Starting phenix.real_space_refine on Sun Aug 24 13:20:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pko_13474/08_2025/7pko_13474.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pko_13474/08_2025/7pko_13474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pko_13474/08_2025/7pko_13474.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pko_13474/08_2025/7pko_13474.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pko_13474/08_2025/7pko_13474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pko_13474/08_2025/7pko_13474.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 120 5.16 5 C 13064 2.51 5 N 3456 2.21 5 O 3728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 182 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20368 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "B" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "C" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "D" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "E" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "F" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "G" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "U" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Time building chain proxies: 4.46, per 1000 atoms: 0.22 Number of scatterers: 20368 At special positions: 0 Unit cell: (135.255, 135.255, 109.695, 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 120 16.00 O 3728 8.00 N 3456 7.00 C 13064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 822.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4848 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 27 sheets defined 46.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 3 through 6 Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.759A pdb=" N THR A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 61 removed outlier: 3.532A pdb=" N PHE A 57 " --> pdb=" O PRO A 54 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS A 59 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR A 61 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 89 removed outlier: 4.243A pdb=" N THR A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 removed outlier: 3.726A pdb=" N LEU A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.715A pdb=" N LEU A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 198 through 213 removed outlier: 3.920A pdb=" N VAL A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.583A pdb=" N HIS A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.689A pdb=" N GLY A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 291 removed outlier: 3.543A pdb=" N LYS A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU A 289 " --> pdb=" O CYS A 285 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'B' and resid 3 through 7 removed outlier: 3.660A pdb=" N PHE B 7 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 Processing helix chain 'B' and resid 54 through 61 removed outlier: 4.363A pdb=" N LYS B 59 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR B 61 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 91 removed outlier: 4.255A pdb=" N THR B 78 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 removed outlier: 3.814A pdb=" N LEU B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.835A pdb=" N LEU B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 141 Processing helix chain 'B' and resid 148 through 152 Processing helix chain 'B' and resid 198 through 213 removed outlier: 3.944A pdb=" N VAL B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 233 through 250 removed outlier: 3.582A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.711A pdb=" N GLY B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 291 removed outlier: 3.717A pdb=" N LYS B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU B 289 " --> pdb=" O CYS B 285 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE B 290 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 311 Processing helix chain 'C' and resid 3 through 6 Processing helix chain 'C' and resid 23 through 32 removed outlier: 3.569A pdb=" N THR C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 61 removed outlier: 3.529A pdb=" N PHE C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS C 59 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR C 61 " --> pdb=" O LYS C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 91 removed outlier: 4.101A pdb=" N THR C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.683A pdb=" N LEU C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 141 Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 198 through 213 removed outlier: 3.922A pdb=" N VAL C 202 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 250 removed outlier: 4.484A pdb=" N ALA C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASN C 236 " --> pdb=" O SER C 232 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN C 248 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 250 " --> pdb=" O LYS C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 279 removed outlier: 3.748A pdb=" N GLY C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 291 removed outlier: 3.720A pdb=" N LYS C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU C 289 " --> pdb=" O CYS C 285 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE C 290 " --> pdb=" O LYS C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 311 Processing helix chain 'D' and resid 3 through 6 Processing helix chain 'D' and resid 23 through 32 removed outlier: 3.885A pdb=" N THR D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 60 removed outlier: 4.497A pdb=" N LYS D 59 " --> pdb=" O GLN D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 89 removed outlier: 4.163A pdb=" N THR D 78 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 107 through 119 removed outlier: 3.774A pdb=" N LEU D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 removed outlier: 4.148A pdb=" N HIS D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 141 Processing helix chain 'D' and resid 198 through 213 removed outlier: 3.954A pdb=" N VAL D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 233 through 250 removed outlier: 3.588A pdb=" N HIS D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN D 248 " --> pdb=" O THR D 244 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 282 through 291 removed outlier: 3.750A pdb=" N LYS D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU D 288 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU D 289 " --> pdb=" O CYS D 285 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE D 290 " --> pdb=" O LYS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 removed outlier: 3.755A pdb=" N VAL D 312 " --> pdb=" O LYS D 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 33 removed outlier: 3.751A pdb=" N THR E 32 " --> pdb=" O LYS E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 60 removed outlier: 4.555A pdb=" N LYS E 59 " --> pdb=" O GLN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 89 removed outlier: 4.273A pdb=" N THR E 78 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 102 removed outlier: 3.673A pdb=" N LEU E 102 " --> pdb=" O VAL E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 119 removed outlier: 3.704A pdb=" N LEU E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU E 119 " --> pdb=" O VAL E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 128 through 141 Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 199 through 213 Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 233 through 247 removed outlier: 4.346A pdb=" N THR E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 279 removed outlier: 3.557A pdb=" N GLY E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 289 Processing helix chain 'E' and resid 303 through 311 Processing helix chain 'F' and resid 3 through 7 removed outlier: 3.639A pdb=" N PHE F 7 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 32 removed outlier: 3.791A pdb=" N THR F 32 " --> pdb=" O LYS F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 61 removed outlier: 3.545A pdb=" N PHE F 57 " --> pdb=" O PRO F 54 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS F 59 " --> pdb=" O GLN F 56 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR F 61 " --> pdb=" O LYS F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 91 removed outlier: 4.064A