Starting phenix.real_space_refine on Sat Sep 28 21:41:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/09_2024/6kfh_9973.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/09_2024/6kfh_9973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/09_2024/6kfh_9973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/09_2024/6kfh_9973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/09_2024/6kfh_9973.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/09_2024/6kfh_9973.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 13832 2.51 5 N 3344 2.21 5 O 3568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20840 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Restraints were copied for chains: C, B, E, D, G, F, H Time building chain proxies: 6.46, per 1000 atoms: 0.31 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=2, 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.71 Conformation dependent library (CDL) restraints added in 2.7 seconds 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4880 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 8 sheets defined 71.1% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 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: 6.03 Time building geometry restraints manager: 6.57 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: 10550 15.88 - 31.77: 1270 31.77 - 47.65: 346 47.65 - 63.53: 8 63.53 - 79.41: 24 Dihedral angle restraints: 12198 sinusoidal: 4662 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 12195 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: 2.03 - 2.60: 187 2.60 - 3.18: 19434 3.18 - 3.75: 31393 3.75 - 4.33: 41559 4.33 - 4.90: 68853 Nonbonded interactions: 161426 Sorted by model distance: nonbonded pdb=" SG CYS B 76 " pdb=" SG CYS B 248 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS G 76 " pdb=" SG CYS G 248 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS F 76 " pdb=" SG CYS F 248 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS C 76 " pdb=" SG CYS C 248 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS D 76 " pdb=" SG CYS D 248 " model vdw 2.028 3.760 ... (remaining 161421 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 40.090 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.030 ------------------------------------------------------------------------------- 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 21472 Z= 0.451 Angle : 0.735 11.650 29272 Z= 0.389 Chirality : 0.045 0.178 3232 Planarity : 0.003 0.021 3584 Dihedral : 14.752 79.413 7312 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.15), residues: 2480 helix: -0.95 (0.11), residues: 1680 sheet: -5.11 (0.18), residues: 40 loop : -4.48 (0.16), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.004 0.001 HIS G 50 PHE 0.012 0.002 PHE D 119 TYR 0.008 0.001 TYR A 172 ARG 0.003 0.000 ARG E 168 *********************** 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 fitting. rotamer outliers: 0 poor density : 772 time to evaluate : 2.335 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: 0.3302 time to fit residues: 382.0298 Evaluate side-chains 556 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 556 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 225 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21472 Z= 0.196 Angle : 0.623 6.531 29272 Z= 0.326 Chirality : 0.042 0.162 3232 Planarity : 0.004 0.068 3584 Dihedral : 4.951 20.901 2752 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.54 % Allowed : 19.84 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.16), residues: 2480 helix: 0.29 (0.12), residues: 1696 sheet: None (None), residues: 0 loop : -3.93 (0.17), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 68 HIS 0.012 0.001 HIS G 50 PHE 0.013 0.001 PHE A 242 TYR 0.017 0.001 TYR C 301 ARG 0.006 0.000 ARG B 244 *********************** 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 fitting. rotamer outliers: 56 poor density : 640 time to evaluate : 2.364 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: A 54 ASP cc_start: 0.7404 (p0) cc_final: 0.7149 (p0) REVERT: A 103 GLN cc_start: 0.6999 (pt0) cc_final: 0.6690 (pt0) REVERT: A 107 TRP cc_start: 0.8027 (m100) cc_final: 0.7792 (m-10) REVERT: A 145 ASP cc_start: 0.8587 (t70) cc_final: 0.8347 (t0) REVERT: A 156 ASP cc_start: 0.8316 (t0) cc_final: 0.8090 (t0) REVERT: A 313 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8499 (mtmm) REVERT: B 58 CYS cc_start: 0.8128 (m) cc_final: 0.7593 (m) REVERT: B 103 GLN cc_start: 0.6817 (pt0) cc_final: 0.6540 (pt0) REVERT: B 130 ILE cc_start: 0.9187 (tp) cc_final: 0.8625 (tp) REVERT: B 145 ASP cc_start: 0.8552 (t70) cc_final: 0.8286 (t0) REVERT: B 159 LYS cc_start: 0.7991 (mptt) cc_final: 0.7670 (mptt) REVERT: B 264 LEU cc_start: 0.8769 (tp) cc_final: 0.8348 (tt) REVERT: B 313 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8424 (mtmm) REVERT: C 45 LEU cc_start: 0.8288 (tp) cc_final: 0.8006 (tp) REVERT: C 49 SER cc_start: 0.8941 (t) cc_final: 0.8660 (m) REVERT: C 103 GLN cc_start: 0.7039 (pt0) cc_final: 0.6654 (pt0) REVERT: C 107 TRP cc_start: 0.8068 (m100) cc_final: 0.7762 (m-10) REVERT: C 186 ARG cc_start: 0.6683 (mtp180) cc_final: 0.6447 (mtp85) REVERT: C 