Starting phenix.real_space_refine on Thu Sep 18 21:49:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kfh_9973/09_2025/6kfh_9973.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kfh_9973/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6kfh_9973/09_2025/6kfh_9973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kfh_9973/09_2025/6kfh_9973.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kfh_9973/09_2025/6kfh_9973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kfh_9973/09_2025/6kfh_9973.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D, E, F, G, H Time building chain proxies: 2.66, per 1000 atoms: 0.13 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 B 58 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 58 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 58 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 58 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 58 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS H 58 " - pdb=" SG CYS H 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 76 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 76 " - pdb=" SG CYS G 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: 1.44 Conformation dependent library (CDL) restraints added in 528.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.41 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: 2.64 Time building geometry restraints manager: 1.86 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.060 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.200 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG E 168 TYR 0.008 0.001 TYR A 172 PHE 0.012 0.002 PHE D 119 TRP 0.009 0.001 TRP A 68 HIS 0.004 0.001 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00706 (21472) covalent geometry : angle 0.73493 (29272) SS BOND : bond 0.00262 ( 16) SS BOND : angle 0.70845 ( 32) hydrogen bonds : bond 0.13705 ( 1224) hydrogen bonds : angle 6.28556 ( 3648) *********************** 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 : 0.790 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: 0.1436 time to fit residues: 168.1233 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 : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 247 optimal weight: 0.0030 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.129528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.107929 restraints weight = 29977.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.111874 restraints weight = 15632.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.114506 restraints weight = 10167.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116280 restraints weight = 7567.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117428 restraints weight = 6144.004| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1676 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= 0.136 Angle : 0.612 6.195 29304 Z= 0.320 Chirality : 0.041 0.162 3232 Planarity : 0.004 0.062 3584 Dihedral : 4.872 20.650 2752 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.54 % Allowed : 19.66 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.16), residues: 2480 helix: 0.29 (0.12), residues: 1712 sheet: None (None), residues: 0 loop : -4.01 (0.17), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 244 TYR 0.017 0.001 TYR C 301 PHE 0.017 0.001 PHE G 242 TRP 0.026 0.001 TRP D 68 HIS 0.011 0.001 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00287 (21472) covalent geometry : angle 0.61102 (29272) SS BOND : bond 0.00062 ( 16) SS BOND : angle 0.95953 ( 32) hydrogen bonds : bond 0.04613 ( 1224) hydrogen bonds : angle 4.60022 ( 3648) *********************** 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 696 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 640 time to evaluate : 0.747 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: A 54 ASP cc_start: 0.7796 (p0) cc_final: 0.7516 (p0) REVERT: A 103 GLN cc_start: 0.7032 (pt0) cc_final: 0.6829 (pt0) REVERT: A 107 TRP cc_start: 0.8294 (m100) cc_final: 0.7629 (m-10) REVERT: A 145 ASP cc_start: 0.8608 (t70) cc_final: 0.8372 (t0) REVERT: A 156 ASP cc_start: 0.8318 (t0) cc_final: 0.8114 (t0) REVERT: A 313 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8589 (mtmm) REVERT: B 107 TRP cc_start: 0.7920 (m100) cc_final: 0.7408 (m-10) REVERT: B 130 ILE cc_start: 0.9020 (tp) cc_final: 0.8513 (tp) REVERT: B 145 ASP cc_start: 0.8573 (t70) cc_final: 0.8319 (t0) REVERT: B 159 LYS cc_start: 0.7985 (mptt) cc_final: 0.7719 (mptt) REVERT: B 313 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8457 (mtmm) REVERT: C 45 LEU cc_start: 0.8094 (tp) cc_final: 0.7869 (tp) REVERT: C 49 SER cc_start: 0.8965 (t) cc_final: 0.8526 (m) REVERT: C 67 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7521 (mp10) REVERT: C 103 GLN cc_start: 0.7081 (pt0) cc_final: 0.6812 (pt0) REVERT: C 107 TRP cc_start: 0.8309 (m100) cc_final: 0.7615 (m-10) REVERT: C 186 ARG cc_start: 0.6978 (mtp180) cc_final: 0.6665 (mtp85) REVERT: C 300 TYR cc_start: 0.8258 (t80) cc_final: 0.7994 (t80) REVERT: D 107 TRP cc_start: 0.7923 (m100) cc_final: 0.7535 (m-10) REVERT: D 130 ILE cc_start: 0.8918 (tp) cc_final: 0.8435 (tp) REVERT: D 313 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8256 (mtmm) REVERT: E 103 GLN cc_start: 0.6802 (pt0) cc_final: 0.6577 (pt0) REVERT: E 107 TRP cc_start: 0.8293 (m100) cc_final: 0.7657 (m-10) REVERT: E 142 LYS cc_start: 0.9124 (mtmm) cc_final: 0.8762 (mtpp) REVERT: E 313 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8369 (mtmm) REVERT: E 327 ASP cc_start: 0.8697 (m-30) cc_final: 0.8482 (m-30) REVERT: E 334 LEU cc_start: 0.7852 (tp) cc_final: 0.7623 (tp) REVERT: F 307 LYS cc_start: 0.8308 (tmtt) cc_final: 0.7960 (tptt) REVERT: F 313 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8438 (mtmm) REVERT: G 54 ASP cc_start: 0.7826 (p0) cc_final: 0.7553 (p0) REVERT: G 103 GLN cc_start: 0.6988 (pt0) cc_final: 0.6767 (pt0) REVERT: G 107 TRP cc_start: 0.8284 (m100) cc_final: 0.7595 (m-10) REVERT: G 142 LYS cc_start: 0.9146 (mtmm) cc_final: 0.8864 (mtpp) REVERT: G 145 ASP cc_start: 0.8714 (t70) cc_final: 0.8446 (t0) REVERT: G 177 ILE cc_start: 0.9279 (mm) cc_final: 0.9051 (mt) REVERT: G 303 CYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8170 (t) REVERT: G 313 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8482 (mtmm) REVERT: G 329 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8333 (pt0) REVERT: G 332 SER cc_start: 0.9236 (t) cc_final: 0.8941 (p) REVERT: H 107 TRP cc_start: 0.8106 (m100) cc_final: 0.7566 (m-10) REVERT: H 307 LYS cc_start: 0.8298 (tmtt) cc_final: 0.7892 (tptt) REVERT: H 313 LYS cc_start: 0.8813 (mtpt) cc_final: 0.8470 (mtmm) outliers start: 56 outliers final: 38 residues processed: 677 average time/residue: 0.1378 time to fit residues: 144.5962 Evaluate side-chains 599 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 559 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 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 211 THR 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 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 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 299 ILE 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 18 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 231 optimal weight: 0.3980 chunk 209 optimal weight: 0.