cc_start: 0.7043 (mtp180) cc_final: 0.6708 (mtp85) REVERT: D 107 TRP cc_start: 0.7992 (m100) cc_final: 0.7533 (m-10) REVERT: D 130 ILE cc_start: 0.8932 (tp) cc_final: 0.8444 (tp) REVERT: D 313 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8258 (mtmm) REVERT: E 103 GLN cc_start: 0.6831 (pt0) cc_final: 0.6615 (pt0) REVERT: E 107 TRP cc_start: 0.8314 (m100) cc_final: 0.7679 (m-10) REVERT: E 142 LYS cc_start: 0.9154 (mtmm) cc_final: 0.8790 (mtpp) REVERT: E 313 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8429 (mtmm) REVERT: E 327 ASP cc_start: 0.8800 (m-30) cc_final: 0.8571 (m-30) REVERT: E 334 LEU cc_start: 0.7843 (tp) cc_final: 0.7617 (tp) REVERT: F 313 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8467 (mtmm) REVERT: G 54 ASP cc_start: 0.7882 (p0) cc_final: 0.7625 (p0) REVERT: G 103 GLN cc_start: 0.7040 (pt0) cc_final: 0.6822 (pt0) REVERT: G 107 TRP cc_start: 0.8299 (m100) cc_final: 0.7606 (m-10) REVERT: G 142 LYS cc_start: 0.9171 (mtmm) cc_final: 0.8886 (mtpp) REVERT: G 145 ASP cc_start: 0.8717 (t70) cc_final: 0.8457 (t0) REVERT: G 177 ILE cc_start: 0.9287 (mm) cc_final: 0.9054 (mt) REVERT: G 303 CYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8226 (t) REVERT: G 313 LYS cc_start: 0.8827 (mtpt) cc_final: 0.8495 (mtmm) REVERT: G 329 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8381 (pt0) REVERT: G 332 SER cc_start: 0.9240 (t) cc_final: 0.8939 (p) REVERT: H 107 TRP cc_start: 0.8125 (m100) cc_final: 0.7573 (m-10) REVERT: H 303 CYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7899 (t) REVERT: H 307 LYS cc_start: 0.8303 (tmtt) cc_final: 0.7852 (tptt) REVERT: H 313 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8486 (mtmm) outliers start: 56 outliers final: 41 residues processed: 668 average time/residue: 0.3112 time to fit residues: 318.6696 Evaluate side-chains 595 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 551 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 303 CYS Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN C 50 HIS ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN G 329 GLN H 151 ASN H 314 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.101711 restraints weight = 29861.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.105535 restraints weight = 15720.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.108103 restraints weight = 10291.224| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21488 Z= 0.145 Angle : 0.612 10.328 29304 Z= 0.313 Chirality : 0.042 0.168 3232 Planarity : 0.003 0.042 3584 Dihedral : 4.677 19.712 2752 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 2.90 % Allowed : 22.46 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.95 (0.17), residues: 2480 helix: 0.69 (0.12), residues: 1720 sheet: -4.32 (0.32), residues: 40 loop : -3.78 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 59 HIS 0.020 0.002 HIS A 50 PHE 0.012 0.001 PHE B 51 TYR 0.021 0.001 TYR F 300 ARG 0.004 0.000 ARG B 244 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 1224) hydrogen bonds : angle 4.40634 ( 3648) SS BOND : bond 0.00597 ( 16) SS BOND : angle 0.94287 ( 32) covalent geometry : bond 0.00325 (21472) covalent geometry : angle 0.61172 (29272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 581 time to evaluate : 2.420 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: 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: A 107 TRP cc_start: 0.8365 (m100) cc_final: 0.7603 (m-10) REVERT: A 145 ASP cc_start: 0.8688 (t70) cc_final: 0.8417 (t0) REVERT: A 313 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8625 (mtmm) REVERT: B 50 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7560 (p-80) REVERT: B 107 TRP cc_start: 0.7993 (m100) cc_final: 0.7376 (m-10) REVERT: B 145 ASP cc_start: 0.8595 (t70) cc_final: 0.8372 (t0) REVERT: B 156 ASP cc_start: 0.8603 (t0) cc_final: 0.8388 (t0) REVERT: B 159 LYS cc_start: 0.8123 (mptt) cc_final: 0.7829 (mptt) REVERT: B 236 TRP cc_start: 0.8116 (p90) cc_final: 0.7869 (p90) REVERT: B 264 LEU cc_start: 0.8935 (tp) cc_final: 0.8575 (tt) REVERT: B 313 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8431 (mtmm) REVERT: C 49 SER cc_start: 0.8957 (t) cc_final: 0.8505 (m) REVERT: C 67 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7487 (mp10) REVERT: C 103 GLN cc_start: 0.7076 (pt0) cc_final: 0.6822 (pt0) REVERT: C 107 TRP cc_start: 0.8310 (m100) cc_final: 0.7581 (m-10) REVERT: C 186 ARG cc_start: 0.7197 (mtp180) cc_final: 0.6810 (mtp85) REVERT: C 264 LEU cc_start: 0.8916 (tp) cc_final: 0.8492 (tt) REVERT: D 107 TRP cc_start: 0.7937 (m100) cc_final: 0.7455 (m-10) REVERT: D 130 ILE cc_start: 0.8910 (tp) cc_final: 0.8436 (tp) REVERT: D 313 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8256 (mtmm) REVERT: E 67 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7337 (mp10) REVERT: E 103 GLN cc_start: 0.6945 (pt0) cc_final: 0.6726 (pt0) REVERT: E 107 TRP cc_start: 0.8376 (m100) cc_final: 0.7700 (m-10) REVERT: E 186 ARG cc_start: 0.7221 (mtm110) cc_final: 0.7012 (mtp85) REVERT: E 313 LYS cc_start: 0.8844 (mtpt) cc_final: 0.8469 (mtmm) REVERT: E 327 ASP cc_start: 0.8901 (m-30) cc_final: 0.8691 (m-30) REVERT: F 67 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7741 (mp10) REVERT: F 107 TRP cc_start: 0.7979 (m100) cc_final: 0.7451 (m-10) REVERT: F 264 LEU cc_start: 0.8946 (tp) cc_final: 0.8617 (tt) REVERT: F 313 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8413 (mtmm) REVERT: F 332 SER cc_start: 0.9041 (t) cc_final: 0.8719 (p) REVERT: G 54 ASP cc_start: 0.7908 (p0) cc_final: 0.7654 (p0) REVERT: G 107 TRP cc_start: 0.8292 (m100) cc_final: 0.7569 (m-10) REVERT: G 142 LYS cc_start: 0.9105 (mtmm) cc_final: 0.8835 (mtpp) REVERT: G 145 ASP cc_start: 0.8710 (t70) cc_final: 0.8465 (t0) REVERT: G 303 CYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8273 (t) REVERT: G 313 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8550 (mtmm) REVERT: G 332 SER cc_start: 0.9349 (t) cc_final: 0.9001 (p) REVERT: H 107 TRP cc_start: 0.8046 (m100) cc_final: 0.7415 (m-10) REVERT: H 130 ILE cc_start: 0.9072 (tp) cc_final: 0.8699 (tp) REVERT: H 264 LEU cc_start: 0.8889 (tp) cc_final: 0.8539 (tt) REVERT: H 303 CYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7910 (t) REVERT: H 313 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8460 (mtmm) REVERT: H 332 SER cc_start: 0.9054 (t) cc_final: 0.8743 (p) outliers start: 64 outliers final: 49 residues processed: 623 average time/residue: 0.3199 time to fit residues: 306.6384 Evaluate side-chains 590 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 538 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 303 CYS Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 62 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 181 optimal weight: 0.0370 chunk 65 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 228 optimal weight: 1.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS B 50 HIS ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS H 50 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.104003 restraints weight = 29989.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107906 restraints weight = 15554.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110615 restraints weight = 10110.669| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21488 Z= 0.122 Angle : 0.585 9.757 29304 Z= 0.298 Chirality : 0.041 0.169 3232 Planarity : 0.003 0.037 3584 Dihedral : 4.471 18.011 2752 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.44 % Allowed : 24.59 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.17), residues: 2480 helix: 0.96 (0.12), residues: 1720 sheet: -4.12 (0.35), residues: 40 loop : -3.54 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 236 HIS 0.012 0.002 HIS E 50 PHE 0.017 0.001 PHE C 51 TYR 0.020 0.001 TYR D 120 ARG 0.003 0.000 ARG B 244 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 1224) hydrogen bonds : angle 4.25196 ( 3648) SS BOND : bond 0.00090 ( 16) SS BOND : angle 0.75797 ( 32) covalent geometry : bond 0.00260 (21472) covalent geometry : angle 0.58486 (29272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 607 time to evaluate : 2.554 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TRP cc_start: 0.8288 (m100) cc_final: 0.7551 (m-10) REVERT: A 145 ASP cc_start: 0.8625 (t70) cc_final: 0.8393 (t0) REVERT: A 264 LEU cc_start: 0.8887 (tp) cc_final: 0.8357 (tt) REVERT: A 313 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8625 (mtmm) REVERT: B 50 HIS cc_start: 0.8090 (OUTLIER) cc_final: 0.7271 (p90) REVERT: B 107 TRP cc_start: 0.7959 (m100) cc_final: 0.7338 (m-10) REVERT: B 130 ILE cc_start: 0.8991 (tp) cc_final: 0.8505 (tp) REVERT: B 145 ASP cc_start: 0.8573 (t70) cc_final: 0.8354 (t0) REVERT: B 236 TRP cc_start: 0.8148 (p90) cc_final: 0.7873 (p90) REVERT: B 264 LEU cc_start: 0.8934 (tp) cc_final: 0.8543 (tt) REVERT: B 274 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.5604 (mp0) REVERT: B 313 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8483 (mtmm) REVERT: B 332 SER cc_start: 0.9044 (t) cc_final: 0.8720 (p) REVERT: C 49 SER cc_start: 0.8961 (t) cc_final: 0.8637 (m) REVERT: C 67 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7525 (mp10) REVERT: C 107 TRP cc_start: 0.8405 (m100) cc_final: 0.7693 (m-10) REVERT: C 186 ARG cc_start: 0.7174 (mtp180) cc_final: 0.6875 (mmm-85) REVERT: C 236 TRP cc_start: 0.7974 (p90) cc_final: 0.7739 (p90) REVERT: C 301 TYR cc_start: 0.8573 (t80) cc_final: 0.8263 (t80) REVERT: C 303 CYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8077 (t) REVERT: D 107 TRP cc_start: 0.7878 (m100) cc_final: 0.7473 (m-10) REVERT: D 130 ILE cc_start: 0.8912 (tp) cc_final: 0.8453 (tp) REVERT: D 236 TRP cc_start: 0.8266 (p90) cc_final: 0.7982 (p90) REVERT: D 264 LEU cc_start: 0.8744 (tp) cc_final: 0.8349 (tt) REVERT: D 313 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8251 (mtmm) REVERT: E 67 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7398 (mp10) REVERT: E 107 TRP cc_start: 0.8309 (m100) cc_final: 0.7700 (m-10) REVERT: E 236 TRP cc_start: 0.7991 (p90) cc_final: 0.7776 (p90) REVERT: E 274 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: E 313 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8478 (mtmm) REVERT: E 327 ASP cc_start: 0.8883 (m-30) cc_final: 0.8646 (m-30) REVERT: F 67 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7748 (mp10) REVERT: F 107 TRP cc_start: 0.7723 (m100) cc_final: 0.7318 (m-10) REVERT: F 130 ILE cc_start: 0.8936 (tp) cc_final: 0.8509 (tp) REVERT: F 156 ASP cc_start: 0.8543 (t0) cc_final: 0.8232 (t0) REVERT: F 159 LYS cc_start: 0.8099 (mptt) cc_final: 0.7757 (mptt) REVERT: F 264 LEU cc_start: 0.8841 (tp) cc_final: 0.8456 (tt) REVERT: F 274 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: F 313 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8395 (mtmm) REVERT: F 332 SER cc_start: 0.9047 (t) cc_final: 0.8705 (p) REVERT: G 54 ASP cc_start: 0.7913 (p0) cc_final: 0.7657 (p0) REVERT: G 107 TRP cc_start: 0.8279 (m100) cc_final: 0.7603 (m-10) REVERT: G 145 ASP cc_start: 0.8646 (t70) cc_final: 0.8396 (t0) REVERT: G 264 LEU cc_start: 0.8894 (tp) cc_final: 0.8398 (tt) REVERT: G 313 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8554 (mtmm) REVERT: G 332 SER cc_start: 0.9345 (t) cc_final: 0.8990 (p) REVERT: H 50 HIS cc_start: 0.8036 (OUTLIER) cc_final: 0.7599 (p90) REVERT: H 107 TRP cc_start: 0.7994 (m100) cc_final: 0.7386 (m-10) REVERT: H 130 ILE cc_start: 0.8925 (tp) cc_final: 0.8559 (tp) REVERT: H 236 TRP cc_start: 0.8285 (p90) cc_final: 0.8021 (p90) REVERT: H 264 LEU cc_start: 0.8855 (tp) cc_final: 0.8474 (tt) REVERT: H 313 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8442 (mtmm) REVERT: H 332 SER cc_start: 0.9052 (t) cc_final: 0.8715 (p) outliers start: 76 outliers final: 53 residues processed: 657 average time/residue: 0.3056 time to fit residues: 312.8773 Evaluate side-chains 618 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 559 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 49 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 219 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS F 50 HIS ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.100305 restraints weight = 30320.