226 ILE cc_start: 0.7808 (mm) cc_final: 0.7530 (mt) REVERT: D 58 CYS cc_start: 0.8158 (m) cc_final: 0.7555 (m) REVERT: D 103 GLN cc_start: 0.6791 (pt0) cc_final: 0.6559 (pt0) REVERT: D 130 ILE cc_start: 0.9144 (tp) cc_final: 0.8595 (tp) REVERT: D 264 LEU cc_start: 0.8700 (tp) cc_final: 0.8230 (tt) REVERT: D 313 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8325 (mtmm) REVERT: E 58 CYS cc_start: 0.8171 (m) cc_final: 0.7349 (m) REVERT: E 59 TRP cc_start: 0.7570 (t-100) cc_final: 0.7276 (t60) REVERT: E 103 GLN cc_start: 0.6820 (pt0) cc_final: 0.6432 (pt0) REVERT: E 107 TRP cc_start: 0.8061 (m100) cc_final: 0.7829 (m-10) REVERT: E 142 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8823 (mtpp) REVERT: E 264 LEU cc_start: 0.8900 (tp) cc_final: 0.8473 (tt) REVERT: E 313 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8359 (mtmm) REVERT: E 327 ASP cc_start: 0.8708 (m-30) cc_final: 0.8490 (m-30) REVERT: E 334 LEU cc_start: 0.7880 (tp) cc_final: 0.7640 (tp) REVERT: F 58 CYS cc_start: 0.8290 (m) cc_final: 0.7804 (m) REVERT: F 264 LEU cc_start: 0.8818 (tp) cc_final: 0.8433 (tt) REVERT: F 313 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8390 (mtmm) REVERT: G 54 ASP cc_start: 0.7394 (p0) cc_final: 0.7158 (p0) REVERT: G 58 CYS cc_start: 0.8215 (m) cc_final: 0.7421 (m) REVERT: G 103 GLN cc_start: 0.7030 (pt0) cc_final: 0.6633 (pt0) REVERT: G 107 TRP cc_start: 0.8034 (m100) cc_final: 0.7768 (m-10) REVERT: G 142 LYS cc_start: 0.9213 (mtmm) cc_final: 0.8928 (mtpp) REVERT: G 145 ASP cc_start: 0.8699 (t70) cc_final: 0.8437 (t0) REVERT: G 177 ILE cc_start: 0.9352 (mm) cc_final: 0.9114 (mt) REVERT: G 313 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8447 (mtmm) REVERT: G 329 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8301 (pt0) REVERT: G 332 SER cc_start: 0.9262 (t) cc_final: 0.8984 (p) REVERT: H 58 CYS cc_start: 0.8246 (m) cc_final: 0.7728 (m) REVERT: H 264 LEU cc_start: 0.8721 (tp) cc_final: 0.8264 (tt) REVERT: H 303 CYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7552 (t) REVERT: H 313 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8447 (mtmm) outliers start: 56 outliers final: 41 residues processed: 676 average time/residue: 0.3086 time to fit residues: 319.6774 Evaluate side-chains 594 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 551 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 47 LEU 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 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 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 271 ILE Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 4.9990 chunk 243 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN B 50 HIS B 73 ASN C 50 HIS ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN D 73 ASN D 151 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS E 73 ASN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN F 50 HIS F 73 ASN F 151 ASN G 73 ASN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN G 329 GLN H 73 ASN H 314 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21472 Z= 0.192 Angle : 0.606 9.861 29272 Z= 0.311 Chirality : 0.042 0.169 3232 Planarity : 0.003 0.042 3584 Dihedral : 4.676 19.731 2752 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.85 % Allowed : 22.78 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.17), residues: 2480 helix: 0.75 (0.12), residues: 1720 sheet: -3.97 (0.41), residues: 40 loop : -3.73 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 68 HIS 0.020 0.002 HIS A 50 PHE 0.012 0.001 PHE B 51 TYR 0.017 0.001 TYR C 301 ARG 0.004 0.000 ARG B 244 *********************** 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 647 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 584 time to evaluate : 3.181 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: A 103 GLN cc_start: 0.7090 (pt0) cc_final: 0.6743 (pt0) REVERT: A 107 TRP cc_start: 0.7980 (m100) cc_final: 0.7777 (m-10) REVERT: A 145 ASP cc_start: 0.8579 (t70) cc_final: 0.8330 (t0) REVERT: A 303 CYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7962 (t) REVERT: B 50 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.7412 (p90) REVERT: B 145 ASP cc_start: 0.8531 (t70) cc_final: 0.8313 (t0) REVERT: B 156 ASP cc_start: 0.8513 (t0) cc_final: 0.8305 (t0) REVERT: B 159 LYS cc_start: 0.8001 (mptt) cc_final: 0.7758 (mptt) REVERT: C 45 LEU cc_start: 0.8223 (tp) cc_final: 0.8019 (tp) REVERT: C 49 SER cc_start: 0.8921 (t) cc_final: 0.8632 (m) REVERT: C 103 GLN cc_start: 0.7029 (pt0) cc_final: 0.6621 (pt0) REVERT: C 107 TRP cc_start: 0.7996 (m100) cc_final: 0.7757 (m-10) REVERT: C 186 ARG cc_start: 0.6657 (mtp180) cc_final: 0.6415 (mtp85) REVERT: C 226 ILE cc_start: 0.7605 (mm) cc_final: 0.7292 (mt) REVERT: D 130 ILE cc_start: 0.9146 (tp) cc_final: 0.8590 (tp) REVERT: D 313 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8260 (mtmm) REVERT: E 103 GLN cc_start: 0.6929 (pt0) cc_final: 0.6555 (pt0) REVERT: E 313 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8484 (mtmm) REVERT: E 327 ASP cc_start: 0.8724 (m-30) cc_final: 0.8515 (m-30) REVERT: F 159 LYS cc_start: 0.7909 (mptt) cc_final: 0.7635 (mptt) REVERT: F 313 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8386 (mtmm) REVERT: F 332 SER cc_start: 0.9020 (t) cc_final: 0.8766 (p) REVERT: G 54 ASP cc_start: 0.7378 (p0) cc_final: 0.7129 (p0) REVERT: G 103 GLN cc_start: 0.7076 (pt0) cc_final: 0.6733 (pt0) REVERT: G 107 TRP cc_start: 0.7952 (m100) cc_final: 0.7715 (m-10) REVERT: G 142 LYS cc_start: 0.9208 (mtmm) cc_final: 0.8931 (mtpp) REVERT: G 145 ASP cc_start: 0.8677 (t70) cc_final: 0.8421 (t0) REVERT: G 226 ILE cc_start: 0.7396 (mm) cc_final: 0.7027 (mt) REVERT: G 313 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8472 (mtmm) REVERT: G 325 ILE cc_start: 0.8667 (mm) cc_final: 0.8446 (mm) REVERT: G 332 SER cc_start: 0.9360 (t) cc_final: 0.9057 (p) REVERT: H 130 ILE cc_start: 0.9233 (tp) cc_final: 0.8823 (tp) REVERT: H 303 CYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7542 (t) REVERT: H 313 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8425 (mtmm) REVERT: H 332 SER cc_start: 0.9029 (t) cc_final: 0.8774 (p) outliers start: 63 outliers final: 49 residues processed: 624 average time/residue: 0.3298 time to fit residues: 316.6658 Evaluate side-chains 579 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 527 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 127 LYS 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 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 268 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 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 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 222 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 226 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 21472 Z= 0.510 Angle : 0.744 8.292 29272 Z= 0.383 Chirality : 0.048 0.198 3232 Planarity : 0.004 0.044 3584 Dihedral : 5.172 24.364 2752 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 5.71 % Allowed : 24.68 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 2480 helix: 0.63 (0.12), residues: 1720 sheet: -2.60 (0.84), residues: 40 loop : -3.62 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 68 HIS 0.021 0.003 HIS E 50 PHE 0.020 0.002 PHE C 51 TYR 0.024 0.002 TYR C 301 ARG 0.006 0.001 ARG B 168 *********************** 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 678 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 552 time to evaluate : 2.414 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: A 107 TRP cc_start: 0.8259 (m100) cc_final: 0.7907 (m-10) REVERT: A 145 ASP cc_start: 0.8679 (t70) cc_final: 0.8391 (t0) REVERT: A 198 TRP cc_start: 0.8690 (t-100) cc_final: 0.8327 (t-100) REVERT: A 274 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.6406 (mp0) REVERT: B 130 ILE cc_start: 0.9282 (tp) cc_final: 0.8868 (tp) REVERT: B 145 ASP cc_start: 0.8670 (t70) cc_final: 0.8416 (t0) REVERT: B 156 ASP cc_start: 0.8475 (t0) cc_final: 0.8212 (t0) REVERT: B 159 LYS cc_start: 0.7995 (mptt) cc_final: 0.7735 (mptt) REVERT: B 274 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.6164 (mp0) REVERT: B 313 LYS cc_start: 0.8939 (mtmm) cc_final: 0.8734 (mtmm) REVERT: B 332 SER cc_start: 0.9009 (t) cc_final: 0.8792 (p) REVERT: C 107 TRP cc_start: 0.8237 (m100) cc_final: 0.7866 (m-10) REVERT: C 186 ARG cc_start: 0.6938 (mtp180) cc_final: 0.6649 (mtp85) REVERT: C 226 ILE cc_start: 0.7665 (mm) cc_final: 0.7401 (mt) REVERT: D 130 ILE cc_start: 0.9311 (tp) cc_final: 0.8871 (tp) REVERT: D 208 TYR cc_start: 0.7807 (t80) cc_final: 0.7596 (t80) REVERT: D 274 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.6415 (mp0) REVERT: D 313 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8416 (mtmm) REVERT: E 74 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7798 (mt0) REVERT: E 313 LYS cc_start: 0.8778 (mtpt) cc_final: 0.8507 (mtmm) REVERT: E 327 ASP cc_start: 0.8794 (m-30) cc_final: 0.8569 (m-30) REVERT: F 130 ILE cc_start: 0.9296 (tp) cc_final: 0.8860 (tp) REVERT: F 274 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.6381 (mp0) REVERT: F 313 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8446 (mtmm) REVERT: F 332 SER cc_start: 0.9044 (t) cc_final: 0.8830 (p) REVERT: G 74 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: G 107 TRP cc_start: 0.8259 (m100) cc_final: 0.7868 (m-10) REVERT: G 145 ASP cc_start: 0.8697 (t70) cc_final: 0.8430 (t0) REVERT: G 198 TRP cc_start: 0.8706 (t-100) cc_final: 0.8409 (t-100) REVERT: G 274 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: G 332 SER cc_start: 0.9406 (t) cc_final: 0.9094 (p) REVERT: H 130 ILE cc_start: 0.9240 (tp) cc_final: 0.8766 (tp) REVERT: H 274 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.6399 (mp0) REVERT: H 313 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8440 (mtmm) REVERT: H 332 SER cc_start: 0.9068 (t) cc_final: 0.8857 (p) outliers start: 126 outliers final: 95 residues processed: 632 average time/residue: 0.3156 time to fit residues: 313.6193 Evaluate side-chains 621 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 518 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE 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 274 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 197 VAL 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 290 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 197 VAL 