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN C 50 HIS ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN D 151 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN F 151 ASN G 314 ASN G 329 GLN H 151 ASN H 314 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.099798 restraints weight = 30551.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.103625 restraints weight = 15825.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.106217 restraints weight = 10340.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.107941 restraints weight = 7746.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.109107 restraints weight = 6334.173| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21488 Z= 0.148 Angle : 0.613 10.183 29304 Z= 0.313 Chirality : 0.042 0.165 3232 Planarity : 0.003 0.041 3584 Dihedral : 4.668 19.631 2752 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.08 % Allowed : 22.19 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.17), residues: 2480 helix: 0.69 (0.12), residues: 1720 sheet: -4.32 (0.31), residues: 40 loop : -3.79 (0.18), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 244 TYR 0.020 0.001 TYR F 300 PHE 0.012 0.001 PHE B 51 TRP 0.012 0.001 TRP E 59 HIS 0.010 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00335 (21472) covalent geometry : angle 0.61289 (29272) SS BOND : bond 0.00061 ( 16) SS BOND : angle 0.92384 ( 32) hydrogen bonds : bond 0.04274 ( 1224) hydrogen bonds : angle 4.39924 ( 3648) *********************** 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 635 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 567 time to evaluate : 0.819 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 103 GLN cc_start: 0.7104 (pt0) cc_final: 0.6860 (pt0) REVERT: A 107 TRP cc_start: 0.8320 (m100) cc_final: 0.7637 (m-10) REVERT: A 145 ASP cc_start: 0.8601 (t70) cc_final: 0.8367 (t0) REVERT: A 313 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8620 (mtmm) REVERT: B 107 TRP cc_start: 0.7962 (m100) cc_final: 0.7410 (m-10) REVERT: B 145 ASP cc_start: 0.8569 (t70) cc_final: 0.8349 (t0) REVERT: B 156 ASP cc_start: 0.8518 (t0) cc_final: 0.8313 (t0) REVERT: B 159 LYS cc_start: 0.8039 (mptt) cc_final: 0.7808 (mptt) REVERT: B 236 TRP cc_start: 0.8104 (p90) cc_final: 0.7863 (p90) REVERT: B 264 LEU cc_start: 0.8924 (tp) cc_final: 0.8577 (tt) REVERT: B 313 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8450 (mtmm) REVERT: C 49 SER cc_start: 0.9020 (t) cc_final: 0.8587 (m) REVERT: C 67 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7519 (mp10) REVERT: C 103 GLN cc_start: 0.7070 (pt0) cc_final: 0.6783 (pt0) REVERT: C 107 TRP cc_start: 0.8274 (m100) cc_final: 0.7607 (m-10) REVERT: C 186 ARG cc_start: 0.7036 (mtp180) cc_final: 0.6709 (mtp85) REVERT: C 264 LEU cc_start: 0.8914 (tp) cc_final: 0.8503 (tt) REVERT: D 107 TRP cc_start: 0.7866 (m100) cc_final: 0.7481 (m-10) REVERT: D 130 ILE cc_start: 0.8989 (tp) cc_final: 0.8504 (tp) REVERT: D 313 LYS cc_start: 0.8727 (mtpt) cc_final: 0.8278 (mtmm) REVERT: E 103 GLN cc_start: 0.6944 (pt0) cc_final: 0.6687 (pt0) REVERT: E 107 TRP cc_start: 0.8308 (m100) cc_final: 0.7672 (m-10) REVERT: E 313 LYS cc_start: 0.8827 (mtpt) cc_final: 0.8485 (mtmm) REVERT: E 327 ASP cc_start: 0.8790 (m-30) cc_final: 0.8583 (m-30) REVERT: E 361 MET cc_start: 0.9275 (mtp) cc_final: 0.9009 (mtm) REVERT: F 67 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7758 (mp10) REVERT: F 107 TRP cc_start: 0.7969 (m100) cc_final: 0.7449 (m-10) REVERT: F 159 LYS cc_start: 0.7956 (mptt) cc_final: 0.7699 (mptt) REVERT: F 264 LEU cc_start: 0.8942 (tp) cc_final: 0.8619 (tt) REVERT: F 303 CYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7948 (t) REVERT: F 313 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8433 (mtmm) REVERT: F 332 SER cc_start: 0.9028 (t) cc_final: 0.8737 (p) REVERT: G 54 ASP cc_start: 0.7791 (p0) cc_final: 0.7528 (p0) REVERT: G 103 GLN cc_start: 0.7062 (pt0) cc_final: 0.6814 (pt0) REVERT: G 107 TRP cc_start: 0.8263 (m100) cc_final: 0.7624 (m-10) REVERT: G 145 ASP cc_start: 0.8660 (t70) cc_final: 0.8417 (t0) REVERT: G 303 CYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8163 (t) REVERT: G 313 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8534 (mtmm) REVERT: G 332 SER cc_start: 0.9356 (t) cc_final: 0.9027 (p) REVERT: H 107 TRP cc_start: 0.8020 (m100) cc_final: 0.7462 (m-10) REVERT: H 130 ILE cc_start: 0.9124 (tp) cc_final: 0.8749 (tp) REVERT: H 264 LEU cc_start: 0.8884 (tp) cc_final: 0.8541 (tt) REVERT: H 303 CYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7794 (t) REVERT: H 313 LYS cc_start: 0.8787 (mtpt) cc_final: 0.8469 (mtmm) REVERT: H 332 SER cc_start: 0.9042 (t) cc_final: 0.8749 (p) outliers start: 68 outliers final: 52 residues processed: 609 average time/residue: 0.1334 time to fit residues: 126.8662 Evaluate side-chains 582 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 527 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 341 ILE 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 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 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 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 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 303 CYS 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 271 ILE 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 231 LEU 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 131 optimal weight: 3.9990 chunk 92 optimal weight: 0.0970 chunk 29 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS ** C 50 HIS ** 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** G 329 GLN H 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105917 restraints weight = 30092.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.109822 restraints weight = 15694.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.112461 restraints weight = 10238.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.114260 restraints weight = 7654.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.115430 restraints weight = 6211.269| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21488 Z= 0.126 Angle : 0.590 9.855 29304 Z= 0.300 Chirality : 0.041 0.170 3232 Planarity : 0.003 0.039 3584 Dihedral : 4.486 18.220 2752 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.44 % Allowed : 24.73 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.17), residues: 2480 helix: 0.95 (0.12), residues: 1720 sheet: -4.10 (0.35), residues: 40 loop : -3.55 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 186 TYR 0.021 0.001 TYR D 120 PHE 0.017 0.001 PHE C 51 TRP 0.009 0.001 TRP E 236 HIS 0.016 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00274 (21472) covalent geometry : angle 0.58984 (29272) SS BOND : bond 0.00105 ( 16) SS BOND : angle 0.76105 ( 32) hydrogen bonds : bond 0.03946 ( 1224) hydrogen bonds : angle 4.25515 ( 3648) *********************** 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 665 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 589 time to evaluate : 0.610 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: 0.8297 (m100) cc_final: 0.7602 (m-10) REVERT: A 145 ASP cc_start: 0.8617 (t70) cc_final: 0.8384 (t0) REVERT: A 313 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8617 (mtmm) REVERT: B 50 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7257 (p90) REVERT: B 107 TRP cc_start: 0.7958 (m100) cc_final: 0.7363 (m-10) REVERT: B 130 ILE cc_start: 0.9014 (tp) cc_final: 0.8529 (tp) REVERT: B 145 ASP cc_start: 0.8581 (t70) cc_final: 0.8349 (t0) REVERT: B 264 LEU cc_start: 0.8935 (tp) cc_final: 0.8544 (tt) REVERT: B 274 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.5702 (mp0) REVERT: B 313 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8486 (mtmm) REVERT: B 332 SER cc_start: 0.9038 (t) cc_final: 0.8726 (p) REVERT: C 67 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7526 (mp10) REVERT: C 107 TRP cc_start: 0.8312 (m100) cc_final: 0.7637 (m-10) REVERT: C 186 ARG cc_start: 0.7055 (mtp180) cc_final: 0.6831 (mmm-85) REVERT: C 236 TRP cc_start: 0.7963 (p90) cc_final: 0.7742 (p90) REVERT: C 301 TYR cc_start: 0.8596 (t80) cc_final: 0.8281 (t80) REVERT: C 303 CYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8034 (t) REVERT: D 107 TRP cc_start: 0.7854 (m100) cc_final: 0.7494 (m-10) REVERT: D 130 ILE cc_start: 0.8954 (tp) cc_final: 0.8485 (tp) REVERT: D 236 TRP cc_start: 0.8237 (p90) cc_final: 0.7986 (p90) REVERT: D 264 LEU cc_start: 0.8737 (tp) cc_final: 0.8345 (tt) REVERT: D 274 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: D 313 LYS cc_start: 0.8727 (mtpt) cc_final: 0.8259 (mtmm) REVERT: E 67 GLN cc_start: 0.7438 (mm-40) cc_final: 0.7222 (mp10) REVERT: E 107 TRP cc_start: 0.8303 (m100) cc_final: 0.7713 (m-10) REVERT: E 236 TRP cc_start: 0.7967 (p90) cc_final: 0.7764 (p90) REVERT: E 313 LYS cc_start: 0.8827 (mtpt) cc_final: 0.8510 (mtmm) REVERT: E 361 MET cc_start: 0.9346 (mtp) cc_final: 0.9128 (mtm) REVERT: F 67 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7743 (mp10) REVERT: F 107 TRP cc_start: 0.7937 (m100) cc_final: 0.7421 (m-10) REVERT: F 130 ILE cc_start: 0.8960 (tp) cc_final: 0.8530 (tp) REVERT: F 159 LYS cc_start: 0.8068 (mptt) cc_final: 0.7776 (mptt) REVERT: F 264 LEU cc_start: 0.8842 (tp) cc_final: 0.8471 (tt) REVERT: F 274 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: F 313 LYS cc_start: 0.8757 (mtpt) cc_final: 0.8403 (mtmm) REVERT: F 332 SER cc_start: 0.9037 (t) cc_final: 0.8718 (p) REVERT: G 54 ASP cc_start: 0.7826 (p0) cc_final: 0.7570 (p0) REVERT: G 107 TRP cc_start: 0.8248 (m100) cc_final: 0.7593 (m-10) REVERT: G 145 ASP cc_start: 0.8631 (t70) cc_final: 0.8378 (t0) REVERT: G 313 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8550 (mtmm) REVERT: G 332 SER cc_start: 0.9339 (t) cc_final: 0.8989 (p) REVERT: H 50 HIS cc_start: 0.7986 (OUTLIER) cc_final: 0.7654 (p90) REVERT: H 107 TRP cc_start: 0.7986 (m100) cc_final: 0.7406 (m-10) REVERT: H 130 ILE cc_start: 0.8983 (tp) cc_final: 0.8562 (tp) REVERT: H 236 TRP cc_start: 0.8243 (p90) cc_final: 0.8016 (p90) REVERT: H 264 LEU cc_start: 0.8854 (tp) cc_final: 0.8485 (tt) REVERT: H 274 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: H 313 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8412 (mtmm) REVERT: H 332 SER cc_start: 0.9044 (t) cc_final: 0.8717 (p) outliers start: 76 outliers final: 57 residues processed: 642 average time/residue: 0.1283 time to fit residues: 130.0666 Evaluate side-chains 593 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 529 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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 47 LEU Chi-restraints excluded: chain D residue 49 SER 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 263 VAL 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 47 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 170 SER 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 Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 195 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 56 optimal weight: 0.0570 chunk 41 optimal weight: 2.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS D 50 HIS ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS ** F 50 HIS ** 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 = 0.3481 r_free = 0.3481 target = 0.132594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.110334 restraints weight = 29673.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114408 restraints weight = 15405.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117188 restraints weight = 9978.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.118959 restraints weight = 7376.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120346 restraints weight = 5989.241| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21488 Z= 0.122 Angle : 0.589 12.826 29304 Z= 0.299 Chirality : 0.041 0.179 3232 Planarity : 0.003 0.033 3584 Dihedral : 4.362 16.933 2752 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.99 % Allowed : 26.68 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.17), residues: 2480 helix: 1.14 (0.13), residues: 1720 sheet: -4.02 (0.37), residues: 40 loop : -3.46 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 244 TYR 0.023 0.001 TYR D 120 PHE 0.016 0.001 PHE B 51 TRP 0.009 0.001 TRP E 236 HIS 0.013 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00261 (21472) covalent geometry : angle 0.58851 (29272) SS BOND : bond 0.00082 ( 16) SS BOND : angle 0.93559 ( 32) hydrogen bonds : bond 0.03789 ( 1224) hydrogen bonds : angle 4.19253 ( 3648) *********************** 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 679 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 591 time to evaluate : 0.586 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 50 HIS cc_start: 0.7796 (OUTLIER) cc_final: 0.7535 (p90) REVERT: A 107 TRP cc_start: 0.8289 (m100) cc_final: 0.7654 (m-10) REVERT: A 145 ASP cc_start: 0.8587 (t70) cc_final: 0.8358 (t0) REVERT: A 274 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.5889 (mp0) REVERT: A 313 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8603 (mtmm) REVERT: B 67 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7703 (mp10) REVERT: B 107 TRP cc_start: 0.7907 (m100) cc_final: 0.7361 (m-10) REVERT: B 130 ILE cc_start: 0.8942 (tp) cc_final: 0.8521 (tp) REVERT: B 145 ASP cc_start: 0.8551 (t70) cc_final: 0.8343 (t0) REVERT: B 159 LYS cc_start: 0.7823 (mppt) cc_final: 0.7536 (mptt) REVERT: B 264 LEU cc_start: 0.8903 (tp) cc_final: 0.8522 (tt) REVERT: B 274 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.5626 (mp0) REVERT: B 313 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8473 (mtmm) REVERT: B 332 SER cc_start: 0.9024 (t) cc_final: 0.8697 (p) REVERT: C 107 TRP cc_start: 0.8268 (m100) cc_final: 0.7695 (m-10) REVERT: C 236 TRP cc_start: 0.8011 (p90) cc_final: 0.7795 (p90) REVERT: C 301 TYR cc_start: 0.8599 (t80) cc_final: 0.8258 (t80) REVERT: C 303 CYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8158 (t) REVERT: D 107 TRP cc_start: 0.7792 (m100) cc_final: 0.7466 (m-10) REVERT: D 130 ILE cc_start: 0.8947 (tp) cc_final: 0.8482 (tp) REVERT: D 236 TRP cc_start: 0.8204 (p90) cc_final: 0.7954 (p90) REVERT: D 264 LEU cc_start: 0.8676 (tp) cc_final: 0.8132 (tt) REVERT: D 274 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6438 (mp0) REVERT: D 313 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8252 (mtmm) REVERT: E 107 TRP cc_start: 0.8268 (m100) cc_final: 0.7705 (m-10) REVERT: E 303 CYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8285 (t) REVERT: E 313 LYS cc_start: 0.8810 (mtpt) cc_final: 0.8486 (mtmm) REVERT: E 361 MET cc_start: 0.9308 (mtp) cc_final: 0.9082 (mtm) REVERT: F 67 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7721 (mp10) REVERT: F 107 TRP cc_start: 0.7843 (m100) cc_final: 0.7345 (m-10) REVERT: F 156 ASP cc_start: 0.8413 (t0) cc_final: 0.8127 (t0) REVERT: F 159 LYS cc_start: 0.8155 (mptt) cc_final: 0.7848 (mptt) REVERT: F 236 TRP cc_start: 0.8206 (p90) cc_final: 0.7927 (p90) REVERT: F 264 LEU cc_start: 0.8746 (tp) cc_final: 0.8358 (tt) REVERT: F 274 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: F 313 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8398 (mtmm) REVERT: F 332 SER cc_start: 0.9038 (t) cc_final: 0.8665 (p) REVERT: G 107 TRP cc_start: 0.8294 (m100) cc_final: 0.7707 (m-10) REVERT: G 145 ASP cc_start: 0.8620 (t70) cc_final: 0.8378 (t0) REVERT: G 236 TRP cc_start: 0.8185 (p90) cc_final: 0.7823 (p90) REVERT: G 274 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.6009 (mp0) REVERT: G 313 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8531 (mtmm) REVERT: G 332 SER cc_start: 0.9282 (t) cc_final: 0.8786 (p) REVERT: H 107 TRP cc_start: 0.7913 (m100) cc_final: 0.7377 (m-10) REVERT: H 130 ILE cc_start: 0.8867 (tp) cc_final: 0.8461 (tp) REVERT: H 236 TRP cc_start: 0.8213 (p90) cc_final: 0.7997 (p90) REVERT: H 264 LEU cc_start: 0.8803 (tp) cc_final: 0.8436 (tt) REVERT: H 274 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: H 313 LYS cc_start: 0.8778 (mtpt) cc_final: 0.8427 (mtmm) REVERT: H 332 SER cc_start: 0.9051 (t) cc_final: 0.8662 (p) outliers start: 88 outliers final: 67 residues processed: 647 average time/residue: 0.1277 time to fit residues: 130.8291 Evaluate side-chains 628 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 552 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 50 HIS 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 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 39 LEU Chi-restraints excluded: chain C residue 50 HIS 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 341 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 127 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 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 74 GLN 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 42 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 129 MET 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 49 SER 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 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 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 Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 37 optimal weight: 7.9990 chunk 232 optimal weight: 0.9980 chunk 235 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 217 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS C 50 HIS 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.103349 restraints weight = 30714.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.107305 restraints weight = 15955.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109932 restraints weight = 10394.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.111637 restraints weight = 7776.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.112952 restraints weight = 6351.576| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21488 Z= 0.154 Angle : 0.600 11.319 29304 Z= 0.305 Chirality : 0.042 0.185 3232 Planarity : 0.003 0.032 3584 Dihedral : 4.392 16.715 2752 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 4.94 % Allowed : 26.81 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.17), residues: 2480 helix: 1.17 (0.13), residues: 1720 sheet: -4.03 (0.39), residues: 40 loop : -3.46 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 244 TYR 0.027 0.001 TYR B 120 PHE 0.015 0.001 PHE C 340 TRP 0.014 0.001 TRP B 236 HIS 0.008 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00355 (21472) covalent geometry : angle 0.59886 (29272) SS BOND : bond 0.00258 ( 16) SS BOND : angle 1.35684 ( 32) hydrogen bonds : bond 0.03896 ( 1224) hydrogen bonds : angle 4.18685 ( 3648) *********************** 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 674 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 565 time to evaluate : 0.532 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 50 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7571 (p90) REVERT: A 107 TRP cc_start: 0.8378 (m100) cc_final: 0.7675 (m-10) REVERT: A 142 LYS cc_start: 0.9051 (mtmm) cc_final: 0.8773 (mtpp) REVERT: A 145 ASP cc_start: 0.8655 (t70) cc_final: 0.8381 (t0) REVERT: A 274 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.5726 (mp0) REVERT: A 313 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8593 (mtmm) REVERT: B 107 TRP cc_start: 0.7999 (m100) cc_final: 0.7387 (m-10) REVERT: B 130 ILE cc_start: 0.8840 (tp) cc_final: 0.8430 (tp) REVERT: B 145 ASP cc_start: 0.8581 (t70) cc_final: 0.8352 (t0) REVERT: B 156 ASP cc_start: 0.8553 (t0) cc_final: 0.8337 (t0) REVERT: B 159 LYS cc_start: 0.7877 (mppt) cc_final: 0.7537 (mptt) REVERT: B 274 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.5590 (mp0) REVERT: B 313 LYS cc_start: 0.8734 (mtpt) cc_final: 0.8405 (mtmm) REVERT: B 332 SER cc_start: 0.9041 (t) cc_final: 0.8695 (p) REVERT: C 50 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.7441 (p90) REVERT: C 67 GLN cc_start: 0.6871 (mp10) cc_final: 0.6551 (mp10) REVERT: C 107 TRP cc_start: 0.8366 (m100) cc_final: 0.7684 (m-10) REVERT: C 236 TRP cc_start: 0.8034 (p90) cc_final: 0.7771 (p90) REVERT: C 274 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.6339 (mp0) REVERT: C 303 CYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8274 (t) REVERT: D 107 TRP cc_start: 0.7965 (m100) cc_final: 0.7453 (m-10) REVERT: D 130 ILE cc_start: 0.8989 (tp) cc_final: 0.8549 (tp) REVERT: D 264 LEU cc_start: 0.8726 (tp) cc_final: 0.8192 (tt) REVERT: D 274 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.5946 (mp0) REVERT: D 313 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8246 (mtmm) REVERT: E 107 TRP cc_start: 0.8343 (m100) cc_final: 0.7717 (m-10) REVERT: E 303 CYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8304 (t) REVERT: E 313 LYS cc_start: 0.8820 (mtpt) cc_final: 0.8467 (mtmm) REVERT: F 67 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7711 (mp10) REVERT: F 107 TRP cc_start: 0.7955 (m100) cc_final: 0.7353 (m-10) REVERT: F 156 ASP cc_start: 0.8481 (t0) cc_final: 0.8239 (t0) REVERT: F 159 LYS cc_start: 0.8219 (mptt) cc_final: 0.7910 (mptt) REVERT: F 264 LEU cc_start: 0.8781 (tp) cc_final: 0.8439 (tt) REVERT: F 274 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.5875 (mp0) REVERT: F 303 CYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8038 (t) REVERT: F 313 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8389 (mtmm) REVERT: F 332 SER cc_start: 0.9066 (t) cc_final: 0.8656 (p) REVERT: G 50 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.7236 (p90) REVERT: G 107 TRP cc_start: 0.8336 (m100) cc_final: 0.7637 (m-10) REVERT: G 145 ASP cc_start: 0.8657 (t70) cc_final: 0.8400 (t0) REVERT: G 274 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.5876 (mp0) REVERT: G 313 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8625 (mtmm) REVERT: G 332 SER cc_start: 0.9355 (t) cc_final: 0.8834 (p) REVERT: H 107 TRP cc_start: 0.7996 (m100) cc_final: 0.7385 (m-10) REVERT: H 130 ILE cc_start: 0.8961 (tp) cc_final: 0.8552 (tp) REVERT: H 274 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.5887 (mp0) REVERT: H 313 LYS cc_start: 0.8757 (mtpt) cc_final: 0.8441 (mtmm) REVERT: H 332 SER cc_start: 0.9068 (t) cc_final: 0.8661 (p) outliers start: 109 outliers final: 68 residues processed: 638 average time/residue: 0.1270 time to fit residues: 128.9379 Evaluate side-chains 635 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 554 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU 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 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 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 50 HIS 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 341 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 47 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 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 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 42 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 129 MET 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 292 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 49 SER 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 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 170 SER 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 Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 173 optimal weight: 0.0010 chunk 195 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 216 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS ** C 50 HIS ** 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** H 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.102695 restraints weight = 30753.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.106494 restraints weight = 16828.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109074 restraints weight = 11276.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110773 restraints weight = 8539.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111964 restraints weight = 7028.329| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2724 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= 0.125 Angle : 0.597 10.532 29304 Z= 0.303 Chirality : 0.041 0.192 3232 Planarity : 0.003 0.040 3584 Dihedral : 4.316 16.121 2752 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.03 % Allowed : 28.49 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.17), residues: 2480 helix: 1.27 (0.13), residues: 1720 sheet: -4.01 (0.40), residues: 40 loop : -3.39 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 244 TYR 0.026 0.001 TYR B 120 PHE 0.013 0.001 PHE D 147 TRP 0.021 0.001 TRP B 236 HIS 0.007 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00271 (21472) covalent geometry : angle 0.59668 (29272) SS BOND : bond 0.00125 ( 16) SS BOND : angle 0.94624 ( 32) hydrogen bonds : bond 0.03736 ( 1224) hydrogen bonds : angle 4.16629 ( 3648) *********************** 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 704 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 615 time to evaluate : 0.536 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 50 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7363 (p90) REVERT: A 107 TRP cc_start: 0.8386 (m100) cc_final: 0.7720 (m-10) REVERT: A 145 ASP cc_start: 0.8637 (t70) cc_final: 0.8384 (t0) REVERT: A 236 TRP cc_start: 0.8229 (p90) cc_final: 0.7809 (p90) REVERT: A 274 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.5721 (mp0) REVERT: A 313 LYS cc_start: 0.8897 (mtpt) cc_final: 0.8609 (mtmm) REVERT: B 67 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7698 (mp10) REVERT: B 107 TRP cc_start: 0.7941 (m100) cc_final: 0.7396 (m-10) REVERT: B 145 ASP cc_start: 0.8568 (t70) cc_final: 0.8342 (t0) REVERT: B 156 ASP cc_start: 0.8513 (t0) cc_final: 0.8309 (t0) REVERT: B 159 LYS cc_start: 0.7768 (mppt) cc_final: 0.7462 (mptt) REVERT: B 264 LEU cc_start: 0.8787 (tp) cc_final: 0.8445 (tt) REVERT: B 274 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.5555 (mp0) REVERT: B 313 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8496 (mtmm) REVERT: B 332 SER cc_start: 0.9011 (t) cc_final: 0.8634 (p) REVERT: C 67 GLN cc_start: 0.6863 (mp10) cc_final: 0.6616 (mp10) REVERT: C 107 TRP cc_start: 0.8307 (m100) cc_final: 0.7692 (m-10) REVERT: C 236 TRP cc_start: 0.8072 (p90) cc_final: 0.7817 (p90) REVERT: C 274 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.6266 (mp0) REVERT: C 303 CYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8198 (t) REVERT: D 67 GLN cc_start: 0.7069 (mp10) cc_final: 0.6684 (mp10) REVERT: D 107 TRP cc_start: 0.7976 (m100) cc_final: 0.7474 (m-10) REVERT: D 130 ILE cc_start: 0.8968 (tp) cc_final: 0.8502 (tp) REVERT: D 151 ASN cc_start: 0.8074 (p0) cc_final: 0.7849 (m-40) REVERT: D 208 TYR cc_start: 0.7677 (t80) cc_final: 0.7424 (t80) REVERT: D 236 TRP cc_start: 0.8133 (p90) cc_final: 0.7859 (p90) REVERT: D 264 LEU cc_start: 0.8689 (tp) cc_final: 0.8169 (tt) REVERT: D 274 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.5909 (mp0) REVERT: D 313 LYS cc_start: 0.8696 (mtpt) cc_final: 0.8374 (mtmm) REVERT: E 107 TRP cc_start: 0.8300 (m100) cc_final: 0.7698 (m-10) REVERT: E 274 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.6483 (mp0) REVERT: E 303 CYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8272 (t) REVERT: E 313 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8465 (mtmm) REVERT: F 67 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7726 (mp10) REVERT: F 107 TRP cc_start: 0.7933 (m100) cc_final: 0.7452 (m-10) REVERT: F 130 ILE cc_start: 0.8929 (tp) cc_final: 0.8424 (tp) REVERT: F 151 ASN cc_start: 0.8093 (p0) cc_final: 0.7834 (m-40) REVERT: F 156 ASP cc_start: 0.8424 (t0) cc_final: 0.8206 (t0) REVERT: F 264 LEU cc_start: 0.8742 (tp) cc_final: 0.8399 (tt) REVERT: F 274 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.5912 (mp0) REVERT: F 303 CYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8045 (t) REVERT: F 313 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8488 (mtmm) REVERT: F 332 SER cc_start: 0.9040 (t) cc_final: 0.8634 (p) REVERT: G 50 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.7128 (p90) REVERT: G 107 TRP cc_start: 0.8342 (m100) cc_final: 0.7714 (m-10) REVERT: G 145 ASP cc_start: 0.8624 (t70) cc_final: 0.8388 (t0) REVERT: G 210 LEU cc_start: 0.8947 (tp) cc_final: 0.8713 (tp) REVERT: G 236 TRP cc_start: 0.8225 (p90) cc_final: 0.7825 (p90) REVERT: G 274 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.5839 (mp0) REVERT: G 313 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8627 (mtmm) REVERT: G 331 PHE cc_start: 0.8543 (m-80) cc_final: 0.8205 (m-80) REVERT: G 332 SER cc_start: 0.9323 (t) cc_final: 0.8786 (p) REVERT: H 107 TRP cc_start: 0.7965 (m100) cc_final: 0.7404 (m-10) REVERT: H 236 TRP cc_start: 0.8208 (p90) cc_final: 0.7960 (p90) REVERT: H 264 LEU cc_start: 0.8761 (tp) cc_final: 0.8455 (tt) REVERT: H 274 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.5920 (mp0) REVERT: H 303 CYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8006 (t) REVERT: H 313 