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.104199 restraints weight = 15937.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.106788 restraints weight = 10433.216| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21488 Z= 0.139 Angle : 0.596 13.011 29304 Z= 0.303 Chirality : 0.042 0.179 3232 Planarity : 0.003 0.034 3584 Dihedral : 4.430 17.225 2752 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 4.12 % Allowed : 26.45 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.17), residues: 2480 helix: 1.08 (0.12), residues: 1720 sheet: -4.05 (0.37), residues: 40 loop : -3.50 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 236 HIS 0.009 0.001 HIS H 50 PHE 0.017 0.001 PHE B 51 TYR 0.023 0.001 TYR B 120 ARG 0.003 0.000 ARG B 244 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 1224) hydrogen bonds : angle 4.23352 ( 3648) SS BOND : bond 0.00106 ( 16) SS BOND : angle 0.94093 ( 32) covalent geometry : bond 0.00316 (21472) covalent geometry : angle 0.59567 (29272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 579 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TRP cc_start: 0.8296 (m100) cc_final: 0.7582 (m-10) REVERT: A 145 ASP cc_start: 0.8644 (t70) cc_final: 0.8386 (t0) REVERT: A 274 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.5901 (mp0) REVERT: A 303 CYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8307 (t) REVERT: A 313 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8621 (mtmm) REVERT: B 107 TRP cc_start: 0.7976 (m100) cc_final: 0.7394 (m-10) REVERT: B 130 ILE cc_start: 0.8942 (tp) cc_final: 0.8493 (tp) REVERT: B 145 ASP cc_start: 0.8556 (t70) cc_final: 0.8350 (t0) REVERT: B 159 LYS cc_start: 0.7897 (mppt) cc_final: 0.7557 (mptt) REVERT: B 264 LEU cc_start: 0.8929 (tp) cc_final: 0.8575 (tt) REVERT: B 274 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.5656 (mp0) REVERT: B 313 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8482 (mtmm) REVERT: B 332 SER cc_start: 0.9044 (t) cc_final: 0.8708 (p) REVERT: C 49 SER cc_start: 0.8978 (t) cc_final: 0.8522 (m) REVERT: C 67 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7535 (mp10) REVERT: C 107 TRP cc_start: 0.8380 (m100) cc_final: 0.7709 (m-10) REVERT: C 186 ARG cc_start: 0.7163 (mtp180) cc_final: 0.6889 (mmm-85) REVERT: C 236 TRP cc_start: 0.8007 (p90) cc_final: 0.7750 (p90) REVERT: C 303 CYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8293 (t) REVERT: D 107 TRP cc_start: 0.7889 (m100) cc_final: 0.7495 (m-10) REVERT: D 130 ILE cc_start: 0.8964 (tp) cc_final: 0.8494 (tp) REVERT: D 264 LEU cc_start: 0.8716 (tp) cc_final: 0.8365 (tt) REVERT: D 274 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.6415 (mp0) REVERT: D 313 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8215 (mtmm) REVERT: E 67 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7437 (mp10) REVERT: E 107 TRP cc_start: 0.8313 (m100) cc_final: 0.7725 (m-10) REVERT: E 236 TRP cc_start: 0.8014 (p90) cc_final: 0.7782 (p90) REVERT: E 303 CYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8379 (t) REVERT: E 313 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8508 (mtmm) REVERT: F 67 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7729 (mp10) REVERT: F 107 TRP cc_start: 0.7791 (m100) cc_final: 0.7374 (m-10) REVERT: F 156 ASP cc_start: 0.8506 (t0) cc_final: 0.8206 (t0) REVERT: F 159 LYS cc_start: 0.8191 (mptt) cc_final: 0.7852 (mptt) REVERT: F 229 ASP cc_start: 0.8625 (m-30) cc_final: 0.8421 (m-30) REVERT: F 264 LEU cc_start: 0.8828 (tp) cc_final: 0.8474 (tt) REVERT: F 274 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: F 313 LYS cc_start: 0.8763 (mtpt) cc_final: 0.8403 (mtmm) REVERT: F 332 SER cc_start: 0.9061 (t) cc_final: 0.8677 (p) REVERT: G 107 TRP cc_start: 0.8271 (m100) cc_final: 0.7619 (m-10) REVERT: G 142 LYS cc_start: 0.9146 (mtmm) cc_final: 0.8871 (mtpp) REVERT: G 145 ASP cc_start: 0.8640 (t70) cc_final: 0.8398 (t0) REVERT: G 264 LEU cc_start: 0.8904 (tp) cc_final: 0.8461 (tt) REVERT: G 274 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.5954 (mp0) REVERT: G 313 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8566 (mtmm) REVERT: G 332 SER cc_start: 0.9350 (t) cc_final: 0.8985 (p) REVERT: H 107 TRP cc_start: 0.7986 (m100) cc_final: 0.7414 (m-10) REVERT: H 130 ILE cc_start: 0.8901 (tp) cc_final: 0.8521 (tp) REVERT: H 229 ASP cc_start: 0.8635 (m-30) cc_final: 0.8415 (m-30) REVERT: H 236 TRP cc_start: 0.8361 (p90) cc_final: 0.8130 (p90) REVERT: H 264 LEU cc_start: 0.8851 (tp) cc_final: 0.8520 (tt) REVERT: H 274 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.6490 (mp0) REVERT: H 313 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8433 (mtmm) REVERT: H 332 SER cc_start: 0.9068 (t) cc_final: 0.8675 (p) outliers start: 91 outliers final: 63 residues processed: 640 average time/residue: 0.3929 time to fit residues: 393.5536 Evaluate side-chains 618 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 546 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 35 optimal weight: 0.0570 chunk 166 optimal weight: 0.9990 chunk 206 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 196 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 8 optimal weight: 0.0370 chunk 16 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 ASN ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 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 = 0.3403 r_free = 0.3403 target = 0.126316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.103954 restraints weight = 29683.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.107861 restraints weight = 15611.