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 38 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 56 ILE Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 209 ILE 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 271 ILE Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 301 TYR Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 226 ILE 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 289 VAL Chi-restraints excluded: chain E residue 290 VAL 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 56 ILE Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 197 VAL 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 292 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 301 TYR Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 74 GLN 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 289 VAL 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 65 ASN Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 197 VAL 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 290 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 301 TYR 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 199 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS B 73 ASN C 50 HIS C 314 ASN D 50 HIS E 50 HIS ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS F 63 GLN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 50 HIS H 63 GLN H 73 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21472 Z= 0.192 Angle : 0.608 7.353 29272 Z= 0.313 Chirality : 0.041 0.188 3232 Planarity : 0.004 0.043 3584 Dihedral : 4.722 18.718 2752 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.94 % Allowed : 27.90 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2480 helix: 0.92 (0.12), residues: 1728 sheet: -2.83 (0.94), residues: 40 loop : -3.63 (0.19), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 236 HIS 0.012 0.001 HIS F 50 PHE 0.012 0.001 PHE F 51 TYR 0.024 0.001 TYR H 300 ARG 0.004 0.000 ARG E 186 *********************** 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 650 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 563 time to evaluate : 2.212 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 107 TRP cc_start: 0.8080 (m100) cc_final: 0.7811 (m-10) REVERT: A 145 ASP cc_start: 0.8681 (t70) cc_final: 0.8416 (t0) REVERT: A 264 LEU cc_start: 0.8731 (tp) cc_final: 0.8355 (tt) REVERT: A 274 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.6130 (mp0) REVERT: B 130 ILE cc_start: 0.9169 (tp) cc_final: 0.8643 (tp) REVERT: B 145 ASP cc_start: 0.8616 (t70) cc_final: 0.8379 (t0) REVERT: B 274 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.5919 (mp0) REVERT: B 332 SER cc_start: 0.8975 (t) cc_final: 0.8759 (p) REVERT: C 107 TRP cc_start: 0.8065 (m100) cc_final: 0.7800 (m-10) REVERT: C 186 ARG cc_start: 0.6782 (mtp180) cc_final: 0.6557 (mtp85) REVERT: C 226 ILE cc_start: 0.7648 (mm) cc_final: 0.7363 (mt) REVERT: D 50 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7042 (p90) REVERT: D 130 ILE cc_start: 0.9229 (tp) cc_final: 0.8741 (tp) REVERT: D 208 TYR cc_start: 0.7812 (t80) cc_final: 0.7599 (t80) REVERT: D 274 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.6201 (mp0) REVERT: D 313 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8389 (mtmm) REVERT: D 325 ILE cc_start: 0.8448 (mm) cc_final: 0.8225 (mm) REVERT: E 74 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7735 (mt0) REVERT: E 142 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8933 (mtpp) REVERT: E 313 LYS cc_start: 0.8723 (mtpt) cc_final: 0.8481 (mtmm) REVERT: F 156 ASP cc_start: 0.8478 (t0) cc_final: 0.8153 (t0) REVERT: F 159 LYS cc_start: 0.7930 (mptt) cc_final: 0.7713 (mptt) REVERT: F 274 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.6156 (mp0) REVERT: F 313 LYS cc_start: 0.8633 (mtpt) cc_final: 0.8419 (mtmm) REVERT: F 332 SER cc_start: 0.8999 (t) cc_final: 0.8751 (p) REVERT: G 107 TRP cc_start: 0.8075 (m100) cc_final: 0.7793 (m-10) REVERT: G 145 ASP cc_start: 0.8700 (t70) cc_final: 0.8448 (t0) REVERT: G 332 SER cc_start: 0.9354 (t) cc_final: 0.9030 (p) REVERT: H 50 HIS cc_start: 0.7606 (OUTLIER) cc_final: 0.6956 (p90) REVERT: H 130 ILE cc_start: 0.9134 (tp) cc_final: 0.8608 (tp) REVERT: H 274 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.6406 (mp0) REVERT: H 313 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8442 (mtmm) REVERT: H 332 SER cc_start: 0.9033 (t) cc_final: 0.8769 (p) outliers start: 87 outliers final: 58 residues processed: 619 average time/residue: 0.2961 time to fit residues: 285.6660 Evaluate side-chains 572 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 506 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 74 GLN Chi-restraints excluded: chain A residue 127 LYS 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 38 ILE Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 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 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 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 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 47 LEU Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 38 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 268 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS C 73 ASN ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN F 63 GLN F 363 ASN G 314 ASN ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21472 Z= 0.168 Angle : 0.596 8.413 29272 Z= 0.306 Chirality : 0.041 0.190 3232 Planarity : 0.004 0.041 3584 Dihedral : 4.505 17.401 2752 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.40 % Allowed : 29.39 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2480 helix: 1.15 (0.13), residues: 1704 sheet: -2.56 (0.96), residues: 40 loop : -3.65 (0.19), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 236 HIS 0.014 0.001 HIS D 50 PHE 0.016 0.001 PHE H 51 TYR 0.024 0.001 TYR D 300 ARG 0.004 0.000 ARG C 184 *********************** 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 625 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 550 time to evaluate : 2.392 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: A 107 TRP cc_start: 0.8037 (m100) cc_final: 0.7781 (m-10) REVERT: A 145 ASP cc_start: 0.8661 (t70) cc_final: 0.8406 (t0) REVERT: A 274 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.6001 (mp0) REVERT: B 130 ILE cc_start: 0.9073 (tp) cc_final: 0.8618 (tp) REVERT: B 145 ASP cc_start: 0.8568 (t70) cc_final: 0.8334 (t0) REVERT: B 274 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.5977 (mp0) REVERT: B 325 ILE cc_start: 0.8568 (mm) cc_final: 0.8340 (mm) REVERT: B 332 SER cc_start: 0.9012 (t) cc_final: 0.8734 (p) REVERT: C 28 ASP cc_start: 0.7279 (m-30) cc_final: 0.7065 (m-30) REVERT: C 67 GLN cc_start: 0.6858 (mp10) cc_final: 0.6593 (mp10) REVERT: C 107 TRP cc_start: 0.8026 (m100) cc_final: 0.7806 (m-10) REVERT: C 274 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: C 361 MET cc_start: 0.9398 (mtp) cc_final: 0.9170 (ttm) REVERT: D 130 ILE cc_start: 0.9209 (tp) cc_final: 0.8698 (tp) REVERT: D 274 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.6225 (mp0) REVERT: D 313 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8375 (mtmm) REVERT: E 274 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: E 313 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8483 (mtmm) REVERT: F 130 ILE cc_start: 0.9134 (tp) cc_final: 0.8629 (tp) REVERT: F 159 LYS cc_start: 0.8117 (mptt) cc_final: 0.7859 (mptt) REVERT: F 274 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.6195 (mp0) REVERT: F 313 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8454 (mtmm) REVERT: F 332 SER cc_start: 0.9022 (t) cc_final: 0.8728 (p) REVERT: G 107 TRP cc_start: 0.7995 (m100) cc_final: 0.7760 (m-10) REVERT: G 145 ASP cc_start: 0.8649 (t70) cc_final: 0.8377 (t0) REVERT: G 274 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.6134 (mp0) REVERT: G 313 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8637 (mtmm) REVERT: G 332 SER cc_start: 0.9335 (t) cc_final: 0.9005 (p) REVERT: G 361 MET cc_start: 0.9132 (mtm) cc_final: 0.8896 (mtm) REVERT: H 130 ILE cc_start: 0.9129 (tp) cc_final: 0.8648 (tp) REVERT: H 274 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.6217 (mp0) REVERT: H 313 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8497 (mtmm) REVERT: H 332 SER cc_start: 0.9030 (t) cc_final: 0.8722 (p) outliers start: 75 outliers final: 50 residues processed: 599 average time/residue: 0.3047 time to fit residues: 283.1716 Evaluate side-chains 571 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 513 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 127 LYS 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 129 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 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 268 THR Chi-restraints excluded: chain C residue 274 GLU 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 121 ILE 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 231 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 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 231 LEU 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 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 47 LEU Chi-restraints excluded: chain H residue 129 MET 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 231 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 239 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21472 Z= 0.206 Angle : 0.613 8.376 29272 Z= 0.313 Chirality : 0.042 0.200 3232 Planarity : 0.003 0.038 3584 Dihedral : 4.474 16.774 2752 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.80 % Allowed : 30.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2480 helix: 1.28 (0.13), residues: 1688 sheet: -2.64 (0.93), residues: 40 loop : -3.58 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 236 HIS 0.005 0.001 HIS G 50 PHE 0.018 0.001 PHE G 51 TYR 0.026 0.001 TYR B 120 ARG 0.004 0.000 ARG B 244 *********************** 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 618 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 534 time to evaluate : 2.437 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: A 145 ASP cc_start: 0.8690 (t70) cc_final: 0.8433 (t0) REVERT: A 274 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.5971 (mp0) REVERT: B 50 HIS cc_start: 0.7629 (OUTLIER) cc_final: 0.6660 (p90) REVERT: B 130 ILE cc_start: 0.9175 (tp) cc_final: 0.8719 (tp) REVERT: B 145 ASP cc_start: 0.8561 (t70) cc_final: 0.8343 (t0) REVERT: B 274 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.5972 (mp0) REVERT: B 325 ILE cc_start: 0.8590 (mm) cc_final: 0.8381 (mm) REVERT: B 332 SER cc_start: 0.9019 (t) cc_final: 0.8714 (p) REVERT: C 28 ASP cc_start: 0.7292 (m-30) cc_final: 0.7081 (m-30) REVERT: C 107 TRP cc_start: 0.8023 (m100) cc_final: 0.7782 (m-10) REVERT: C 274 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: D 67 GLN cc_start: 0.7064 (mp10) cc_final: 0.6755 (mp10) REVERT: D 130 ILE cc_start: 0.9147 (tp) cc_final: 0.8688 (tp) REVERT: D 274 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.6142 (mp0) REVERT: D 313 LYS cc_start: 0.8633 (mtpt) cc_final: 0.8376 (mtmm) REVERT: E 142 LYS cc_start: 0.9187 (mtmm) cc_final: 0.8913 (mtpp) REVERT: E 274 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: E 313 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8472 (mtmm) REVERT: F 159 LYS cc_start: 0.8053 (mptt) cc_final: 0.7797 (mptt) REVERT: F 274 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.6197 (mp0) REVERT: F 313 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8485 (mtmm) REVERT: G 54 ASP cc_start: 0.7497 (p0) cc_final: 0.7264 (p0) REVERT: G 107 TRP cc_start: 0.8077 (m100) cc_final: 0.7832 (m-10) REVERT: G 145 ASP cc_start: 0.8648 (t70) cc_final: 0.8393 (t0) REVERT: G 274 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.6076 (mp0) REVERT: G 313 LYS cc_start: 0.8947 (mtmm) cc_final: 0.8656 (mtmm) REVERT: G 332 SER cc_start: 0.9297 (t) cc_final: 0.8826 (p) REVERT: H 274 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.6196 (mp0) REVERT: H 313 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8478 (mtmm) REVERT: H 332 SER cc_start: 0.9035 (t) cc_final: 0.8703 (p) outliers start: 84 outliers final: 57 residues processed: 591 average time/residue: 0.2962 time to fit residues: 273.5287 Evaluate side-chains 584 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 518 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 127 LYS 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 129 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 38 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 341 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 179 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 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 341 ILE Chi-restraints excluded: chain F residue 38 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 231 LEU 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 38 ILE Chi-restraints excluded: chain G residue 39 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 187 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 329 GLN ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21472 Z= 0.205 Angle : 0.621 10.209 29272 Z= 0.313 Chirality : 0.042 0.199 3232 Planarity : 0.003 0.042 3584 Dihedral : 4.450 16.411 2752 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 3.44 % Allowed : 30.93 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2480 helix: 1.36 (0.13), residues: 1688 sheet: -2.66 (0.92), residues: 40 loop : -3.50 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 236 HIS 0.005 0.001 HIS G 50 PHE 0.015 0.001 PHE D 147 TYR 0.028 0.001 TYR F 120 ARG 0.002 0.000 ARG B 244 *********************** 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 614 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 538 time to evaluate : 2.274 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: A 145 ASP cc_start: 0.8706 (t70) cc_final: 0.8432 (t0) REVERT: A 274 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.5982 (mp0) REVERT: B 50 HIS cc_start: 0.7595 (OUTLIER) cc_final: 0.6704 (p90) REVERT: B 130 ILE cc_start: 0.9063 (tp) cc_final: 0.8605 (tp) REVERT: B 145 ASP cc_start: 0.8575 (t70) cc_final: 0.8336 (t0) REVERT: B 274 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.5913 (mp0) REVERT: B 332 SER cc_start: 0.9019 (t) cc_final: 0.8664 (p) REVERT: C 107 TRP cc_start: 0.8040 (m100) cc_final: 0.7778 (m-10) REVERT: C 274 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.6480 (mp0) REVERT: C 303 CYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7857 (t) REVERT: D 130 ILE cc_start: 0.9182 (tp) cc_final: 0.8730 (tp) REVERT: D 151 ASN cc_start: 0.8028 (p0) cc_final: 0.7750 (m-40) REVERT: D 274 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.6075 (mp0) REVERT: D 313 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8352 (mtmm) REVERT: E 274 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: E 313 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8517 (mtmm) REVERT: F 130 ILE cc_start: 0.9208 (tp) cc_final: 0.8731 (tp) REVERT: F 151 ASN cc_start: 0.8137 (p0) cc_final: 0.7832 (m-40) REVERT: F 156 ASP cc_start: 0.8469 (t0) cc_final: 0.8170 (t70) REVERT: F 188 MET cc_start: 0.8503 (mmm) cc_final: 0.8209 (mtp) REVERT: F 274 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.6099 (mp0) REVERT: F 313 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8466 (mtmm) REVERT: F 332 SER cc_start: 0.9041 (t) cc_final: 0.8655 (p) REVERT: G 107 TRP cc_start: 0.8060 (m100) cc_final: 0.7821 (m-10) REVERT: G 145 ASP cc_start: 0.8654 (t70) cc_final: 