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8496 (mtmm) REVERT: H 332 SER cc_start: 0.9047 (t) cc_final: 0.8643 (p) outliers start: 89 outliers final: 67 residues processed: 664 average time/residue: 0.1333 time to fit residues: 138.8054 Evaluate side-chains 672 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 591 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 50 HIS 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 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 49 SER 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 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 127 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 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 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 39 LEU 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 121 ILE Chi-restraints excluded: chain F residue 129 MET 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 303 CYS 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 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 303 CYS Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 107 optimal weight: 0.4980 chunk 42 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 186 optimal weight: 0.0270 chunk 191 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 overall best weight: 0.6640 ------------------------------------------------------------------------------- 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 C 50 HIS C 314 ASN ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.106719 restraints weight = 30413.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110762 restraints weight = 15953.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.113505 restraints weight = 10433.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.115303 restraints weight = 7779.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116658 restraints weight = 6340.431| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21488 Z= 0.120 Angle : 0.596 8.721 29304 Z= 0.304 Chirality : 0.040 0.177 3232 Planarity : 0.003 0.032 3584 Dihedral : 4.212 15.915 2752 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.79 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.17), residues: 2480 helix: 1.34 (0.13), residues: 1728 sheet: -4.06 (0.40), residues: 40 loop : -3.26 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 244 TYR 0.028 0.001 TYR D 300 PHE 0.014 0.001 PHE H 147 TRP 0.022 0.001 TRP B 236 HIS 0.020 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00249 (21472) covalent geometry : angle 0.59554 (29272) SS BOND : bond 0.00074 ( 16) SS BOND : angle 0.84637 ( 32) hydrogen bonds : bond 0.03547 ( 1224) hydrogen bonds : angle 4.14145 ( 3648) *********************** 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 693 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 617 time to evaluate : 0.784 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 50 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.7163 (p90) REVERT: A 107 TRP cc_start: 0.8302 (m100) cc_final: 0.7703 (m-10) REVERT: A 145 ASP cc_start: 0.8589 (t70) cc_final: 0.8354 (t0) REVERT: A 274 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.5730 (mp0) REVERT: A 313 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8621 (mtmm) REVERT: B 67 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7706 (mp10) REVERT: B 107 TRP cc_start: 0.7919 (m100) cc_final: 0.7399 (m-10) REVERT: B 130 ILE cc_start: 0.8859 (tp) cc_final: 0.8409 (tp) REVERT: B 156 ASP cc_start: 0.8516 (t0) cc_final: 0.8302 (t0) REVERT: B 159 LYS cc_start: 0.7688 (mppt) cc_final: 0.7405 (mptt) REVERT: B 264 LEU cc_start: 0.8740 (tp) cc_final: 0.8401 (tt) REVERT: B 274 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.5524 (mp0) REVERT: B 313 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8489 (mtmm) REVERT: B 332 SER cc_start: 0.9021 (t) cc_final: 0.8627 (p) REVERT: C 67 GLN cc_start: 0.6848 (mp10) cc_final: 0.6598 (mp10) REVERT: C 107 TRP cc_start: 0.8222 (m100) cc_final: 0.7643 (m-10) REVERT: C 151 ASN cc_start: 0.8202 (p0) cc_final: 0.7945 (m-40) REVERT: C 236 TRP cc_start: 0.7983 (p90) cc_final: 0.7711 (p90) REVERT: C 274 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.6180 (mp0) REVERT: C 303 CYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8214 (t) REVERT: D 67 GLN cc_start: 0.7087 (mp10) cc_final: 0.6702 (mp10) REVERT: D 107 TRP cc_start: 0.7838 (m100) cc_final: 0.7439 (m-10) REVERT: D 208 TYR cc_start: 0.7726 (t80) cc_final: 0.7462 (t80) REVERT: D 236 TRP cc_start: 0.8108 (p90) cc_final: 0.7889 (p90) REVERT: D 274 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.5897 (mp0) REVERT: D 313 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8372 (mtmm) REVERT: E 107 TRP cc_start: 0.8218 (m100) cc_final: 0.7689 (m-10) REVERT: E 274 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.6359 (mp0) REVERT: E 313 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8569 (mtmm) REVERT: F 67 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7727 (mp10) REVERT: F 107 TRP cc_start: 0.7748 (m100) cc_final: 0.7402 (m-10) REVERT: F 130 ILE cc_start: 0.8771 (tp) cc_final: 0.8227 (tp) REVERT: F 236 TRP cc_start: 0.8054 (p90) cc_final: 0.7802 (p90) REVERT: F 274 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.5867 (mp0) REVERT: F 303 CYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8002 (t) REVERT: F 313 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8466 (mtmm) REVERT: F 332 SER cc_start: 0.9030 (t) cc_final: 0.8622 (p) REVERT: G 50 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.7070 (p90) REVERT: G 107 TRP cc_start: 0.8287 (m100) cc_final: 0.7722 (m-10) REVERT: G 145 ASP cc_start: 0.8628 (t70) cc_final: 0.8383 (t0) REVERT: G 210 LEU cc_start: 0.8978 (tp) cc_final: 0.8731 (tp) REVERT: G 236 TRP cc_start: 0.8159 (p90) cc_final: 0.7762 (p90) REVERT: G 264 LEU cc_start: 0.8793 (tp) cc_final: 0.8419 (tp) REVERT: G 274 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.5676 (mp0) REVERT: G 313 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8622 (mtmm) REVERT: G 332 SER cc_start: 0.9332 (t) cc_final: 0.8787 (p) REVERT: H 67 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7717 (mp10) REVERT: H 107 TRP cc_start: 0.7885 (m100) cc_final: 0.7446 (m-10) REVERT: H 130 ILE cc_start: 0.8595 (tp) cc_final: 0.8267 (tp) REVERT: H 151 ASN cc_start: 0.8018 (p0) cc_final: 0.7780 (m-40) REVERT: H 274 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.5883 (mp0) REVERT: H 303 CYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7945 (t) REVERT: H 313 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8530 (mtmm) REVERT: H 332 SER cc_start: 0.9044 (t) cc_final: 0.8630 (p) outliers start: 76 outliers final: 60 residues processed: 658 average time/residue: 0.1299 time to fit residues: 134.1147 Evaluate side-chains 641 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 568 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 HIS 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 63 GLN Chi-restraints excluded: chain B residue 125 ILE 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 50 HIS 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 341 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 125 ILE 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 211 THR 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 129 MET 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 303 CYS 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 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 303 CYS Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 121 optimal weight: 2.9990 chunk 240 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 187 optimal weight: 0.6980 chunk 96 optimal weight: 0.0870 chunk 155 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- 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 C 50 HIS ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.103152 restraints weight = 30618.