pdb=" N THR F 78 " --> pdb=" O THR F 74 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER F 90 " --> pdb=" O GLU F 86 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 102 Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.863A pdb=" N LEU F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN F 120 " --> pdb=" O ILE F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 141 removed outlier: 3.540A pdb=" N LEU F 132 " --> pdb=" O SER F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 152 Processing helix chain 'F' and resid 198 through 213 removed outlier: 3.937A pdb=" N VAL F 202 " --> pdb=" O SER F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 233 through 250 removed outlier: 3.603A pdb=" N ASP F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 243 " --> pdb=" O ASP F 239 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN F 248 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS F 250 " --> pdb=" O LYS F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 279 removed outlier: 3.751A pdb=" N GLY F 279 " --> pdb=" O SER F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 291 removed outlier: 3.980A pdb=" N LYS F 286 " --> pdb=" O LEU F 282 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU F 288 " --> pdb=" O VAL F 284 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE F 290 " --> pdb=" O LYS F 286 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 311 Processing helix chain 'G' and resid 5 through 7 No H-bonds generated for 'chain 'G' and resid 5 through 7' Processing helix chain 'G' and resid 23 through 32 removed outlier: 3.564A pdb=" N THR G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 61 removed outlier: 3.618A pdb=" N PHE G 57 " --> pdb=" O PRO G 54 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS G 59 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR G 61 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 91 removed outlier: 4.110A pdb=" N THR G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER G 90 " --> pdb=" O GLU G 86 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 102 Processing helix chain 'G' and resid 107 through 119 removed outlier: 3.719A pdb=" N LEU G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG G 117 " --> pdb=" O ASN G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 141 Processing helix chain 'G' and resid 148 through 152 Processing helix chain 'G' and resid 199 through 213 Processing helix chain 'G' and resid 230 through 250 removed outlier: 4.483A pdb=" N ALA G 235 " --> pdb=" O TYR G 231 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN G 236 " --> pdb=" O SER G 232 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR G 244 " --> pdb=" O ARG G 240 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN G 248 " --> pdb=" O THR G 244 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS G 250 " --> pdb=" O LYS G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 279 removed outlier: 3.776A pdb=" N GLY G 279 " --> pdb=" O SER G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 291 removed outlier: 3.528A pdb=" N LYS G 286 " --> pdb=" O LEU G 282 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU G 288 " --> pdb=" O VAL G 284 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU G 289 " --> pdb=" O CYS G 285 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE G 290 " --> pdb=" O LYS G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 311 Processing helix chain 'U' and resid 3 through 6 Processing helix chain 'U' and resid 23 through 32 removed outlier: 3.683A pdb=" N THR U 32 " --> pdb=" O LYS U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 61 removed outlier: 4.492A pdb=" N LYS U 59 " --> pdb=" O GLN U 56 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR U 61 " --> pdb=" O LYS U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 89 Processing helix chain 'U' and resid 97 through 102 removed outlier: 3.726A pdb=" N LEU U 102 " --> pdb=" O VAL U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 120 removed outlier: 3.699A pdb=" N LEU U 111 " --> pdb=" O SER U 107 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN U 120 " --> pdb=" O ILE U 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 141 Processing helix chain 'U' and resid 199 through 213 Processing helix chain 'U' and resid 230 through 250 removed outlier: 4.508A pdb=" N ALA U 235 " --> pdb=" O TYR U 231 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN U 236 " --> pdb=" O SER U 232 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR U 244 " --> pdb=" O ARG U 240 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE U 245 " --> pdb=" O VAL U 241 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN U 248 " --> pdb=" O THR U 244 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS U 250 " --> pdb=" O LYS U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 278 Processing helix chain 'U' and resid 282 through 291 removed outlier: 3.687A pdb=" N LYS U 286 " --> pdb=" O LEU U 282 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU U 288 " --> pdb=" O VAL U 284 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU U 289 " --> pdb=" O CYS U 285 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE U 290 " --> pdb=" O LYS U 286 " (cutoff:3.500A) Processing helix chain 'U' and resid 303 through 312 removed outlier: 3.519A pdb=" N VAL U 312 " --> pdb=" O LYS U 308 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46 removed outlier: 3.519A pdb=" N SER A 46 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 160 removed outlier: 6.717A pdb=" N ILE A 157 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS A 168 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE A 159 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU A 186 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 9 through 12 Processing sheet with id=AA5, first strand: chain 'B' and resid 44 through 46 removed outlier: 3.514A pdb=" N SER B 46 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.507A pdb=" N ILE B 157 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS B 168 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 159 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU B 186 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 8 through 12 Processing sheet with id=AA8, first strand: chain 'C' and resid 44 through 46 Processing sheet with id=AA9, first strand: chain 'C' and resid 156 through 160 removed outlier: 6.595A pdb=" N ILE C 157 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LYS C 168 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE C 159 " --> pdb=" O MET C 166 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU C 186 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 217 through 220 removed outlier: 3.510A pdb=" N VAL C 229 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 8 through 12 Processing sheet with id=AB3, first strand: chain 'D' and resid 44 through 46 Processing sheet with id=AB4, first strand: chain 'D' and resid 156 through 160 removed outlier: 6.387A pdb=" N ILE D 157 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LYS D 168 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE D 159 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU D 186 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 2 through 3 Processing sheet with id=AB6, first strand: chain 'E' and resid 8 through 12 Processing sheet with id=AB7, first strand: chain 'E' and resid 44 through 46 Processing sheet with id=AB8, first strand: chain 'E' and resid 156 through 160 removed outlier: 6.421A pdb=" N ILE E 157 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LYS E 168 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE E 159 " --> pdb=" O MET E 166 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU E 186 " --> pdb=" O LEU E 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 9 through 12 Processing sheet with id=AC1, first strand: chain 'F' and resid 44 through 46 Processing sheet with id=AC2, first strand: chain 'F' and resid 156 through 160 removed outlier: 6.475A pdb=" N ILE F 157 " --> pdb=" O LYS F 168 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LYS F 168 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE F 159 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU F 186 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 2 through 3 Processing