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.110495 restraints weight = 10215.666| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21488 Z= 0.118 Angle : 0.579 11.150 29304 Z= 0.295 Chirality : 0.040 0.179 3232 Planarity : 0.003 0.030 3584 Dihedral : 4.256 16.188 2752 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.89 % Allowed : 28.03 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.17), residues: 2480 helix: 1.27 (0.13), residues: 1720 sheet: -4.08 (0.36), residues: 40 loop : -3.40 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 236 HIS 0.015 0.001 HIS H 50 PHE 0.018 0.001 PHE F 51 TYR 0.025 0.001 TYR F 120 ARG 0.003 0.000 ARG B 244 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 1224) hydrogen bonds : angle 4.13971 ( 3648) SS BOND : bond 0.00187 ( 16) SS BOND : angle 1.32180 ( 32) covalent geometry : bond 0.00245 (21472) covalent geometry : angle 0.57731 (29272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 614 time to evaluate : 3.629 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TRP cc_start: 0.8333 (m100) cc_final: 0.7711 (m-10) REVERT: A 145 ASP cc_start: 0.8600 (t70) cc_final: 0.8360 (t0) REVERT: A 274 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.5814 (mp0) REVERT: A 313 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8613 (mtmm) REVERT: B 67 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7693 (mp10) REVERT: B 107 TRP cc_start: 0.7897 (m100) cc_final: 0.7369 (m-10) REVERT: B 145 ASP cc_start: 0.8543 (t70) cc_final: 0.8328 (t0) REVERT: B 159 LYS cc_start: 0.7787 (mppt) cc_final: 0.7450 (mptt) REVERT: B 264 LEU cc_start: 0.8755 (tp) cc_final: 0.8356 (tt) REVERT: B 274 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.5544 (mp0) REVERT: B 313 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8483 (mtmm) REVERT: B 332 SER cc_start: 0.9025 (t) cc_final: 0.8671 (p) REVERT: C 67 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7520 (mp10) REVERT: C 107 TRP cc_start: 0.8250 (m100) cc_final: 0.7656 (m-10) REVERT: C 186 ARG cc_start: 0.7185 (mtp180) cc_final: 0.6950 (mmm-85) REVERT: C 236 TRP cc_start: 0.8041 (p90) cc_final: 0.7774 (p90) REVERT: C 301 TYR cc_start: 0.8553 (t80) cc_final: 0.8248 (t80) REVERT: C 303 CYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8260 (t) REVERT: D 67 GLN cc_start: 0.7010 (mp10) cc_final: 0.6802 (mp10) REVERT: D 107 TRP cc_start: 0.7877 (m100) cc_final: 0.7438 (m-10) REVERT: D 236 TRP cc_start: 0.8179 (p90) cc_final: 0.7925 (p90) REVERT: D 274 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.6023 (mp0) REVERT: D 313 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8237 (mtmm) REVERT: E 67 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7399 (mp10) REVERT: E 107 TRP cc_start: 0.8249 (m100) cc_final: 0.7684 (m-10) REVERT: E 236 TRP cc_start: 0.8054 (p90) cc_final: 0.7813 (p90) REVERT: E 303 CYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8348 (t) REVERT: E 313 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8542 (mtmm) REVERT: F 67 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7723 (mp10) REVERT: F 107 TRP cc_start: 0.7770 (m100) cc_final: 0.7350 (m-10) REVERT: F 130 ILE cc_start: 0.8915 (tp) cc_final: 0.8459 (tp) REVERT: F 156 ASP cc_start: 0.8529 (t0) cc_final: 0.8282 (t0) REVERT: F 159 LYS cc_start: 0.7997 (mptt) cc_final: 0.7736 (mptt) REVERT: F 236 TRP cc_start: 0.8207 (p90) cc_final: 0.7908 (p90) REVERT: F 274 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.6017 (mp0) REVERT: F 313 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8477 (mtmm) REVERT: F 332 SER cc_start: 0.9051 (t) cc_final: 0.8633 (p) REVERT: G 50 HIS cc_start: 0.7479 (OUTLIER) cc_final: 0.7018 (p90) REVERT: G 107 TRP cc_start: 0.8284 (m100) cc_final: 0.7668 (m-10) REVERT: G 145 ASP cc_start: 0.8627 (t70) cc_final: 0.8375 (t0) REVERT: G 274 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.5818 (mp0) REVERT: G 313 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8606 (mtmm) REVERT: G 332 SER cc_start: 0.9330 (t) cc_final: 0.8895 (p) REVERT: H 67 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7724 (mp10) REVERT: H 107 TRP cc_start: 0.7890 (m100) cc_final: 0.7407 (m-10) REVERT: H 130 ILE cc_start: 0.8847 (tp) cc_final: 0.8464 (tp) REVERT: H 264 LEU cc_start: 0.8697 (tp) cc_final: 0.8346 (tt) REVERT: H 274 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.6030 (mp0) REVERT: H 313 LYS cc_start: 0.8758 (mtpt) cc_final: 0.8443 (mtmm) REVERT: H 332 SER cc_start: 0.9048 (t) cc_final: 0.8635 (p) outliers start: 86 outliers final: 53 residues processed: 673 average time/residue: 0.3133 time to fit residues: 329.2645 Evaluate side-chains 627 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 565 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 204 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS H 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.101662 restraints weight = 30561.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.105591 restraints weight = 16143.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.108266 restraints weight = 10662.924| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21488 Z= 0.132 Angle : 0.595 12.996 29304 Z= 0.302 Chirality : 0.041 0.190 3232 Planarity : 0.003 0.028 3584 Dihedral : 4.257 16.068 2752 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.62 % Allowed : 29.12 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.17), residues: 2480 helix: 1.32 (0.13), residues: 1720 sheet: -4.12 (0.38), residues: 40 loop : -3.34 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 236 HIS 0.008 0.001 HIS D 50 PHE 0.020 0.001 PHE D 51 TYR 0.027 0.001 TYR H 120 ARG 0.004 0.000 ARG B 244 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 1224) hydrogen bonds : angle 4.14489 ( 3648) SS BOND : bond 0.00152 ( 16) SS BOND : angle 0.97045 ( 32) covalent geometry : bond 0.00294 (21472) covalent geometry : angle 0.59438 (29272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 576 