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.106962 restraints weight = 16772.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109519 restraints weight = 11267.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.111206 restraints weight = 8563.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.112340 restraints weight = 7065.508| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2969 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= 0.135 Angle : 0.607 10.563 29304 Z= 0.309 Chirality : 0.041 0.153 3232 Planarity : 0.003 0.032 3584 Dihedral : 4.223 15.945 2752 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.44 % Allowed : 30.34 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.17), residues: 2480 helix: 1.36 (0.13), residues: 1728 sheet: -4.06 (0.42), residues: 40 loop : -3.20 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 184 TYR 0.028 0.001 TYR F 120 PHE 0.020 0.001 PHE A 51 TRP 0.036 0.001 TRP B 236 HIS 0.020 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00303 (21472) covalent geometry : angle 0.60650 (29272) SS BOND : bond 0.00211 ( 16) SS BOND : angle 1.21703 ( 32) hydrogen bonds : bond 0.03609 ( 1224) hydrogen bonds : angle 4.12864 ( 3648) *********************** 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 659 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 583 time to evaluate : 0.664 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 50 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.7120 (p90) REVERT: A 107 TRP cc_start: 0.8346 (m100) cc_final: 0.7707 (m-10) REVERT: A 145 ASP cc_start: 0.8643 (t70) cc_final: 0.8376 (t0) REVERT: A 236 TRP cc_start: 0.8228 (p90) cc_final: 0.7784 (p90) REVERT: A 264 LEU cc_start: 0.8806 (tp) cc_final: 0.8484 (tp) REVERT: A 274 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.5707 (mp0) REVERT: A 313 LYS cc_start: 0.8911 (mtpt) cc_final: 0.8624 (mtmm) REVERT: B 67 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7633 (mp10) REVERT: B 107 TRP cc_start: 0.7984 (m100) cc_final: 0.7414 (m-10) REVERT: B 145 ASP cc_start: 0.8567 (t70) cc_final: 0.8354 (t0) REVERT: B 264 LEU cc_start: 0.8768 (tp) cc_final: 0.8448 (tt) REVERT: B 274 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.5513 (mp0) REVERT: B 313 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8496 (mtmm) REVERT: B 332 SER cc_start: 0.9059 (t) cc_final: 0.8634 (p) REVERT: C 67 GLN cc_start: 0.6849 (mp10) cc_final: 0.6613 (mp10) REVERT: C 107 TRP cc_start: 0.8275 (m100) cc_final: 0.7658 (m-10) REVERT: C 264 LEU cc_start: 0.8837 (tp) cc_final: 0.8533 (tp) REVERT: C 274 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.6058 (mp0) REVERT: C 303 CYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8240 (t) REVERT: D 107 TRP cc_start: 0.7944 (m100) cc_final: 0.7450 (m-10) REVERT: D 208 TYR cc_start: 0.7740 (t80) cc_final: 0.7454 (t80) REVERT: D 274 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.5854 (mp0) REVERT: D 313 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8399 (mtmm) REVERT: E 107 TRP cc_start: 0.8245 (m100) cc_final: 0.7703 (m-10) REVERT: E 274 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.6198 (mp0) REVERT: E 313 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8545 (mtmm) REVERT: F 67 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7712 (mp10) REVERT: F 107 TRP cc_start: 0.7782 (m100) cc_final: 0.7388 (m-10) REVERT: F 236 TRP cc_start: 0.8098 (p90) cc_final: 0.7818 (p90) REVERT: F 274 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.5830 (mp0) REVERT: F 303 CYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8046 (t) REVERT: F 313 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8554 (mtmm) REVERT: F 332 SER cc_start: 0.9056 (t) cc_final: 0.8633 (p) REVERT: G 50 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7109 (p90) REVERT: G 107 TRP cc_start: 0.8326 (m100) cc_final: 0.7727 (m-10) REVERT: G 145 ASP cc_start: 0.8653 (t70) cc_final: 0.8407 (t0) REVERT: G 210 LEU cc_start: 0.8970 (tp) cc_final: 0.8742 (tp) REVERT: G 236 TRP cc_start: 0.8152 (p90) cc_final: 0.7729 (p90) REVERT: G 274 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.5610 (mp0) REVERT: G 313 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8627 (mtmm) REVERT: G 332 SER cc_start: 0.9346 (t) cc_final: 0.8786 (p) REVERT: H 67 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7720 (mp10) REVERT: H 107 TRP cc_start: 0.7789 (m100) cc_final: 0.7417 (m-10) REVERT: H 130 ILE cc_start: 0.8638 (tp) cc_final: 0.8295 (tp) REVERT: H 264 LEU cc_start: 0.8712 (tp) cc_final: 0.8390 (tt) REVERT: H 274 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.5848 (mp0) REVERT: H 303 CYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7998 (t) REVERT: H 313 LYS cc_start: 0.8763 (mtpt) cc_final: 0.8478 (mtmm) REVERT: H 332 SER cc_start: 0.9088 (t) cc_final: 0.8666 (p) outliers start: 76 outliers final: 60 residues processed: 624 average time/residue: 0.1307 time to fit residues: 128.9616 Evaluate side-chains 637 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 564 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 HIS 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 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 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 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 211 THR 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 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 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 303 CYS 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 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 303 CYS 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 115 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 112 optimal weight: 20.0000 chunk 199 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN D 50 HIS D 63 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.102112 restraints weight = 31067.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.105876 restraints weight = 17026.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108415 restraints weight = 11485.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110124 restraints weight = 8752.