sheet with id=AC4, first strand: chain 'G' and resid 9 through 12 Processing sheet with id=AC5, first strand: chain 'G' and resid 44 through 46 Processing sheet with id=AC6, first strand: chain 'G' and resid 156 through 160 removed outlier: 6.484A pdb=" N ILE G 157 " --> pdb=" O LYS G 168 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS G 168 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE G 159 " --> pdb=" O MET G 166 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU G 186 " --> pdb=" O LEU G 169 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 8 through 12 Processing sheet with id=AC8, first strand: chain 'U' and resid 44 through 46 removed outlier: 3.712A pdb=" N SER U 46 " --> pdb=" O GLY U 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 156 through 160 removed outlier: 6.280A pdb=" N ILE U 157 " --> pdb=" O LYS U 168 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS U 168 " --> pdb=" O ILE U 157 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE U 159 " --> pdb=" O MET U 166 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU U 186 " --> pdb=" O LEU U 169 " (cutoff:3.500A) 790 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6516 1.34 - 1.46: 4261 1.46 - 1.58: 9815 1.58 - 1.69: 0 1.69 - 1.81: 208 Bond restraints: 20800 Sorted by residual: bond pdb=" CA SER D 232 " pdb=" C SER D 232 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.34e-02 5.57e+03 5.83e+00 bond pdb=" CA SER A 232 " pdb=" C SER A 232 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.34e-02 5.57e+03 5.71e+00 bond pdb=" CA ARG U 210 " pdb=" C ARG U 210 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.72e-02 3.38e+03 5.44e+00 bond pdb=" CA ARG E 210 " pdb=" C ARG E 210 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.41e-02 5.03e+03 3.31e+00 bond pdb=" C ILE D 264 " pdb=" N ILE D 265 " ideal model delta sigma weight residual 1.334 1.312 0.022 1.29e-02 6.01e+03 2.89e+00 ... (remaining 20795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 26684 1.38 - 2.76: 1207 2.76 - 4.14: 149 4.14 - 5.52: 40 5.52 - 6.90: 8 Bond angle restraints: 28088 Sorted by residual: angle pdb=" C GLN A 160 " pdb=" N ASN A 161 " pdb=" CA ASN A 161 " ideal model delta sigma weight residual 121.90 116.31 5.59 1.26e+00 6.30e-01 1.97e+01 angle pdb=" C GLN D 160 " pdb=" N ASN D 161 " pdb=" CA ASN D 161 " ideal model delta sigma weight residual 121.90 116.60 5.30 1.26e+00 6.30e-01 1.77e+01 angle pdb=" C GLN C 160 " pdb=" N ASN C 161 " pdb=" CA ASN C 161 " ideal model delta sigma weight residual 121.90 116.79 5.11 1.26e+00 6.30e-01 1.65e+01 angle pdb=" N ASP G 41 " pdb=" CA ASP G 41 " pdb=" C ASP G 41 " ideal model delta sigma weight residual 114.09 108.05 6.04 1.55e+00 4.16e-01 1.52e+01 angle pdb=" N ASP C 15 " pdb=" CA ASP C 15 " pdb=" C ASP C 15 " ideal model delta sigma weight residual 114.75 109.85 4.90 1.26e+00 6.30e-01 1.51e+01 ... (remaining 28083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 11396 17.70 - 35.39: 1012 35.39 - 53.09: 158 53.09 - 70.78: 55 70.78 - 88.48: 27 Dihedral angle restraints: 12648 sinusoidal: 5208 harmonic: 7440 Sorted by residual: dihedral pdb=" CA MET G 40 " pdb=" C MET G 40 " pdb=" N ASP G 41 " pdb=" CA ASP G 41 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA TYR G 17 " pdb=" C TYR G 17 " pdb=" N LYS G 18 " pdb=" CA LYS G 18 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA SER C 46 " pdb=" C SER C 46 " pdb=" N ILE C 47 " pdb=" CA ILE C 47 " ideal model delta harmonic sigma weight residual -180.00 -163.80 -16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 12645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2051 0.037 - 0.073: 859 0.073 - 0.110: 206 0.110 - 0.147: 19 0.147 - 0.183: 1 Chirality restraints: 3136 Sorted by residual: chirality pdb=" CB THR U 170 " pdb=" CA THR U 170 " pdb=" OG1 THR U 170 " pdb=" CG2 THR U 170 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA ILE G 228 " pdb=" N ILE G 228 " pdb=" C ILE G 228 " pdb=" CB ILE G 228 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE U 228 " pdb=" N ILE U 228 " pdb=" C ILE U 228 " pdb=" CB ILE U 228 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 3133 not shown) Planarity restraints: 3560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 294 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO C 295 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 231 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C TYR E 231 " 0.023 2.00e-02 2.50e+03 pdb=" O TYR E 231 " -0.009 2.00e-02 2.50e+03 pdb=" N SER E 232 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR F 231 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C TYR F 231 " 0.023 2.00e-02 2.50e+03 pdb=" O TYR F 231 " -0.009 2.00e-02 2.50e+03 pdb=" N SER F 232 " -0.008 2.00e-02 2.50e+03 ... (remaining 3557 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2359 2.74 - 3.28: 21218 3.28 - 3.82: 31813 3.82 - 4.36: 37885 4.36 - 4.90: 62861 Nonbonded interactions: 156136 Sorted by model distance: nonbonded pdb=" OE2 GLU E 13 " pdb=" OG SER E 16 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR E 231 " pdb=" NZ LYS U 308 " model vdw 2.259 3.120 nonbonded pdb=" ND2 ASN C 62 " pdb=" OD1 ASN C 71 " model vdw 2.265 3.120 nonbonded pdb=" ND2 ASN G 62 " pdb=" OD1 ASN G 71 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASN A 161 " pdb=" ND1 HIS A 201 " model vdw 2.269 3.120 ... (remaining 156131 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: 0.01 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 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.910 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.750 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.004 0.040 20800 Z= 0.192 Angle : 0.659 6.897 28088 Z= 0.400 Chirality : 0.040 0.183 3136 Planarity : 0.003 0.034 3560 Dihedral : 14.592 88.477 7800 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.16 (0.13), residues: 2488 helix: -2.31 (0.13), residues: 800 sheet: -2.74 (0.25), residues: 280 loop : -3.15 (0.14), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 117 TYR 0.017 0.002 TYR B 242 PHE 0.018 0.001 PHE D 257 TRP 0.006 0.001 TRP C 266 HIS 0.003 0.001 HIS F 110 Details of bonding type rmsd covalent geometry : bond 0.00399 (20800) covalent geometry : angle 0.65894 (28088) hydrogen bonds : bond 0.17185 ( 790) hydrogen bonds : angle 7.20397 ( 2160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 549 time to evaluate : 0.485 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: A 76 MET cc_start: 0.8367 (mmt) cc_final: 0.7493 (mmt) REVERT: A 94 THR cc_start: 0.8378 (p) cc_final: 0.8169 (p) REVERT: A 142 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8512 (mp10) REVERT: A 144 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8313 (tppt) REVERT: A 262 GLN cc_start: 0.8353 (pt0) cc_final: 0.8082 (pp30) REVERT: B 76 MET cc_start: 0.8452 (mmt) cc_final: 0.7235 (mmt) REVERT: B 133 LEU cc_start: 0.9318 (tt) cc_final: 0.9080 (tt) REVERT: B 153 GLU cc_start: 0.8509 (tt0) cc_final: 0.8113 (tt0) REVERT: B 293 MET cc_start: 0.6085 (tmm) cc_final: 0.5564 (tmm) REVERT: C 59 LYS cc_start: 0.8911 (ptpp) cc_final: 0.8273 (ttpt) REVERT: C 76 MET cc_start: 0.8378 (mmt) cc_final: 0.7113 (mmt) REVERT: C 144 LYS cc_start: 0.7729 (tptp) cc_final: 0.7404 (tppt) REVERT: C 161 ASN cc_start: 0.8168 (p0) cc_final: 0.7867 (p0) REVERT: C 287 ARG cc_start: 0.8370 (mpt180) cc_final: 0.8099 (mpt180) REVERT: D 76 MET cc_start: 0.8355 (mmt) cc_final: 0.7377 (mmt) REVERT: D 112 GLU cc_start: 0.8630 (tp30) cc_final: 0.7955 (tp30) REVERT: D 144 LYS cc_start: 0.7866 (tppt) cc_final: 0.7151 (tppt) REVERT: D 183 ASN cc_start: 0.9353 (t0) cc_final: 0.9098 (t0) REVERT: D 276 MET cc_start: 0.7683 (ttm) cc_final: 0.7452 (ttm) REVERT: D 287 ARG cc_start: 0.8798 (ttp80) cc_final: 0.8406 (mpt180) REVERT: E 34 LYS cc_start: 0.8398 (tptt) cc_final: 0.8123 (ttmm) REVERT: E 56 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8514 (tp40) REVERT: E 122 GLN cc_start: 0.9270 (mm-40) cc_final: 0.8815 (mm-40) REVERT: E 142 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8755 (mp10) REVERT: E 144 LYS cc_start: 0.7895 (tppt) cc_final: 0.7040 (tppt) REVERT: E 240 ARG cc_start: 0.8843 (ttp-170) cc_final: 0.8539 (ttp80) REVERT: E 262 GLN cc_start: 0.8318 (pt0) cc_final: 0.8083 (pp30) REVERT: E 287 ARG cc_start: 0.9070 (ttp-170) cc_final: 0.8513 (mmt90) REVERT: F 31 LEU cc_start: 0.9386 (tp) cc_final: 0.9178 (tt) REVERT: F 68 ARG cc_start: 0.8115 (mpp-170) cc_final: 0.7901 (tmt170) REVERT: F 76 MET cc_start: 0.8461 (mmt) cc_final: 0.7522 (mmt) REVERT: F 82 MET cc_start: 0.7509 (tpt) cc_final: 0.7124 (tpt) REVERT: F 104 ARG cc_start: 0.8670 (mmm160) cc_final: 0.8464 (tpp80) REVERT: F 112 GLU cc_start: 0.8402 (tp30) cc_final: 0.7935 (tp30) REVERT: F 144 LYS cc_start: 0.8167 (tppt) cc_final: 0.7931 (tppt) REVERT: F 186 GLU cc_start: 0.8180 (tt0) cc_final: 0.7879 (tt0) REVERT: F 293 MET cc_start: 0.5661 (tmm) cc_final: 0.4268 (ptt) REVERT: G 56 GLN cc_start: 0.8885 (tp-100) cc_final: 0.8559 (tp40) REVERT: G 58 LYS cc_start: 0.9356 (ttpt) cc_final: 0.9112 (ttmm) REVERT: G 66 ASN cc_start: 0.8338 (p0) cc_final: 0.8006 (p0) REVERT: G 76 MET cc_start: 0.8431 (mmt) cc_final: 0.7170 (mmt) REVERT: G 82 MET cc_start: 0.7474 (tpt) cc_final: 0.7059 (tpt) REVERT: G 144 LYS cc_start: 0.7958 (tppt) cc_final: 0.7535 (tppt) REVERT: G 184 PHE cc_start: 0.8739 (t80) cc_final: 0.8442 (t80) REVERT: G 186 GLU cc_start: 0.8107 (tt0) cc_final: 0.7639 (mt-10) REVERT: U 22 PHE cc_start: 0.8382 (m-80) cc_final: 0.7914 (m-80) REVERT: U 66 ASN cc_start: 0.7503 (t0) cc_final: 0.6292 (p0) REVERT: U 76 MET cc_start: 0.8645 (mmt) cc_final: 0.7741 (mmt) REVERT: U 113 ASN cc_start: 0.9213 (t0) cc_final: 0.8828 (m-40) REVERT: U 144 LYS cc_start: 0.8111 (tppt) cc_final: 0.7470 (tppt) REVERT: U 153 GLU cc_start: 0.8815 (pt0) cc_final: 0.8396 (pt0) REVERT: U 250 LYS cc_start: 0.7577 (mtpt) cc_final: 0.7052 (mmtt) outliers start: 0 outliers final: 0 residues processed: 549 average time/residue: 0.1578 time to fit residues: 125.2004 Evaluate side-chains 435 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 247 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 GLN A 212 GLN ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN B 142 GLN ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 298 ASN C 56 GLN C 64 ASN C 122 GLN C 142 GLN C 175 GLN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN C 268 ASN ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN D 89 ASN D 142 GLN D 183 ASN D 214 ASN ** D 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN E 142 GLN E 237 HIS E 278 GLN E 280 ASN F 23 ASN F 62 ASN F 89 ASN F 100 ASN F 142 GLN F 221 HIS F 298 ASN G 14 ASN G 23 ASN G 56 GLN G 142 GLN G 298 ASN ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 64 ASN U 71 ASN U 95 GLN U 142 GLN U 175 GLN U 183 ASN U 212 GLN U 237 HIS U 291 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.138270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106198 restraints weight = 35422.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109503 restraints weight = 22742.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111570 restraints weight = 17450.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113046 restraints weight = 14886.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113963 restraints weight = 13414.309| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 20800 Z= 0.295 Angle : 0.682 8.930 28088 Z= 0.357 Chirality : 0.043 0.163 3136 Planarity : 0.004 0.075 3560 Dihedral : 5.349 65.288 2688 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 3.92 % Allowed : 14.61 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.87 (0.15), residues: 2488 helix: -0.87 (0.16), residues: 832 sheet: -2.32 (0.26), residues: 280 loop : -2.56 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 210 TYR 0.024 0.002 TYR E 242 PHE 0.014 0.002 PHE F 272 TRP 0.009 0.002 TRP F 269 HIS 0.005 0.001 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00675 (20800) covalent geometry : angle 0.68206 (28088) hydrogen bonds : bond 0.04385 ( 790) hydrogen bonds : angle 5.86206 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 447 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8608 (mmt) cc_final: 0.7924 (mmt) REVERT: A 92 LYS cc_start: 0.8291 (tppt) cc_final: 0.8079 (tmtt) REVERT: A 144 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8341 (tppt) REVERT: A 262 GLN cc_start: 0.8344 (pt0) cc_final: 0.8083 (pp30) REVERT: B 76 MET cc_start: 0.8452 (mmt) cc_final: 0.7267 (mmt) REVERT: B 104 ARG cc_start: 0.8971 (tpp80) cc_final: 0.8679 (tpp80) REVERT: B 293 MET cc_start: 0.6143 (tmm) cc_final: 0.5624 (tmm) REVERT: C 59 LYS cc_start: 0.8956 (ptpp) cc_final: 0.8272 (ttpt) REVERT: C 76 MET cc_start: 0.8413 (mmt) cc_final: 0.7522 (mmt) REVERT: C 112 GLU cc_start: 0.8644 (tp30) cc_final: 0.8053 (tp30) REVERT: C 144 LYS cc_start: 0.7758 (tptp) cc_final: 0.7461 (tppt) REVERT: C 309 MET cc_start: 0.7819 (mpp) cc_final: 0.7086 (mpp) REVERT: D 76 MET cc_start: 0.8423 (mmt) cc_final: 0.7442 (mmt) REVERT: D 123 ASP cc_start: 0.8395 (t0) cc_final: 0.7776 (m-30) REVERT: D 144 LYS cc_start: 0.7923 (tppt) cc_final: 0.7228 (tppt) REVERT: D 153 GLU cc_start: 0.8565 (pt0) cc_final: 0.8334 (pm20) REVERT: D 183 ASN cc_start: 0.9284 (t0) cc_final: 0.9062 (t0) REVERT: D 263 ARG cc_start: 0.8700 (mtp180) cc_final: 0.8493 (mpp80) REVERT: D 287 ARG cc_start: 0.8813 (ttp80) cc_final: 0.8301 (mmt90) REVERT: E 34 LYS cc_start: 0.8552 (tptt) cc_final: 0.8316 (ttmt) REVERT: E 76 MET cc_start: 0.8554 (mmt) cc_final: 0.7309 (mmt) REVERT: E 104 ARG cc_start: 0.9089 (tpp80) cc_final: 0.8761 (tpp80) REVERT: E 122 GLN cc_start: 0.9257 (mm-40) cc_final: 0.8791 (mm-40) REVERT: E 133 LEU cc_start: 0.9123 (mp) cc_final: 0.8909 (tt) REVERT: E 142 GLN cc_start: 0.8997 (mm110) cc_final: 0.8732 (mp10) REVERT: E 144 LYS cc_start: 0.7831 (tppt) cc_final: 0.7110 (tppt) REVERT: E 153 GLU cc_start: 0.8795 (pt0) cc_final: 0.8586 (pt0) REVERT: E 262 GLN cc_start: 0.8202 (pt0) cc_final: 0.7995 (pp30) REVERT: E 287 ARG cc_start: 0.9037 (ttp-170) cc_final: 0.8675 (mpt180) REVERT: E 293 MET cc_start: 0.6300 (tmm) cc_final: 0.5987 (tmm) REVERT: E 309 MET cc_start: 0.7841 (mpp) cc_final: 0.7607 (mpp) REVERT: F 76 MET cc_start: 0.8461 (mmt) cc_final: 0.7059 (mmt) REVERT: F 82 MET cc_start: 0.7623 (tpt) cc_final: 0.7259 (tpt) REVERT: F 144 LYS cc_start: 0.8079 (tppt) cc_final: 0.7821 (tppt) REVERT: F 287 ARG cc_start: 0.7943 (mmt90) cc_final: 0.7679 (mmt90) REVERT: G 9 TYR cc_start: 0.8027 (p90) cc_final: 0.7656 (p90) REVERT: G 56 GLN cc_start: 0.8938 (tp40) cc_final: 0.8585 (tp40) REVERT: G 57 PHE cc_start: 0.8708 (m-10) cc_final: 0.8059 (m-80) REVERT: G 58 LYS cc_start: 0.9306 (ttpt) cc_final: 0.8956 (tttm) REVERT: G 66 ASN cc_start: 0.8370 (p0) cc_final: 0.8071 (p0) REVERT: G 76 MET cc_start: 0.8392 (mmt) cc_final: 0.7201 (mmt) REVERT: G 82 MET cc_start: 0.7520 (tpt) cc_final: 0.7141 (tpt) REVERT: G 142 GLN cc_start: 0.8952 (mm110) cc_final: 0.8619 (mp10) REVERT: G 144 LYS cc_start: 0.7996 (tppt) cc_final: 0.7558 (tppt) REVERT: G 184 PHE cc_start: 0.8709 (t80) cc_final: 0.8375 (t80) REVERT: G 186 GLU cc_start: 0.8052 (tt0) cc_final: 0.7360 (mt-10) REVERT: U 22 PHE cc_start: 0.8388 (m-80) cc_final: 0.7954 (m-80) REVERT: U 66 ASN cc_start: 0.7737 (t0) cc_final: 0.7420 (p0) REVERT: U 76 MET cc_start: 0.8342 (mmt) cc_final: 0.7347 (mmt) REVERT: U 104 ARG cc_start: 0.9003 (tpp80) cc_final: 0.8588 (tpp80) REVERT: U 144 LYS cc_start: 0.8100 (tppt) cc_final: 0.7423 (tppt) REVERT: U 153 GLU cc_start: 0.8844 (pt0) cc_final: 0.8560 (pt0) REVERT: U 183 ASN cc_start: 0.8890 (t0) cc_final: 0.8352 (t0) REVERT: U 215 LYS cc_start: 0.9238 (ttpp) cc_final: 0.9000 (ttpt) REVERT: U 240 ARG cc_start: 0.8543 (ttm110) cc_final: 0.8201 (ttp80) REVERT: U 250 LYS cc_start: 0.7568 (mtpt) cc_final: 0.7044 (mmtt) REVERT: U 287 ARG cc_start: 0.8217 (mmt180) cc_final: 0.7948 (mmt180) outliers start: 89 outliers final: 72 residues processed: 480 average time/residue: 0.1483 time to fit residues: 106.5369 Evaluate side-chains 489 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 417 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 160 GLN Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 241 VAL Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 90 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 60 optimal weight: 30.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 HIS B 267 GLN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS ** D 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN E 110 HIS ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN G 212 GLN U 23 ASN U 212 GLN U 221 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110158 restraints weight = 35255.