0.8402 (t0) REVERT: G 274 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.6052 (mp0) REVERT: G 313 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8725 (mtmm) REVERT: G 332 SER cc_start: 0.9311 (t) cc_final: 0.8839 (p) REVERT: H 130 ILE cc_start: 0.9151 (tp) cc_final: 0.8686 (tp) REVERT: H 274 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.6101 (mp0) REVERT: H 332 SER cc_start: 0.9038 (t) cc_final: 0.8651 (p) outliers start: 76 outliers final: 62 residues processed: 588 average time/residue: 0.2904 time to fit residues: 267.5163 Evaluate side-chains 598 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 526 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 127 LYS 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 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 38 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 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 179 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 235 ASP 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 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 231 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 74 GLN 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 121 ILE Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 299 ILE 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 228 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 174 optimal weight: 0.0980 chunk 68 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN B 63 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 73 ASN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21472 Z= 0.207 Angle : 0.631 10.606 29272 Z= 0.317 Chirality : 0.042 0.189 3232 Planarity : 0.003 0.043 3584 Dihedral : 4.435 16.383 2752 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.62 % Allowed : 31.75 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2480 helix: 1.41 (0.13), residues: 1688 sheet: -2.75 (0.92), residues: 40 loop : -3.45 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 236 HIS 0.005 0.001 HIS G 50 PHE 0.015 0.001 PHE D 147 TYR 0.029 0.001 TYR H 120 ARG 0.002 0.000 ARG C 184 *********************** 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 639 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 559 time to evaluate : 2.272 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: A 145 ASP cc_start: 0.8706 (t70) cc_final: 0.8435 (t0) REVERT: A 264 LEU cc_start: 0.8685 (tp) cc_final: 0.8457 (tp) REVERT: A 274 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.5970 (mp0) REVERT: B 50 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.6683 (p90) REVERT: B 130 ILE cc_start: 0.9224 (tp) cc_final: 0.8731 (tp) REVERT: B 145 ASP cc_start: 0.8576 (t70) cc_final: 0.8348 (t0) REVERT: B 188 MET cc_start: 0.8512 (mmm) cc_final: 0.8137 (mtp) REVERT: B 274 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.6143 (mp0) REVERT: B 332 SER cc_start: 0.9066 (t) cc_final: 0.8682 (p) REVERT: C 107 TRP cc_start: 0.8031 (m100) cc_final: 0.7770 (m-10) REVERT: C 274 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.6450 (mp0) REVERT: C 303 CYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7841 (t) REVERT: D 63 GLN cc_start: 0.7763 (tp40) cc_final: 0.7546 (tp-100) REVERT: D 130 ILE cc_start: 0.9028 (tp) cc_final: 0.8525 (tp) REVERT: D 151 ASN cc_start: 0.8004 (p0) cc_final: 0.7790 (m-40) REVERT: D 274 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.6154 (mp0) REVERT: D 313 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8447 (mtmm) REVERT: E 274 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.6470 (mp0) REVERT: E 303 CYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7960 (t) REVERT: E 313 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8522 (mtmm) REVERT: F 130 ILE cc_start: 0.9215 (tp) cc_final: 0.8739 (tp) REVERT: F 151 ASN cc_start: 0.7976 (p0) cc_final: 0.7753 (m-40) REVERT: F 153 ASP cc_start: 0.8676 (m-30) cc_final: 0.8458 (m-30) REVERT: F 188 MET cc_start: 0.8390 (mmm) cc_final: 0.8069 (mtp) REVERT: F 274 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.6083 (mp0) REVERT: F 332 SER cc_start: 0.9067 (t) cc_final: 0.8680 (p) REVERT: G 145 ASP cc_start: 0.8713 (t70) cc_final: 0.8441 (t0) REVERT: G 274 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.6074 (mp0) REVERT: G 313 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8735 (mtmm) REVERT: G 332 SER cc_start: 0.9335 (t) cc_final: 0.8854 (p) REVERT: H 130 ILE cc_start: 0.9027 (tp) cc_final: 0.8559 (tp) REVERT: H 274 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.6064 (mp0) REVERT: H 313 LYS cc_start: 0.8855 (mtmm) cc_final: 0.8566 (mtmm) REVERT: H 332 SER cc_start: 0.9040 (t) cc_final: 0.8688 (p) outliers start: 80 outliers final: 62 residues processed: 612 average time/residue: 0.2964 time to fit residues: 285.0376 Evaluate side-chains 616 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 543 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 127 LYS 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 47 LEU Chi-restraints excluded: chain B residue 50 HIS 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 292 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 38 