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111217 restraints weight = 7234.831| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21488 Z= 0.147 Angle : 0.628 11.287 29304 Z= 0.318 Chirality : 0.041 0.152 3232 Planarity : 0.003 0.035 3584 Dihedral : 4.266 16.624 2752 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.49 % Allowed : 30.25 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.17), residues: 2480 helix: 1.35 (0.13), residues: 1728 sheet: -4.05 (0.44), residues: 40 loop : -3.16 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 184 TYR 0.028 0.001 TYR F 120 PHE 0.018 0.001 PHE A 51 TRP 0.044 0.001 TRP B 236 HIS 0.005 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00334 (21472) covalent geometry : angle 0.62590 (29272) SS BOND : bond 0.00215 ( 16) SS BOND : angle 1.50865 ( 32) hydrogen bonds : bond 0.03744 ( 1224) hydrogen bonds : angle 4.16929 ( 3648) ********************** 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 656 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 579 time to evaluate : 0.797 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: A 50 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.7213 (p90) REVERT: A 107 TRP cc_start: 0.8336 (m100) cc_final: 0.7757 (m-10) REVERT: A 145 ASP cc_start: 0.8636 (t70) cc_final: 0.8366 (t0) REVERT: A 156 ASP cc_start: 0.8331 (t0) cc_final: 0.8108 (t0) REVERT: A 236 TRP cc_start: 0.8220 (p90) cc_final: 0.7789 (p90) REVERT: A 264 LEU cc_start: 0.8852 (tp) cc_final: 0.8559 (tp) REVERT: A 274 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.5810 (mp0) REVERT: A 313 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8706 (mtmm) REVERT: B 67 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7667 (mp10) REVERT: B 107 TRP cc_start: 0.7954 (m100) cc_final: 0.7483 (m-10) REVERT: B 130 ILE cc_start: 0.8903 (tp) cc_final: 0.8474 (tp) REVERT: B 145 ASP cc_start: 0.8570 (t70) cc_final: 0.8352 (t0) REVERT: B 274 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.5559 (mp0) REVERT: B 313 LYS cc_start: 0.8800 (mtpt) cc_final: 0.8516 (mtmm) REVERT: B 332 SER cc_start: 0.9062 (t) cc_final: 0.8648 (p) REVERT: C 67 GLN cc_start: 0.6911 (mp10) cc_final: 0.6650 (mp10) REVERT: C 107 TRP cc_start: 0.8279 (m100) cc_final: 0.7703 (m-10) REVERT: C 264 LEU cc_start: 0.8852 (tp) cc_final: 0.8558 (tp) REVERT: C 274 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: C 303 CYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8199 (t) REVERT: C 313 LYS cc_start: 0.8787 (mtpt) cc_final: 0.8564 (mtmm) REVERT: C 332 SER cc_start: 0.9234 (t) cc_final: 0.8899 (p) REVERT: D 67 GLN cc_start: 0.7013 (mp10) cc_final: 0.6690 (mp10) REVERT: D 107 TRP cc_start: 0.7945 (m100) cc_final: 0.7507 (m-10) REVERT: D 208 TYR cc_start: 0.7796 (t80) cc_final: 0.7510 (t80) REVERT: D 274 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.5912 (mp0) REVERT: D 313 LYS cc_start: 0.8663 (mtpt) cc_final: 0.8411 (mtmm) REVERT: E 107 TRP cc_start: 0.8242 (m100) cc_final: 0.7718 (m-10) REVERT: E 151 ASN cc_start: 0.8299 (p0) cc_final: 0.8080 (m-40) REVERT: E 274 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.6223 (mp0) REVERT: E 313 LYS cc_start: 0.8857 (mtpt) cc_final: 0.8573 (mtmm) REVERT: F 67 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7680 (mp10) REVERT: F 107 TRP cc_start: 0.7783 (m100) cc_final: 0.7426 (m-10) REVERT: F 188 MET cc_start: 0.8652 (mmm) cc_final: 0.8173 (mtp) REVERT: F 236 TRP cc_start: 0.8090 (p90) cc_final: 0.7862 (p90) REVERT: F 274 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.5909 (mp0) REVERT: F 303 CYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8009 (t) REVERT: F 313 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8548 (mtmm) REVERT: F 332 SER cc_start: 0.9072 (t) cc_final: 0.8665 (p) REVERT: F 334 LEU cc_start: 0.7673 (tp) cc_final: 0.7461 (tt) REVERT: G 50 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.7201 (p90) REVERT: G 107 TRP cc_start: 0.8328 (m100) cc_final: 0.7726 (m-10) REVERT: G 145 ASP cc_start: 0.8647 (t70) cc_final: 0.8388 (t0) REVERT: G 210 LEU cc_start: 0.9006 (tp) cc_final: 0.8766 (tp) REVERT: G 264 LEU cc_start: 0.8859 (tp) cc_final: 0.8574 (tp) REVERT: G 274 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.5737 (mp0) REVERT: G 313 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8632 (mtmm) REVERT: G 332 SER cc_start: 0.9284 (t) cc_final: 0.8741 (p) REVERT: H 67 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7740 (mp10) REVERT: H 107 TRP cc_start: 0.7798 (m100) cc_final: 0.7363 (m-10) REVERT: H 130 ILE cc_start: 0.8737 (tp) cc_final: 0.8374 (tp) REVERT: H 264 LEU cc_start: 0.8704 (tp) cc_final: 0.8396 (tt) REVERT: H 274 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.5889 (mp0) REVERT: H 303 CYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7961 (t) REVERT: H 313 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8499 (mtmm) REVERT: H 332 SER cc_start: 0.9182 (t) cc_final: 0.8813 (p) outliers start: 77 outliers final: 62 residues processed: 623 average time/residue: 0.1438 time to fit residues: 141.3266 Evaluate side-chains 645 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 570 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 HIS 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 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 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 341 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 ILE 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 211 THR 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 38 ILE Chi-restraints excluded: chain F residue 39 LEU 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 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 303 CYS 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 47 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 170 SER 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 303 CYS 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 19 optimal weight: 9.9990 chunk 38 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 223 optimal weight: 0.2980 chunk 215 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 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 314 ASN F 63 GLN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.101846 restraints weight = 30841.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.105596 restraints weight = 16988.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.108123 restraints weight = 11475.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.109724 restraints weight = 8761.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.110845 restraints weight = 7293.630| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21488 Z= 0.147 Angle : 0.637 10.598 29304 Z= 0.322 Chirality : 0.041 0.152 3232 Planarity : 0.003 0.036 3584 Dihedral : 4.269 17.011 2752 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.44 % Allowed : 30.53 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.17), residues: 2480 helix: 1.34 (0.13), residues: 1728 sheet: -3.98 (0.47), residues: 40 loop : -3.16 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 244 TYR 0.028 0.001 TYR H 120 PHE 0.024 0.001 PHE H 51 TRP 0.039 0.001 TRP B 236 HIS 0.005 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00335 (21472) covalent geometry : angle 0.63632 (29272) SS BOND : bond 0.00234 ( 16) SS BOND : angle 1.33314 ( 32) hydrogen bonds : bond 0.03743 ( 1224) hydrogen bonds : angle 4.17206 ( 3648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3400.87 seconds wall clock time: 59 minutes 26.21 seconds (3566.21 seconds total)