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113624 restraints weight = 22450.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115896 restraints weight = 17154.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117383 restraints weight = 14514.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118242 restraints weight = 13034.162| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20800 Z= 0.157 Angle : 0.567 7.632 28088 Z= 0.297 Chirality : 0.041 0.213 3136 Planarity : 0.004 0.050 3560 Dihedral : 4.898 60.660 2688 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.30 % Allowed : 16.68 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.15), residues: 2488 helix: -0.12 (0.17), residues: 832 sheet: -2.17 (0.26), residues: 280 loop : -2.22 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 104 TYR 0.015 0.002 TYR A 242 PHE 0.011 0.001 PHE A 7 TRP 0.009 0.001 TRP A 211 HIS 0.003 0.001 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00363 (20800) covalent geometry : angle 0.56682 (28088) hydrogen bonds : bond 0.03573 ( 790) hydrogen bonds : angle 5.37395 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 444 time to evaluate : 0.801 Fit side-chains REVERT: A 76 MET cc_start: 0.8472 (mmt) cc_final: 0.7781 (mmt) REVERT: A 144 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8280 (tppt) REVERT: A 153 GLU cc_start: 0.8517 (pt0) cc_final: 0.7898 (pm20) REVERT: A 262 GLN cc_start: 0.8155 (pt0) cc_final: 0.7949 (pp30) REVERT: A 293 MET cc_start: 0.5394 (tmm) cc_final: 0.5099 (tmm) REVERT: B 76 MET cc_start: 0.8372 (mmt) cc_final: 0.7522 (mmt) REVERT: B 92 LYS cc_start: 0.8326 (tppt) cc_final: 0.8116 (tmtt) REVERT: B 293 MET cc_start: 0.6193 (tmm) cc_final: 0.5883 (tmm) REVERT: C 59 LYS cc_start: 0.8905 (ptpp) cc_final: 0.8310 (ttpt) REVERT: C 76 MET cc_start: 0.8364 (mmt) cc_final: 0.7405 (mmt) REVERT: C 112 GLU cc_start: 0.8603 (tp30) cc_final: 0.7982 (tp30) REVERT: C 144 LYS cc_start: 0.7730 (tptp) cc_final: 0.7225 (tppt) REVERT: C 153 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: C 161 ASN cc_start: 0.8154 (p0) cc_final: 0.7819 (p0) REVERT: C 287 ARG cc_start: 0.8327 (mpt180) cc_final: 0.8098 (mpt180) REVERT: C 309 MET cc_start: 0.7833 (mpp) cc_final: 0.7442 (mpp) REVERT: D 76 MET cc_start: 0.8347 (mmt) cc_final: 0.7349 (mmt) REVERT: D 123 ASP cc_start: 0.8258 (t0) cc_final: 0.7546 (m-30) REVERT: D 144 LYS cc_start: 0.7854 (tppt) cc_final: 0.7132 (tppt) REVERT: D 183 ASN cc_start: 0.9267 (t0) cc_final: 0.9031 (t0) REVERT: D 287 ARG cc_start: 0.8755 (ttp80) cc_final: 0.8189 (mmt90) REVERT: D 293 MET cc_start: 0.5648 (mtt) cc_final: 0.3726 (ttt) REVERT: E 1 MET cc_start: 0.4978 (mmp) cc_final: 0.4141 (mpp) REVERT: E 34 LYS cc_start: 0.8467 (tptt) cc_final: 0.8245 (tptt) REVERT: E 60 ARG cc_start: 0.8771 (ttm110) cc_final: 0.7974 (ttp-110) REVERT: E 76 MET cc_start: 0.8604 (mmt) cc_final: 0.7800 (mmt) REVERT: E 122 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8761 (mm-40) REVERT: E 144 LYS cc_start: 0.7786 (tppt) cc_final: 0.7013 (tppt) REVERT: E 153 GLU cc_start: 0.8828 (pt0) cc_final: 0.8589 (pt0) REVERT: E 195 LYS cc_start: 0.9226 (ptpt) cc_final: 0.8916 (mtmt) REVERT: E 240 ARG cc_start: 0.8478 (ttm170) cc_final: 0.8190 (ttp80) REVERT: E 262 GLN cc_start: 0.8154 (pt0) cc_final: 0.7942 (pp30) REVERT: E 287 ARG cc_start: 0.9043 (ttp-170) cc_final: 0.8655 (mpt180) REVERT: E 293 MET cc_start: 0.6247 (tmm) cc_final: 0.5877 (tmm) REVERT: F 76 MET cc_start: 0.8451 (mmt) cc_final: 0.7031 (mmt) REVERT: F 82 MET cc_start: 0.7540 (tpt) cc_final: 0.7197 (tpt) REVERT: F 144 LYS cc_start: 0.8070 (tppt) cc_final: 0.7579 (tppt) REVERT: F 309 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7513 (mpp) REVERT: G 56 GLN cc_start: 0.8895 (tp40) cc_final: 0.8529 (tp40) REVERT: G 57 PHE cc_start: 0.8688 (m-10) cc_final: 0.8076 (m-80) REVERT: G 58 LYS cc_start: 0.9309 (ttpt) cc_final: 0.8986 (tttm) REVERT: G 66 ASN cc_start: 0.8378 (p0) cc_final: 0.8081 (p0) REVERT: G 76 MET cc_start: 0.8362 (mmt) cc_final: 0.7583 (mmt) REVERT: G 82 MET cc_start: 0.7457 (tpt) cc_final: 0.7029 (tpt) REVERT: G 142 GLN cc_start: 0.8956 (mm110) cc_final: 0.8399 (mp10) REVERT: G 144 LYS cc_start: 0.7941 (tppt) cc_final: 0.7467 (tppt) REVERT: G 186 GLU cc_start: 0.8032 (tt0) cc_final: 0.7424 (mt-10) REVERT: G 309 MET cc_start: 0.7951 (mpp) cc_final: 0.7365 (mpp) REVERT: U 66 ASN cc_start: 0.7395 (t0) cc_final: 0.6146 (p0) REVERT: U 76 MET cc_start: 0.8222 (mmt) cc_final: 0.7211 (mmt) REVERT: U 144 LYS cc_start: 0.8111 (tppt) cc_final: 0.7422 (tppt) REVERT: U 153 GLU cc_start: 0.8817 (pt0) cc_final: 0.8455 (pt0) REVERT: U 183 ASN cc_start: 0.8917 (t0) cc_final: 0.8458 (t0) REVERT: U 287 ARG cc_start: 0.8167 (mmt180) cc_final: 0.7845 (mmt180) REVERT: U 309 MET cc_start: 0.7939 (mpp) cc_final: 0.7475 (mpp) outliers start: 75 outliers final: 56 residues processed: 470 average time/residue: 0.1345 time to fit residues: 96.6253 Evaluate side-chains 480 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 422 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 212 GLN Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 239 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 173 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 230 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 258 ASN C 23 ASN C 212 GLN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN G 192 ASN G 212 GLN ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 160 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.103418 restraints weight = 36019.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106908 restraints weight = 22583.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109185 restraints weight = 17179.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110659 restraints weight = 14558.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111582 restraints weight = 13113.545| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 20800 Z= 0.388 Angle : 0.765 9.115 28088 Z= 0.394 Chirality : 0.046 0.228 3136 Planarity : 0.004 0.056 3560 Dihedral : 5.324 57.862 2688 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 6.12 % Allowed : 17.52 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.15), residues: 2488 helix: -0.43 (0.16), residues: 832 sheet: -2.03 (0.26), residues: 280 loop : -2.23 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 117 TYR 0.024 0.003 TYR E 226 PHE 0.020 0.002 PHE E 272 TRP 0.007 0.002 TRP D 167 HIS 0.006 0.002 HIS G 225 Details of bonding type rmsd covalent geometry : bond 0.00880 (20800) covalent geometry : angle 0.76462 (28088) hydrogen bonds : bond 0.04434 ( 790) hydrogen bonds : angle 5.78432 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 413 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.8686 (mmt) cc_final: 0.7857 (mmt) REVERT: A 144 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8290 (tppt) REVERT: B 76 MET cc_start: 0.8445 (mmt) cc_final: 0.7599 (mmt) REVERT: B 133 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9035 (tt) REVERT: B 293 MET cc_start: 0.5974 (tmm) cc_final: 0.5289 (tmm) REVERT: C 34 LYS cc_start: 0.8659 (tmtt) cc_final: 0.8136 (tptp) REVERT: C 76 MET cc_start: 0.8483 (mmt) cc_final: 0.7216 (mmt) REVERT: C 114 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8265 (tt) REVERT: C 144 LYS cc_start: 0.7836 (tptp) cc_final: 0.7489 (tppt) REVERT: C 153 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8466 (pt0) REVERT: C 161 ASN cc_start: 0.8539 (p0) cc_final: 0.8283 (p0) REVERT: C 287 ARG cc_start: 0.8356 (mpt180) cc_final: 0.8049 (mpt180) REVERT: C 309 MET cc_start: 0.7849 (mpp) cc_final: 0.7317 (mpp) REVERT: D 76 MET cc_start: 0.8390 (mmt) cc_final: 0.7348 (mmt) REVERT: D 92 LYS cc_start: 0.8335 (tppt) cc_final: 0.7935 (tmtt) REVERT: D 123 ASP cc_start: 0.8322 (t0) cc_final: 0.7654 (m-30) REVERT: D 133 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9019 (tt) REVERT: D 144 LYS cc_start: 0.7881 (tppt) cc_final: 0.7177 (tppt) REVERT: D 153 GLU cc_start: 0.8653 (pt0) cc_final: 0.8408 (pm20) REVERT: D 183 ASN cc_start: 0.9312 (t0) cc_final: 0.9094 (t0) REVERT: D 287 ARG cc_start: 0.8732 (ttp80) cc_final: 0.8362 (mpt180) REVERT: D 293 MET cc_start: 0.6087 (mtt) cc_final: 0.3900 (ttt) REVERT: E 1 MET cc_start: 0.4949 (mmp) cc_final: 0.4040 (mpp) REVERT: E 34 LYS cc_start: 0.8618 (tptt) cc_final: 0.8373 (tptt) REVERT: E 76 MET cc_start: 0.8654 (mmt) cc_final: 0.7540 (mmt) REVERT: E 122 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8695 (mm-40) REVERT: E 144 LYS cc_start: 0.7958 (tppt) cc_final: 0.7151 (tppt) REVERT: E 153 GLU cc_start: 0.8931 (pt0) cc_final: 0.8668 (pt0) REVERT: E 262 GLN cc_start: 0.8172 (pt0) cc_final: 0.7960 (pp30) REVERT: E 287 ARG cc_start: 0.9071 (ttp-170) cc_final: 0.8663 (mpt180) REVERT: E 293 MET cc_start: 0.6386 (tmm) cc_final: 0.5892 (tmm) REVERT: F 41 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7720 (t0) REVERT: F 76 MET cc_start: 0.8493 (mmt) cc_final: 0.7134 (mmt) REVERT: F 82 MET cc_start: 0.7704 (tpt) cc_final: 0.7334 (tpt) REVERT: F 144 LYS cc_start: 0.8097 (tppt) cc_final: 0.7809 (tppt) REVERT: G 9 TYR cc_start: 0.8198 (p90) cc_final: 0.7884 (p90) REVERT: G 56 GLN cc_start: 0.8984 (tp40) cc_final: 0.8669 (tp40) REVERT: G 57 PHE cc_start: 0.8742 (m-10) cc_final: 0.8039 (m-80) REVERT: G 58 LYS cc_start: 0.9360 (ttpt) cc_final: 0.8964 (tttm) REVERT: G 66 ASN cc_start: 0.8410 (p0) cc_final: 0.8025 (p0) REVERT: G 76 MET cc_start: 0.8458 (mmt) cc_final: 0.7283 (mmt) REVERT: G 82 MET cc_start: 0.7658 (tpt) cc_final: 0.7221 (tpt) REVERT: G 142 GLN cc_start: 0.9033 (mm110) cc_final: 0.8561 (mp10) REVERT: G 144 LYS cc_start: 0.7974 (tppt) cc_final: 0.7549 (tppt) REVERT: G 147 GLU cc_start: 0.8257 (tt0) cc_final: 0.7882 (tt0) REVERT: G 195 LYS cc_start: 0.9333 (ptpp) cc_final: 0.9052 (mtmt) REVERT: G 309 MET cc_start: 0.8023 (mpp) cc_final: 0.7517 (mpp) REVERT: U 66 ASN cc_start: 0.7624 (t0) cc_final: 0.6818 (p0) REVERT: U 76 MET cc_start: 0.8371 (mmt) cc_final: 0.7093 (mmt) REVERT: U 144 LYS cc_start: 0.8080 (tppt) cc_final: 0.7766 (tppt) REVERT: U 183 ASN cc_start: 0.8956 (t0) cc_final: 0.8443 (t0) REVERT: U 283 ASP cc_start: 0.4641 (OUTLIER) cc_final: 0.3991 (t70) REVERT: U 287 ARG cc_start: 0.8134 (mmt180) cc_final: 0.7807 (mmt180) REVERT: U 309 MET cc_start: 0.8065 (mpp) cc_final: 0.7844 (mpp) outliers start: 139 outliers final: 103 residues processed: 486 average time/residue: 0.1355 time to fit residues: 102.7604 Evaluate side-chains 505 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 396 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 212 GLN Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 202 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 247 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 GLN ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.109494 restraints weight = 34813.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113161 restraints weight = 21149.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115596 restraints weight = 15772.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.117174 restraints weight = 13182.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118072 restraints weight = 11774.132| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20800 Z= 0.127 Angle : 0.566 8.143 28088 Z= 0.293 Chirality : 0.040 0.193 3136 Planarity : 0.003 0.042 3560 Dihedral : 4.765 53.156 2688 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.31 % Allowed : 20.03 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.16), residues: 2488 helix: 0.31 (0.18), residues: 832 sheet: -1.90 (0.27), residues: 280 loop : -1.94 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 60 TYR 0.014 0.002 TYR A 61 PHE 0.014 0.001 PHE U 19 TRP 0.011 0.001 TRP A 211 HIS 0.002 0.001 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00296 (20800) covalent geometry : angle 0.56637 (28088) hydrogen bonds : bond 0.03274 ( 790) hydrogen bonds : angle 5.21047 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 437 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.8453 (mmt) cc_final: 0.7723 (mmt) REVERT: A 144 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8277 (tppt) REVERT: A 293 MET cc_start: 0.5744 (tmm) cc_final: 0.5408 (tmm) REVERT: B 76 MET cc_start: 0.8351 (mmt) cc_final: 0.7177 (mmt) REVERT: B 293 MET cc_start: 0.6059 (tmm) cc_final: 0.5480 (tmm) REVERT: C 15 ASP cc_start: 0.7147 (t0) cc_final: 0.6898 (t0) REVERT: C 76 MET cc_start: 0.8351 (mmt) cc_final: 0.7418 (mmt) REVERT: C 112 GLU cc_start: 0.8745 (tp30) cc_final: 0.8108 (tp30) REVERT: C 144 LYS cc_start: 0.7731 (tptp) cc_final: 0.7147 (tppt) REVERT: C 161 ASN cc_start: 0.8237 (p0) cc_final: 0.7895 (p0) REVERT: C 287 ARG cc_start: 0.8339 (mpt180) cc_final: 0.8072 (mpt180) REVERT: C 309 MET cc_start: 0.7732 (mpp) cc_final: 0.7260 (mpp) REVERT: D 76 MET cc_start: 0.8267 (mmt) cc_final: 0.7236 (mmt) REVERT: D 92 LYS cc_start: 0.8349 (tppt) cc_final: 0.8057 (tmtt) REVERT: D 123 ASP cc_start: 0.8179 (t0) cc_final: 0.7633 (m-30) REVERT: D 133 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8961 (tt) REVERT: D 144 LYS cc_start: 0.7820 (tppt) cc_final: 0.7109 (tppt) REVERT: D 183 ASN cc_start: 0.9318 (t0) cc_final: 0.9083 (t0) REVERT: D 287 ARG cc_start: 0.8657 (ttp80) cc_final: 0.8113 (mmt90) REVERT: D 293 MET cc_start: 0.6046 (OUTLIER) cc_final: 0.4167 (ttt) REVERT: E 1 MET cc_start: 0.4863 (mmp) cc_final: 0.3954 (mpp) REVERT: E 60 ARG cc_start: 0.8765 (ttm110) cc_final: 0.7940 (ttp-110) REVERT: E 122 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8680 (mm-40) REVERT: E 144 LYS cc_start: 0.7620 (tppt) cc_final: 0.6851 (tppt) REVERT: E 153 GLU cc_start: 0.8889 (pt0) cc_final: 0.8640 (pt0) REVERT: E 262 GLN cc_start: 0.8192 (pt0) cc_final: 0.7949 (pp30) REVERT: E 287 ARG cc_start: 0.9032 (ttp-170) cc_final: 0.8624 (mpt180) REVERT: E 293 MET cc_start: 0.6137 (tmm) cc_final: 0.5691 (tmm) REVERT: F 76 MET cc_start: 0.8402 (mmt) cc_final: 0.7379 (mmt) REVERT: F 82 MET cc_start: 0.7534 (tpt) cc_final: 0.7157 (tpt) REVERT: F 144 LYS cc_start: 0.8030 (tppt) cc_final: 0.7533 (tppt) REVERT: F 309 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7563 (mpp) REVERT: G 56 GLN cc_start: 0.8937 (tp40) cc_final: 0.8569 (tp40) REVERT: G 57 PHE cc_start: 0.8671 (m-10) cc_final: 0.8016 (m-80) REVERT: G 58 LYS cc_start: 0.9329 (ttpt) cc_final: 0.8942 (tttm) REVERT: G 66 ASN cc_start: 0.8376 (p0) cc_final: 0.8014 (p0) REVERT: G 76 MET cc_start: 0.8289 (mmt) cc_final: 0.7213 (mmt) REVERT: G 82 MET cc_start: 0.7474 (tpt) cc_final: 0.7026 (tpt) REVERT: G 142 GLN cc_start: 0.8920 (mm110) cc_final: 0.8509 (mp10) REVERT: G 144 LYS cc_start: 0.7940 (tppt) cc_final: 0.7450 (tppt) REVERT: G 186 GLU cc_start: 0.8022 (tt0) cc_final: 0.7382 (mt-10) REVERT: G 195 LYS cc_start: 0.9233 (ptpp) cc_final: 0.8942 (mtmt) REVERT: U 66 ASN cc_start: 0.6879 (t0) cc_final: 0.6665 (t0) REVERT: U 76 MET cc_start: 0.8195 (mmt) cc_final: 0.7181 (mmt) REVERT: U 104 ARG cc_start: 0.9141 (tpp80) cc_final: 0.8679 (tpp80) REVERT: U 144 LYS cc_start: 0.8214 (tppt) cc_final: 0.7467 (tppt) REVERT: U 153 GLU cc_start: 0.8869 (pt0) cc_final: 0.8503 (pt0) REVERT: U 183 ASN cc_start: 0.8974 (t0) cc_final: 0.8623 (t0) REVERT: U 287 ARG cc_start: 0.8116 (mmt180) cc_final: 0.7712 (mmt180) REVERT: U 309 MET cc_start: 0.7953 (mpp) cc_final: 0.7331 (mpp) outliers start: 98 outliers final: 68 residues processed: 481 average time/residue: 0.1472 time to fit residues: 107.9338 Evaluate side-chains 488 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 417 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 303 LEU Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 91 optimal weight: 20.0000 chunk 166 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 71 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** D 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113516 restraints weight = 34676.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.116985 restraints weight = 21983.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119238 restraints weight = 16779.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120784 restraints weight = 14217.