time to evaluate : 2.386 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TRP cc_start: 0.8383 (m100) cc_final: 0.7688 (m-10) REVERT: A 145 ASP cc_start: 0.8654 (t70) cc_final: 0.8399 (t0) REVERT: A 236 TRP cc_start: 0.8260 (p90) cc_final: 0.7804 (p90) REVERT: A 274 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.5690 (mp0) REVERT: A 313 LYS cc_start: 0.8937 (mtpt) cc_final: 0.8612 (mtmm) REVERT: B 67 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7671 (mp10) REVERT: B 107 TRP cc_start: 0.7965 (m100) cc_final: 0.7391 (m-10) REVERT: B 130 ILE cc_start: 0.8660 (tp) cc_final: 0.8194 (tp) REVERT: B 145 ASP cc_start: 0.8579 (t70) cc_final: 0.8366 (t0) REVERT: B 159 LYS cc_start: 0.7823 (mppt) cc_final: 0.7471 (mptt) REVERT: B 264 LEU cc_start: 0.8790 (tp) cc_final: 0.8453 (tt) REVERT: B 274 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.5482 (mp0) REVERT: B 313 LYS cc_start: 0.8820 (mtpt) cc_final: 0.8467 (mtmm) REVERT: B 332 SER cc_start: 0.9065 (t) cc_final: 0.8646 (p) REVERT: C 67 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7509 (mp10) REVERT: C 107 TRP cc_start: 0.8312 (m100) cc_final: 0.7663 (m-10) REVERT: C 186 ARG cc_start: 0.7281 (mtp180) cc_final: 0.6978 (mmm-85) REVERT: C 236 TRP cc_start: 0.8059 (p90) cc_final: 0.7779 (p90) REVERT: C 303 CYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8287 (t) REVERT: D 67 GLN cc_start: 0.7055 (mp10) cc_final: 0.6828 (mp10) REVERT: D 107 TRP cc_start: 0.7954 (m100) cc_final: 0.7404 (m-10) REVERT: D 151 ASN cc_start: 0.8116 (p0) cc_final: 0.7841 (m-40) REVERT: D 236 TRP cc_start: 0.8224 (p90) cc_final: 0.7951 (p90) REVERT: D 274 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.5872 (mp0) REVERT: D 313 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8219 (mtmm) REVERT: E 67 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7349 (mp10) REVERT: E 107 TRP cc_start: 0.8297 (m100) cc_final: 0.7690 (m-10) REVERT: E 236 TRP cc_start: 0.8092 (p90) cc_final: 0.7833 (p90) REVERT: E 274 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: E 303 CYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8371 (t) REVERT: E 313 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8454 (mtmm) REVERT: E 361 MET cc_start: 0.9061 (mtp) cc_final: 0.8692 (ttm) REVERT: F 67 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7722 (mp10) REVERT: F 107 TRP cc_start: 0.7841 (m100) cc_final: 0.7332 (m-10) REVERT: F 130 ILE cc_start: 0.8911 (tp) cc_final: 0.8508 (tp) REVERT: F 136 ASP cc_start: 0.8359 (p0) cc_final: 0.8091 (p0) REVERT: F 156 ASP cc_start: 0.8558 (t0) cc_final: 0.8304 (t0) REVERT: F 159 LYS cc_start: 0.8097 (mptt) cc_final: 0.7792 (mptt) REVERT: F 236 TRP cc_start: 0.8154 (p90) cc_final: 0.7836 (p90) REVERT: F 264 LEU cc_start: 0.8809 (tp) cc_final: 0.8480 (tt) REVERT: F 274 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.5828 (mp0) REVERT: F 313 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8411 (mtmm) REVERT: F 332 SER cc_start: 0.9069 (t) cc_final: 0.8610 (p) REVERT: G 50 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.7041 (p90) REVERT: G 107 TRP cc_start: 0.8336 (m100) cc_final: 0.7677 (m-10) REVERT: G 145 ASP cc_start: 0.8663 (t70) cc_final: 0.8415 (t0) REVERT: G 236 TRP cc_start: 0.8250 (p90) cc_final: 0.7802 (p90) REVERT: G 274 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.5753 (mp0) REVERT: G 313 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8609 (mtmm) REVERT: G 332 SER cc_start: 0.9310 (t) cc_final: 0.8847 (p) REVERT: G 361 MET cc_start: 0.9322 (mtp) cc_final: 0.9050 (mtm) REVERT: H 67 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7702 (mp10) REVERT: H 107 TRP cc_start: 0.7827 (m100) cc_final: 0.7392 (m-10) REVERT: H 130 ILE cc_start: 0.8758 (tp) cc_final: 0.8368 (tp) REVERT: H 264 LEU cc_start: 0.8768 (tp) cc_final: 0.8462 (tt) REVERT: H 274 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.5848 (mp0) REVERT: H 313 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8470 (mtmm) REVERT: H 332 SER cc_start: 0.9071 (t) cc_final: 0.8647 (p) outliers start: 80 outliers final: 58 residues processed: 620 average time/residue: 0.2984 time to fit residues: 291.6942 Evaluate side-chains 631 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 563 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 134 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 65 optimal weight: 0.0980 chunk 132 optimal weight: 5.9990 chunk 135 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 242 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN B 50 HIS B 63 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN D 50 HIS ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN H 50 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.125135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.102346 restraints weight = 30843.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.106305 restraints weight = 16141.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108981 restraints weight = 10573.709| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21488 Z= 0.119 Angle : 0.586 12.507 29304 Z= 0.298 Chirality : 0.040 0.179 3232 Planarity : 0.003 0.025 3584 Dihedral : 4.170 16.004 2752 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 3.53 % Allowed : 29.85 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.17), residues: 2480 helix: 1.37 (0.13), residues: 1720 sheet: -4.16 (0.38), residues: 40 loop : -3.28 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 236 HIS 0.006 0.001 HIS F 50 PHE 0.015 0.001 PHE D 51 TYR 0.027 0.001 TYR D 120 ARG 0.006 0.000 ARG D 184 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 1224) hydrogen bonds : angle 4.09847 ( 3648) SS BOND : bond 0.00143 ( 16) SS BOND : angle 0.84227 ( 32) covalent geometry : bond 0.00254 (21472) covalent geometry : angle 0.58575 (29272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 585 time to evaluate : 2.295 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7862 (p0) cc_final: 0.7636 (p0) REVERT: A 107 TRP cc_start: 0.8275 (m100) cc_final: 0.7723 (m-10) REVERT: A 145 ASP cc_start: 0.8561 (t70) cc_final: 0.8338 (t0) REVERT: A 264 LEU cc_start: 0.8843 (tp) cc_final: 0.8514 (tp) REVERT: A 274 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.5764 (mp0) REVERT: A 313 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8647 (mtmm) REVERT: B 67 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7788 (mp10) REVERT: B 107 TRP cc_start: 0.7919 (m100) cc_final: 0.7410 (m-10) REVERT: B 130 ILE cc_start: 0.8851 (tp) cc_final: 0.8504 (tp) REVERT: B 145 ASP cc_start: 0.8533 (t70) cc_final: 0.8331 (t0) REVERT: B 159 LYS cc_start: 0.7691 (mppt) cc_final: 0.7389 (mptt) REVERT: B 264 LEU cc_start: 0.8736 (tp) cc_final: 0.8418 (tt) REVERT: B 274 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.5531 (mp0) REVERT: B 313 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8501 (mtmm) REVERT: B 332 SER cc_start: 0.9047 (t) cc_final: 0.8638 (p) REVERT: C 107 TRP cc_start: 0.8221 (m100) cc_final: 0.7656 (m-10) REVERT: C 186 ARG cc_start: 0.7125 (mtp180) cc_final: 0.6916 (mmm-85) REVERT: C 236 TRP cc_start: 0.7985 (p90) cc_final: 0.7715 (p90) REVERT: C 264 LEU cc_start: 0.8821 (tp) cc_final: 0.8497 (tp) REVERT: C 274 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.6413 (mp0) REVERT: C 303 CYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8259 (t) REVERT: D 107 TRP cc_start: 0.7830 (m100) cc_final: 0.7448 (m-10) REVERT: D 184 ARG cc_start: 0.7945 (ttm110) cc_final: 0.7627 (ttp-110) REVERT: D 208 TYR cc_start: 0.7759 (t80) cc_final: 0.7462 (t80) REVERT: D 236 TRP cc_start: 0.8145 (p90) cc_final: 0.7945 (p90) REVERT: D 274 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.5888 (mp0) REVERT: D 313 LYS cc_start: 0.8677 (mtpt) cc_final: 0.8383 (mtmm) REVERT: E 67 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7526 (mp10) REVERT: E 107 TRP cc_start: 0.8214 (m100) cc_final: 0.7707 (m-10) REVERT: E 210 LEU cc_start: 0.9020 (tp) cc_final: 0.8689 (tp) REVERT: E 236 TRP cc_start: 0.7997 (p90) cc_final: 0.7748 (p90) REVERT: E 274 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.6396 (mp0) REVERT: E 303 CYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8268 (t) REVERT: E 313 LYS cc_start: 0.8855 (mtpt) cc_final: 0.8568 (mtmm) REVERT: F 67 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7762 (mp10) REVERT: F 107 TRP cc_start: 0.7728 (m100) cc_final: 0.7408 (m-10) REVERT: F 130 ILE cc_start: 0.8883 (tp) cc_final: 0.8506 (tp) REVERT: F 151 ASN cc_start: 0.8194 (p0) cc_final: 0.7854 (m-40) REVERT: F 236 TRP cc_start: 0.8136 (p90) cc_final: 0.7915 (p90) REVERT: F 274 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.5892 (mp0) REVERT: F 313 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8554 (mtmm) REVERT: F 332 SER cc_start: 0.9035 (t) cc_final: 0.8602 (p) REVERT: G 50 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.6908 (p90) REVERT: G 107 TRP cc_start: 0.8267 (m100) cc_final: 0.7696 (m-10) REVERT: G 145 ASP cc_start: 0.8584 (t70) cc_final: 0.8358 (t0) REVERT: G 157 LYS cc_start: 0.7713 (mmtt) cc_final: 0.6964 (mmtm) REVERT: G 274 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.5825 (mp0) REVERT: G 313 LYS cc_start: 0.8857 (mtpt) cc_final: 0.8618 (mtmm) REVERT: G 332 SER cc_start: 0.9306 (t) cc_final: 0.8860 (p) REVERT: H 67 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7744 (mp10) REVERT: H 107 TRP cc_start: 0.7699 (m100) cc_final: 0.7356 (m-10) REVERT: H 264 LEU cc_start: 0.8739 (tp) cc_final: 0.8460 (tt) REVERT: H 274 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.5961 (mp0) REVERT: H 313 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8491 (mtmm) REVERT: H 332 SER cc_start: 0.9054 (t) cc_final: 0.8637 (p) outliers start: 78 outliers final: 60 residues processed: 624 average time/residue: 0.2975 time to fit residues: 290.9978 Evaluate side-chains 637 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 566 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 61 optimal weight: 0.0870 chunk 164 optimal weight: 4.9990 chunk 70 optimal weight: 0.0570 chunk 5 optimal weight: 4.9990 chunk 185 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 204 optimal weight: 0.0670 chunk 112 optimal weight: 9.9990 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN B 50 HIS B 63 GLN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 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 = 0.3403 r_free = 0.3403 target = 0.126258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.103373 restraints weight = 30892.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.107398 restraints weight = 16162.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110090 restraints weight = 10546.043| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21488 Z= 0.118 Angle : 0.590 10.783 29304 Z= 0.300 Chirality : 0.040 0.168 3232 Planarity : 0.003 0.023 3584 Dihedral : 4.121 15.698 2752 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.31 % Allowed : 30.30 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.12 (0.17), residues: 2480 helix: 1.44 (0.13), residues: 1720 sheet: -4.20 (0.38), residues: 40 loop : -3.18 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 236 HIS 0.008 0.001 HIS H 50 PHE 0.015 0.001 PHE B 147 TYR 0.027 0.001 TYR F 120 ARG 0.004 0.000 ARG D 184 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 1224) hydrogen bonds : angle 4.07628 ( 3648) SS BOND : bond 0.00110 ( 16) SS BOND : angle 1.22025 ( 32) covalent geometry : bond 0.00248 (21472) covalent geometry : angle 0.58942 (29272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 582 time to evaluate : 2.124 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: 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: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7681 (p0) cc_final: 0.7472 (p0) REVERT: A 107 TRP cc_start: 0.8240 (m100) cc_final: 