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 125 ILE 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 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 42 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 74 GLN 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 39 LEU 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 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21472 Z= 0.177 Angle : 0.639 14.472 29272 Z= 0.318 Chirality : 0.041 0.182 3232 Planarity : 0.003 0.042 3584 Dihedral : 4.326 15.766 2752 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.12 % Allowed : 32.65 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2480 helix: 1.46 (0.13), residues: 1704 sheet: -2.79 (0.91), residues: 40 loop : -3.37 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 236 HIS 0.004 0.001 HIS G 50 PHE 0.024 0.001 PHE D 330 TYR 0.028 0.001 TYR B 120 ARG 0.004 0.000 ARG D 184 ********************** 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 653 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 584 time to evaluate : 2.210 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: A 145 ASP cc_start: 0.8655 (t70) cc_final: 0.8406 (t0) REVERT: A 264 LEU cc_start: 0.8633 (tp) cc_final: 0.8428 (tp) REVERT: A 274 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.5919 (mp0) REVERT: B 130 ILE cc_start: 0.9227 (tp) cc_final: 0.8727 (tp) REVERT: B 145 ASP cc_start: 0.8553 (t70) cc_final: 0.8324 (t0) REVERT: B 188 MET cc_start: 0.8356 (mmm) cc_final: 0.8045 (mtp) REVERT: B 274 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.6092 (mp0) REVERT: B 332 SER cc_start: 0.9050 (t) cc_final: 0.8668 (p) REVERT: C 151 ASN cc_start: 0.8564 (p0) cc_final: 0.8214 (m-40) REVERT: C 274 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: C 303 CYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8073 (t) REVERT: C 332 SER cc_start: 0.9335 (t) cc_final: 0.9009 (p) REVERT: C 361 MET cc_start: 0.9026 (mtp) cc_final: 0.8603 (ttm) REVERT: D 63 GLN cc_start: 0.7810 (tp40) cc_final: 0.7583 (tp-100) REVERT: D 130 ILE cc_start: 0.9152 (tp) cc_final: 0.8667 (tp) REVERT: D 274 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6066 (mp0) REVERT: E 274 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.6371 (mp0) REVERT: E 303 CYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7943 (t) REVERT: E 313 LYS cc_start: 0.8813 (mtpt) cc_final: 0.8602 (mtmm) REVERT: F 130 ILE cc_start: 0.9193 (tp) cc_final: 0.8688 (tp) REVERT: F 188 MET cc_start: 0.8359 (mmm) cc_final: 0.8069 (mtp) REVERT: F 274 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6039 (mp0) REVERT: F 313 LYS cc_start: 0.8943 (mtmm) cc_final: 0.8657 (mtmm) REVERT: F 332 SER cc_start: 0.9065 (t) cc_final: 0.8665 (p) REVERT: G 145 ASP cc_start: 0.8689 (t70) cc_final: 0.8438 (t0) REVERT: G 274 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.6017 (mp0) REVERT: G 313 LYS cc_start: 0.8946 (mtmm) cc_final: 0.8728 (mtmm) REVERT: G 331 PHE cc_start: 0.8664 (m-80) cc_final: 0.8380 (m-80) REVERT: G 332 SER cc_start: 0.9323 (t) cc_final: 0.8832 (p) REVERT: H 130 ILE cc_start: 0.9186 (tp) cc_final: 0.8669 (tp) REVERT: H 188 MET cc_start: 0.8376 (mmm) cc_final: 0.7874 (mtp) REVERT: H 274 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.6042 (mp0) REVERT: H 313 LYS cc_start: 0.8903 (mtmm) cc_final: 0.8651 (mtmm) REVERT: H 332 SER cc_start: 0.9043 (t) cc_final: 0.8662 (p) outliers start: 69 outliers final: 56 residues processed: 628 average time/residue: 0.2989 time to fit residues: 294.0582 Evaluate side-chains 629 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 563 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 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 47 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 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 42 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 74 GLN 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 47 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 181 optimal weight: 0.1980 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 ASN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** H 50 HIS ** 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 = 0.3419 r_free = 0.3419 target = 0.127175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.104250 restraints weight = 30977.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.108168 restraints weight = 16326.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110830 restraints weight = 10819.630| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21472 Z= 0.171 Angle : 0.647 12.210 29272 Z= 0.323 Chirality : 0.041 0.186 3232 Planarity : 0.003 0.047 3584 Dihedral : 4.296 16.123 2752 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.03 % Allowed : 33.38 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2480 helix: 1.46 (0.13), residues: 1712 sheet: -2.78 (0.92), residues: 40 loop : -3.30 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 236 HIS 0.004 0.001 HIS G 50 PHE 0.023 0.001 PHE A 51 TYR 0.028 0.001 TYR B 135 ARG 0.011 0.000 ARG E 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5047.79 seconds wall clock time: 90 minutes 10.58 seconds (5410.58 seconds total)