0.7677 (m-10) REVERT: A 145 ASP cc_start: 0.8572 (t70) cc_final: 0.8348 (t0) REVERT: A 236 TRP cc_start: 0.8122 (p90) cc_final: 0.7672 (p90) REVERT: A 264 LEU cc_start: 0.8828 (tp) cc_final: 0.8501 (tp) REVERT: A 274 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.5674 (mp0) REVERT: A 313 LYS cc_start: 0.8903 (mtpt) cc_final: 0.8646 (mtmm) REVERT: B 107 TRP cc_start: 0.7895 (m100) cc_final: 0.7428 (m-10) REVERT: B 130 ILE cc_start: 0.8694 (tp) cc_final: 0.8331 (tp) REVERT: B 264 LEU cc_start: 0.8671 (tp) cc_final: 0.8360 (tt) REVERT: B 274 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.5550 (mp0) REVERT: B 313 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8471 (mtmm) REVERT: B 331 PHE cc_start: 0.8760 (m-80) cc_final: 0.8515 (m-80) REVERT: C 67 GLN cc_start: 0.6866 (mp10) cc_final: 0.6563 (mp10) REVERT: C 107 TRP cc_start: 0.8188 (m100) cc_final: 0.7658 (m-10) REVERT: C 186 ARG cc_start: 0.7128 (mtp180) cc_final: 0.6915 (mmm-85) REVERT: C 210 LEU cc_start: 0.8983 (tp) cc_final: 0.8714 (tp) REVERT: C 236 TRP cc_start: 0.7946 (p90) cc_final: 0.7663 (p90) REVERT: C 264 LEU cc_start: 0.8805 (tp) cc_final: 0.8484 (tp) REVERT: C 274 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.6308 (mp0) REVERT: C 291 SER cc_start: 0.9149 (t) cc_final: 0.8678 (m) REVERT: C 301 TYR cc_start: 0.8535 (t80) cc_final: 0.8285 (t80) REVERT: C 303 CYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8241 (t) REVERT: D 67 GLN cc_start: 0.7124 (mp10) cc_final: 0.6728 (mp10) REVERT: D 107 TRP cc_start: 0.7807 (m100) cc_final: 0.7437 (m-10) REVERT: D 130 ILE cc_start: 0.8817 (tp) cc_final: 0.8200 (tp) REVERT: D 153 ASP cc_start: 0.8501 (m-30) cc_final: 0.8298 (m-30) REVERT: D 184 ARG cc_start: 0.7921 (ttm110) cc_final: 0.7690 (ttp-110) REVERT: D 208 TYR cc_start: 0.7727 (t80) cc_final: 0.7447 (t80) REVERT: D 274 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.5837 (mp0) REVERT: D 313 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8348 (mtmm) REVERT: E 67 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7464 (mp10) REVERT: E 107 TRP cc_start: 0.8186 (m100) cc_final: 0.7671 (m-10) REVERT: E 210 LEU cc_start: 0.8965 (tp) cc_final: 0.8678 (tp) REVERT: E 236 TRP cc_start: 0.7964 (p90) cc_final: 0.7699 (p90) REVERT: E 274 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.6340 (mp0) REVERT: E 303 CYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8249 (t) REVERT: E 313 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8556 (mtmm) REVERT: F 67 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7755 (mp10) REVERT: F 107 TRP cc_start: 0.7761 (m100) cc_final: 0.7378 (m-10) REVERT: F 130 ILE cc_start: 0.8697 (tp) cc_final: 0.8277 (tp) REVERT: F 151 ASN cc_start: 0.8068 (p0) cc_final: 0.7866 (m-40) REVERT: F 274 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.5826 (mp0) REVERT: F 313 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8482 (mtmm) REVERT: F 331 PHE cc_start: 0.8744 (m-80) cc_final: 0.8499 (m-80) REVERT: F 332 SER cc_start: 0.9051 (t) cc_final: 0.8618 (p) REVERT: G 50 HIS cc_start: 0.7674 (OUTLIER) cc_final: 0.6976 (p90) REVERT: G 107 TRP cc_start: 0.8214 (m100) cc_final: 0.7685 (m-10) REVERT: G 145 ASP cc_start: 0.8602 (t70) cc_final: 0.8352 (t0) REVERT: G 157 LYS cc_start: 0.7667 (mmtt) cc_final: 0.6852 (mmtm) REVERT: G 236 TRP cc_start: 0.8179 (p90) cc_final: 0.7752 (p90) REVERT: G 264 LEU cc_start: 0.8772 (tp) cc_final: 0.8455 (tp) REVERT: G 274 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.5716 (mp0) REVERT: G 313 LYS cc_start: 0.8861 (mtpt) cc_final: 0.8613 (mtmm) REVERT: G 332 SER cc_start: 0.9289 (t) cc_final: 0.8829 (p) REVERT: G 337 ASP cc_start: 0.7964 (m-30) cc_final: 0.7689 (m-30) REVERT: H 67 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7731 (mp10) REVERT: H 107 TRP cc_start: 0.7714 (m100) cc_final: 0.7388 (m-10) REVERT: H 274 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.5870 (mp0) REVERT: H 313 LYS cc_start: 0.8786 (mtpt) cc_final: 0.8529 (mtmm) REVERT: H 331 PHE cc_start: 0.8746 (m-80) cc_final: 0.8519 (m-80) REVERT: H 332 SER cc_start: 0.9071 (t) cc_final: 0.8645 (p) outliers start: 73 outliers final: 60 residues processed: 621 average time/residue: 0.3004 time to fit residues: 290.9841 Evaluate side-chains 638 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 567 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 28 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 164 optimal weight: 0.4980 chunk 72 optimal weight: 6.9990 chunk 13 optimal weight: 0.4980 chunk 88 optimal weight: 4.9990 chunk 209 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 189 optimal weight: 0.1980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN B 63 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104931 restraints weight = 30649.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.108750 restraints weight = 16769.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.111334 restraints weight = 11281.097| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21488 Z= 0.123 Angle : 0.597 10.490 29304 Z= 0.303 Chirality : 0.040 0.156 3232 Planarity : 0.003 0.033 3584 Dihedral : 4.113 15.323 2752 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 3.44 % Allowed : 30.16 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.17), residues: 2480 helix: 1.47 (0.13), residues: 1720 sheet: -4.20 (0.40), residues: 40 loop : -3.13 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B 236 HIS 0.010 0.001 HIS B 50 PHE 0.023 0.001 PHE A 51 TYR 0.028 0.001 TYR F 120 ARG 0.008 0.000 ARG H 184 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 1224) hydrogen bonds : angle 4.07790 ( 3648) SS BOND : bond 0.00144 ( 16) SS BOND : angle 1.07761 ( 32) covalent geometry : bond 0.00265 (21472) covalent geometry : angle 0.59648 (29272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 586 time to evaluate : 2.140 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: 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: A 54 ASP cc_start: 0.7682 (p0) cc_final: 0.7476 (p0) REVERT: A 107 TRP cc_start: 0.8233 (m100) cc_final: 0.7688 (m-10) REVERT: A 145 ASP cc_start: 0.8575 (t70) cc_final: 0.8341 (t0) REVERT: A 236 TRP cc_start: 0.8106 (p90) cc_final: 0.7516 (p90) REVERT: A 264 LEU cc_start: 0.8815 (tp) cc_final: 0.8501 (tp) REVERT: A 274 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.5716 (mp0) REVERT: A 313 LYS cc_start: 0.8969 (mtpt) cc_final: 0.8697 (mtmm) REVERT: B 107 TRP cc_start: 0.7919 (m100) cc_final: 0.7469 (m-10) REVERT: B 130 ILE cc_start: 0.8865 (tp) cc_final: 0.8502 (tp) REVERT: B 145 ASP cc_start: 0.8548 (t70) cc_final: 0.8338 (t0) REVERT: B 188 MET cc_start: 0.8690 (mmm) cc_final: 0.8342 (mtp) REVERT: B 264 LEU cc_start: 0.8692 (tp) cc_final: 0.8370 (tt) REVERT: B 274 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.5592 (mp0) REVERT: B 313 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8510 (mtmm) REVERT: B 331 PHE cc_start: 0.8804 (m-80) cc_final: 0.8548 (m-80) REVERT: B 332 SER cc_start: 0.9049 (t) cc_final: 0.8620 (p) REVERT: C 67 GLN cc_start: 0.6908 (mp10) cc_final: 0.6572 (mp10) REVERT: C 107 TRP cc_start: 0.8195 (m100) cc_final: 0.7667 (m-10) REVERT: C 210 LEU cc_start: 0.8968 (tp) cc_final: 0.8687 (tp) REVERT: C 264 LEU cc_start: 0.8785 (tp) cc_final: 0.8468 (tp) REVERT: C 274 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.6059 (mp0) REVERT: C 291 SER cc_start: 0.9153 (t) cc_final: 0.8681 (m) REVERT: C 301 TYR cc_start: 0.8551 (t80) cc_final: 0.8304 (t80) REVERT: C 303 CYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8215 (t) REVERT: C 332 SER cc_start: 0.9202 (t) cc_final: 0.8847 (p) REVERT: D 67 GLN cc_start: 0.7115 (mp10) cc_final: 0.6776 (mp10) REVERT: D 107 TRP cc_start: 0.7816 (m100) cc_final: 0.7454 (m-10) REVERT: D 208 TYR cc_start: 0.7830 (t80) cc_final: 0.7554 (t80) REVERT: D 274 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.5790 (mp0) REVERT: D 313 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8439 (mtmm) REVERT: E 67 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7563 (mp10) REVERT: E 107 TRP cc_start: 0.8146 (m100) cc_final: 0.7687 (m-10) REVERT: E 210 LEU cc_start: 0.8982 (tp) cc_final: 0.8695 (tp) REVERT: E 236 TRP cc_start: 0.7961 (p90) cc_final: 0.7686 (p90) REVERT: E 274 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.6175 (mp0) REVERT: E 313 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8571 (mtmm) REVERT: E 332 SER cc_start: 0.9265 (t) cc_final: 0.8878 (p) REVERT: F 67 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7756 (mp10) REVERT: F 107 TRP cc_start: 0.7754 (m100) cc_final: 0.7367 (m-10) REVERT: F 130 ILE cc_start: 0.8892 (tp) cc_final: 0.8477 (tp) REVERT: F 188 MET cc_start: 0.8668 (mmm) cc_final: 0.8145 (mtp) REVERT: F 270 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.7481 (t0) REVERT: F 274 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.5850 (mp0) REVERT: F 313 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8538 (mtmm) REVERT: F 331 PHE cc_start: 0.8768 (m-80) cc_final: 0.8499 (m-80) REVERT: F 332 SER cc_start: 0.9057 (t) cc_final: 0.8634 (p) REVERT: G 50 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.6995 (p90) REVERT: G 107 TRP cc_start: 0.8204 (m100) cc_final: 0.7714 (m-10) REVERT: G 145 ASP cc_start: 0.8601 (t70) cc_final: 0.8350 (t0) REVERT: G 151 ASN cc_start: 0.7932 (p0) cc_final: 0.7723 (m-40) REVERT: G 157 LYS cc_start: 0.7536 (mmtt) cc_final: 0.6844 (mmtm) REVERT: G 236 TRP cc_start: 0.8094 (p90) cc_final: 0.7640 (p90) REVERT: G 264 LEU cc_start: 0.8815 (tp) cc_final: 0.8492 (tp) REVERT: G 274 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.5847 (mp0) REVERT: G 313 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8618 (mtmm) REVERT: G 332 SER cc_start: 0.9284 (t) cc_final: 0.8836 (p) REVERT: H 67 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7742 (mp10) REVERT: H 107 TRP cc_start: 0.7678 (m100) cc_final: 0.7369 (m-10) REVERT: H 130 ILE cc_start: 0.8845 (tp) cc_final: 0.8413 (tp) REVERT: H 274 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.5782 (mp0) REVERT: H 313 LYS cc_start: 0.8786 (mtpt) cc_final: 0.8538 (mtmm) REVERT: H 331 PHE cc_start: 0.8760 (m-80) cc_final: 0.8527 (m-80) REVERT: H 332 SER cc_start: 0.9163 (t) cc_final: 0.8781 (p) outliers start: 76 outliers final: 60 residues processed: 624 average time/residue: 0.3054 time to fit residues: 297.5160 Evaluate side-chains 646 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 575 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 211 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN B 63 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 HIS E 314 ASN ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104662 restraints weight = 30647.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.108516 restraints weight = 16726.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111059 restraints weight = 11205.261| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 21488 Z= 0.147 Angle : 0.720 42.002 29304 Z= 0.388 Chirality : 0.041 0.299 3232 Planarity : 0.004 0.100 3584 Dihedral : 4.146 19.756 2752 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.40 % Allowed : 30.25 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.17), residues: 2480 helix: 1.47 (0.13), residues: 1720 sheet: -4.21 (0.41), residues: 40 loop : -3.11 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP H 236 HIS 0.007 0.001 HIS B 50 PHE 0.019 0.001 PHE A 51 TYR 0.027 0.001 TYR F 120 ARG 0.019 0.001 ARG D 184 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 1224) hydrogen bonds : angle 4.07260 ( 3648) SS BOND : bond 0.00449 ( 16) SS BOND : angle 1.69519 ( 32) covalent geometry : bond 0.00319 (21472) covalent geometry : angle 0.71772 (29272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7368.84 seconds wall clock time: 129 minutes 12.79 seconds (7752.79 seconds total)