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121785 restraints weight = 12751.389| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20800 Z= 0.111 Angle : 0.545 9.510 28088 Z= 0.282 Chirality : 0.040 0.210 3136 Planarity : 0.003 0.038 3560 Dihedral : 4.363 45.879 2688 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.79 % Allowed : 20.99 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.16), residues: 2488 helix: 0.73 (0.18), residues: 824 sheet: -1.73 (0.27), residues: 280 loop : -1.67 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 104 TYR 0.012 0.001 TYR G 226 PHE 0.013 0.001 PHE U 19 TRP 0.012 0.001 TRP G 211 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00261 (20800) covalent geometry : angle 0.54520 (28088) hydrogen bonds : bond 0.02890 ( 790) hydrogen bonds : angle 4.89956 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 460 time to evaluate : 0.814 Fit side-chains REVERT: A 76 MET cc_start: 0.8455 (mmt) cc_final: 0.7767 (mmt) REVERT: A 135 SER cc_start: 0.9417 (t) cc_final: 0.9147 (p) REVERT: A 144 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8258 (tppt) REVERT: A 293 MET cc_start: 0.5571 (tmm) cc_final: 0.5267 (tmm) REVERT: B 22 PHE cc_start: 0.8324 (m-80) cc_final: 0.7928 (m-80) REVERT: B 76 MET cc_start: 0.8192 (mmt) cc_final: 0.7370 (mmt) REVERT: B 113 ASN cc_start: 0.9210 (t0) cc_final: 0.8976 (m-40) REVERT: C 76 MET cc_start: 0.8357 (mmt) cc_final: 0.7434 (mmt) REVERT: C 112 GLU cc_start: 0.8675 (tp30) cc_final: 0.8071 (tp30) REVERT: C 123 ASP cc_start: 0.8608 (m-30) cc_final: 0.8175 (m-30) REVERT: C 133 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8949 (tt) REVERT: C 144 LYS cc_start: 0.7660 (tptp) cc_final: 0.7093 (tppt) REVERT: C 309 MET cc_start: 0.7794 (mpp) cc_final: 0.7403 (mpp) REVERT: D 57 PHE cc_start: 0.8692 (m-80) cc_final: 0.8222 (m-80) REVERT: D 76 MET cc_start: 0.8190 (mmt) cc_final: 0.7292 (mmt) REVERT: D 104 ARG cc_start: 0.9018 (tpp80) cc_final: 0.8588 (tpp80) REVERT: D 133 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8998 (tt) REVERT: D 144 LYS cc_start: 0.7885 (tppt) cc_final: 0.7163 (tppt) REVERT: D 183 ASN cc_start: 0.9253 (t0) cc_final: 0.9029 (t0) REVERT: D 287 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8231 (mpt180) REVERT: D 293 MET cc_start: 0.5860 (OUTLIER) cc_final: 0.4091 (ttt) REVERT: E 1 MET cc_start: 0.4818 (mmp) cc_final: 0.4001 (mpp) REVERT: E 60 ARG cc_start: 0.8663 (ttm110) cc_final: 0.7927 (ttp-110) REVERT: E 76 MET cc_start: 0.8426 (mmt) cc_final: 0.7829 (mmt) REVERT: E 104 ARG cc_start: 0.9354 (ttm-80) cc_final: 0.8958 (tpp80) REVERT: E 122 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8821 (mm-40) REVERT: E 144 LYS cc_start: 0.7552 (tppt) cc_final: 0.6830 (tppt) REVERT: E 153 GLU cc_start: 0.8874 (pt0) cc_final: 0.8649 (pt0) REVERT: E 287 ARG cc_start: 0.9009 (ttp-170) cc_final: 0.8579 (mpt180) REVERT: F 44 TYR cc_start: 0.8183 (t80) cc_final: 0.7903 (t80) REVERT: F 76 MET cc_start: 0.8370 (mmt) cc_final: 0.7327 (mmt) REVERT: F 82 MET cc_start: 0.7472 (tpt) cc_final: 0.7118 (tpt) REVERT: F 104 ARG cc_start: 0.9126 (ttm-80) cc_final: 0.8574 (tpp80) REVERT: F 144 LYS cc_start: 0.8010 (tppt) cc_final: 0.7506 (tppt) REVERT: G 57 PHE cc_start: 0.8662 (m-10) cc_final: 0.7888 (m-80) REVERT: G 58 LYS cc_start: 0.9303 (ttpt) cc_final: 0.8953 (tttm) REVERT: G 66 ASN cc_start: 0.8512 (p0) cc_final: 0.8217 (p0) REVERT: G 70 MET cc_start: 0.7241 (mtm) cc_final: 0.6988 (mtt) REVERT: G 76 MET cc_start: 0.8304 (mmt) cc_final: 0.7290 (mmt) REVERT: G 82 MET cc_start: 0.7202 (tpt) cc_final: 0.6850 (tpt) REVERT: G 144 LYS cc_start: 0.7815 (tppt) cc_final: 0.7342 (tppt) REVERT: G 195 LYS cc_start: 0.9159 (ptpp) cc_final: 0.8870 (mtmt) REVERT: G 309 MET cc_start: 0.7815 (mpp) cc_final: 0.7292 (mpp) REVERT: U 57 PHE cc_start: 0.8697 (m-80) cc_final: 0.8161 (m-80) REVERT: U 66 ASN cc_start: 0.7121 (t0) cc_final: 0.6885 (t0) REVERT: U 76 MET cc_start: 0.8224 (mmt) cc_final: 0.7246 (mmt) REVERT: U 82 MET cc_start: 0.7405 (tpt) cc_final: 0.7176 (tpt) REVERT: U 104 ARG cc_start: 0.9200 (tpp80) cc_final: 0.8792 (tpp80) REVERT: U 144 LYS cc_start: 0.8184 (tppt) cc_final: 0.7404 (tppt) REVERT: U 153 GLU cc_start: 0.8803 (pt0) cc_final: 0.8449 (pt0) REVERT: U 183 ASN cc_start: 0.8801 (t0) cc_final: 0.8369 (t0) REVERT: U 283 ASP cc_start: 0.4432 (OUTLIER) cc_final: 0.3495 (t70) REVERT: U 287 ARG cc_start: 0.8051 (mmt180) cc_final: 0.7590 (mmt180) REVERT: U 309 MET cc_start: 0.7920 (mpp) cc_final: 0.7479 (mpp) outliers start: 86 outliers final: 63 residues processed: 498 average time/residue: 0.1538 time to fit residues: 116.5874 Evaluate side-chains 491 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 424 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain U residue 303 LEU Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 227 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 242 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 71 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN G 212 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.143640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111468 restraints weight = 35169.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114915 restraints weight = 22422.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.117214 restraints weight = 17187.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118697 restraints weight = 14601.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119665 restraints weight = 13146.120| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20800 Z= 0.129 Angle : 0.556 8.820 28088 Z= 0.286 Chirality : 0.040 0.211 3136 Planarity : 0.003 0.039 3560 Dihedral : 4.244 41.520 2688 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.09 % Allowed : 20.86 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.17), residues: 2488 helix: 0.86 (0.18), residues: 832 sheet: -1.70 (0.27), residues: 280 loop : -1.53 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 60 TYR 0.019 0.001 TYR A 61 PHE 0.010 0.001 PHE A 7 TRP 0.010 0.001 TRP G 211 HIS 0.002 0.001 HIS G 225 Details of bonding type rmsd covalent geometry : bond 0.00306 (20800) covalent geometry : angle 0.55587 (28088) hydrogen bonds : bond 0.02934 ( 790) hydrogen bonds : angle 4.85494 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 429 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8458 (mmt) cc_final: 0.7712 (mmt) REVERT: A 135 SER cc_start: 0.9490 (t) cc_final: 0.9149 (p) REVERT: A 144 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8249 (tppt) REVERT: A 293 MET cc_start: 0.5279 (tmm) cc_final: 0.4968 (tmm) REVERT: B 57 PHE cc_start: 0.8523 (m-80) cc_final: 0.8171 (m-80) REVERT: B 76 MET cc_start: 0.8211 (mmt) cc_final: 0.7376 (mmt) REVERT: B 113 ASN cc_start: 0.9229 (t0) cc_final: 0.8976 (m-40) REVERT: B 309 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7627 (mpp) REVERT: C 76 MET cc_start: 0.8389 (mmt) cc_final: 0.7457 (mmt) REVERT: C 112 GLU cc_start: 0.8635 (tp30) cc_final: 0.8017 (tp30) REVERT: C 133 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8983 (tt) REVERT: C 144 LYS cc_start: 0.7658 (tptp) cc_final: 0.7108 (tppt) REVERT: C 260 LEU cc_start: 0.8701 (mt) cc_final: 0.8384 (mp) REVERT: C 309 MET cc_start: 0.7829 (mpp) cc_final: 0.7392 (mpp) REVERT: D 57 PHE cc_start: 0.8691 (m-80) cc_final: 0.8068 (m-80) REVERT: D 76 MET cc_start: 0.8231 (mmt) cc_final: 0.7358 (mmt) REVERT: D 104 ARG cc_start: 0.9016 (tpp80) cc_final: 0.8596 (tpp80) REVERT: D 133 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8984 (tt) REVERT: D 144 LYS cc_start: 0.7897 (tppt) cc_final: 0.7162 (tppt) REVERT: D 183 ASN cc_start: 0.9209 (t0) cc_final: 0.8989 (t0) REVERT: D 195 LYS cc_start: 0.9151 (ptpp) cc_final: 0.8764 (mtmm) REVERT: D 287 ARG cc_start: 0.8594 (ttp80) cc_final: 0.8073 (mmt90) REVERT: D 293 MET cc_start: 0.5959 (OUTLIER) cc_final: 0.4132 (ttt) REVERT: D 309 MET cc_start: 0.7638 (mpp) cc_final: 0.6874 (mpp) REVERT: E 1 MET cc_start: 0.4735 (mmp) cc_final: 0.3975 (mpp) REVERT: E 60 ARG cc_start: 0.8692 (ttm110) cc_final: 0.7899 (ttp-110) REVERT: E 104 ARG cc_start: 0.9336 (ttm-80) cc_final: 0.8929 (tpp80) REVERT: E 122 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8819 (mm-40) REVERT: E 144 LYS cc_start: 0.7520 (tppt) cc_final: 0.6734 (tppt) REVERT: E 287 ARG cc_start: 0.9015 (ttp-170) cc_final: 0.8478 (mmt180) REVERT: E 293 MET cc_start: 0.6177 (tmm) cc_final: 0.5702 (tmm) REVERT: F 44 TYR cc_start: 0.8161 (t80) cc_final: 0.7900 (t80) REVERT: F 76 MET cc_start: 0.8241 (mmt) cc_final: 0.7311 (mmt) REVERT: F 82 MET cc_start: 0.7549 (tpt) cc_final: 0.7176 (tpt) REVERT: F 144 LYS cc_start: 0.8025 (tppt) cc_final: 0.7518 (tppt) REVERT: G 57 PHE cc_start: 0.8652 (m-10) cc_final: 0.7852 (m-80) REVERT: G 58 LYS cc_start: 0.9326 (ttpt) cc_final: 0.8945 (tttm) REVERT: G 66 ASN cc_start: 0.8526 (p0) cc_final: 0.8224 (p0) REVERT: G 70 MET cc_start: 0.7235 (mtm) cc_final: 0.7013 (mtt) REVERT: G 76 MET cc_start: 0.8329 (mmt) cc_final: 0.7315 (mmt) REVERT: G 82 MET cc_start: 0.7282 (tpt) cc_final: 0.6956 (tpt) REVERT: G 144 LYS cc_start: 0.7814 (tppt) cc_final: 0.7327 (tppt) REVERT: G 195 LYS cc_start: 0.9175 (ptpp) cc_final: 0.8891 (mtmt) REVERT: G 212 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8389 (tm130) REVERT: U 57 PHE cc_start: 0.8612 (m-80) cc_final: 0.7988 (m-80) REVERT: U 66 ASN cc_start: 0.7119 (t0) cc_final: 0.5636 (p0) REVERT: U 76 MET cc_start: 0.8240 (mmt) cc_final: 0.7244 (mmt) REVERT: U 104 ARG cc_start: 0.9195 (tpp80) cc_final: 0.8779 (tpp80) REVERT: U 144 LYS cc_start: 0.8156 (tppt) cc_final: 0.7775 (tppt) REVERT: U 183 ASN cc_start: 0.8845 (t0) cc_final: 0.8418 (t0) REVERT: U 195 LYS cc_start: 0.9295 (ptpp) cc_final: 0.9017 (mtmm) REVERT: U 309 MET cc_start: 0.7930 (mpp) cc_final: 0.7614 (mpp) outliers start: 93 outliers final: 80 residues processed: 470 average time/residue: 0.1331 time to fit residues: 96.4125 Evaluate side-chains 499 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 414 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 212 GLN Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 303 LEU Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 152 optimal weight: 0.0000 chunk 86 optimal weight: 0.2980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 258 ASN ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** D 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN G 183 ASN ** G 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.146207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114578 restraints weight = 34674.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118095 restraints weight = 21825.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120429 restraints weight = 16543.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121929 restraints weight = 13956.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122835 restraints weight = 12542.298| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20800 Z= 0.100 Angle : 0.554 10.186 28088 Z= 0.281 Chirality : 0.040 0.206 3136 Planarity : 0.003 0.038 3560 Dihedral : 4.084 35.600 2688 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.65 % Allowed : 21.70 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.17), residues: 2488 helix: 1.20 (0.18), residues: 824 sheet: -1.91 (0.26), residues: 296 loop : -1.38 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 104 TYR 0.020 0.001 TYR A 61 PHE 0.011 0.001 PHE U 19 TRP 0.019 0.001 TRP G 211 HIS 0.002 0.000 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00234 (20800) covalent geometry : angle 0.55377 (28088) hydrogen bonds : bond 0.02708 ( 790) hydrogen bonds : angle 4.71393 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 437 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8368 (mmt) cc_final: 0.7608 (mmt) REVERT: A 92 LYS cc_start: 0.8098 (tppt) cc_final: 0.7848 (tmtt) REVERT: A 135 SER cc_start: 0.9461 (t) cc_final: 0.9101 (p) REVERT: A 144 LYS cc_start: 0.8661 (mmtt) cc_final: 0.8195 (tppt) REVERT: A 293 MET cc_start: 0.5264 (tmm) cc_final: 0.4901 (tmm) REVERT: A 309 MET cc_start: 0.7618 (mpp) cc_final: 0.7071 (mpp) REVERT: B 22 PHE cc_start: 0.8214 (m-80) cc_final: 0.7900 (m-80) REVERT: B 57 PHE cc_start: 0.8467 (m-80) cc_final: 0.8126 (m-80) REVERT: B 76 MET cc_start: 0.8161 (mmt) cc_final: 0.7414 (mmt) REVERT: B 113 ASN cc_start: 0.9168 (t0) cc_final: 0.8883 (m-40) REVERT: B 133 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9028 (tt) REVERT: B 287 ARG cc_start: 0.8240 (mpt180) cc_final: 0.7825 (mpt180) REVERT: C 76 MET cc_start: 0.8307 (mmt) cc_final: 0.7368 (mmt) REVERT: C 112 GLU cc_start: 0.8606 (tp30) cc_final: 0.8012 (tp30) REVERT: C 133 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8983 (tt) REVERT: C 144 LYS cc_start: 0.7602 (tptp) cc_final: 0.7064 (tppt) REVERT: C 260 LEU cc_start: 0.8683 (mt) cc_final: 0.8372 (mp) REVERT: C 293 MET cc_start: 0.5189 (tpt) cc_final: 0.3138 (mtt) REVERT: C 309 MET cc_start: 0.7754 (mpp) cc_final: 0.7200 (mpp) REVERT: D 60 ARG cc_start: 0.8509 (ttm-80) cc_final: 0.8290 (ttp80) REVERT: D 76 MET cc_start: 0.8197 (mmt) cc_final: 0.7878 (mpp) REVERT: D 104 ARG cc_start: 0.9009 (tpp80) cc_final: 0.8603 (tpp80) REVERT: D 112 GLU cc_start: 0.8710 (tp30) cc_final: 0.8354 (tp30) REVERT: D 144 LYS cc_start: 0.7883 (tppt) cc_final: 0.7168 (tppt) REVERT: D 287 ARG cc_start: 0.8539 (ttp80) cc_final: 0.8004 (mmt90) REVERT: D 293 MET cc_start: 0.5620 (OUTLIER) cc_final: 0.4043 (ttt) REVERT: E 1 MET cc_start: 0.4791 (mmp) cc_final: 0.4127 (mpp) REVERT: E 60 ARG cc_start: 0.8660 (ttm110) cc_final: 0.8041 (ttp-110) REVERT: E 76 MET cc_start: 0.8330 (mmt) cc_final: 0.7790 (mmt) REVERT: E 104 ARG cc_start: 0.9305 (ttm-80) cc_final: 0.8902 (tpp80) REVERT: E 122 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8798 (mm-40) REVERT: E 144 LYS cc_start: 0.7438 (tppt) cc_final: 0.6706 (tppt) REVERT: E 287 ARG cc_start: 0.8998 (ttp-170) cc_final: 0.8467 (mmt180) REVERT: E 309 MET cc_start: 0.7790 (mpp) cc_final: 0.6992 (mpp) REVERT: F 22 PHE cc_start: 0.8661 (m-80) cc_final: 0.8223 (m-80) REVERT: F 44 TYR cc_start: 0.8119 (t80) cc_final: 0.7827 (t80) REVERT: F 76 MET cc_start: 0.8195 (mmt) cc_final: 0.7470 (mmt) REVERT: F 82 MET cc_start: 0.7518 (tpt) cc_final: 0.7134 (tpt) REVERT: F 144 LYS cc_start: 0.7992 (tppt) cc_final: 0.7505 (tppt) REVERT: G 22 PHE cc_start: 0.8170 (m-80) cc_final: 0.7945 (m-80) REVERT: G 57 PHE cc_start: 0.8651 (m-10) cc_final: 0.7826 (m-80) REVERT: G 58 LYS cc_start: 0.9296 (ttpt) cc_final: 0.9033 (tttp) REVERT: G 66 ASN cc_start: 0.8446 (p0) cc_final: 0.8213 (p0) REVERT: G 76 MET cc_start: 0.8261 (mmt) cc_final: 0.7516 (mmt) REVERT: G 82 MET cc_start: 0.7116 (tpt) cc_final: 0.6801 (tpt) REVERT: G 144 LYS cc_start: 0.7792 (tppt) cc_final: 0.7312 (tppt) REVERT: G 195 LYS cc_start: 0.9110 (ptpp) cc_final: 0.8807 (mtmt) REVERT: G 309 MET cc_start: 0.7526 (mpp) cc_final: 0.7015 (mpp) REVERT: U 57 PHE cc_start: 0.8590 (m-80) cc_final: 0.7995 (m-80) REVERT: U 66 ASN cc_start: 0.7125 (t0) cc_final: 0.6845 (t0) REVERT: U 76 MET cc_start: 0.8191 (mmt) cc_final: 0.7236 (mmt) REVERT: U 104 ARG cc_start: 0.9224 (tpp80) cc_final: 0.8820 (tpp80) REVERT: U 144 LYS cc_start: 0.8129 (tppt) cc_final: 0.7544 (tppt) REVERT: U 183 ASN cc_start: 0.8839 (t0) cc_final: 0.8439 (t0) REVERT: U 195 LYS cc_start: 0.9251 (ptpp) cc_final: 0.9003 (mtmm) REVERT: U 309 MET cc_start: 0.7876 (mpp) cc_final: 0.7546 (mpp) outliers start: 83 outliers final: 68 residues processed: 478 average time/residue: 0.1512 time to fit residues: 110.7293 Evaluate side-chains 492 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 421 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain U residue 27 ILE Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 303 LEU Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 59 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 74 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS E 278 GLN G 183 ASN G 212 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113448 restraints weight = 34763.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116881 restraints weight = 22197.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119180 restraints weight = 17044.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120667 restraints weight = 14426.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121531 restraints weight = 12969.963| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20800 Z= 0.113 Angle : 0.564 9.568 28088 Z= 0.285 Chirality : 0.040 0.198 3136 Planarity : 0.003 0.037 3560 Dihedral : 3.988 31.667 2688 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.87 % Allowed : 22.05 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.17), residues: 2488 helix: 1.23 (0.18), residues: 832 sheet: -1.87 (0.26), residues: 296 loop : -1.29 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 210 TYR 0.015 0.001 TYR F 61 PHE 0.019 0.001 PHE A 272 TRP 0.011 0.001 TRP G 211 HIS 0.002 0.000 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00267 (20800) covalent geometry : angle 0.56392 (28088) hydrogen bonds : bond 0.02766 ( 790) hydrogen bonds : angle 4.66912 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 432 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8386 (mmt) cc_final: 0.7697 (mmt) REVERT: A 135 SER cc_start: 0.9482 (t) cc_final: 0.9157 (p) REVERT: A 144 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8192 (tppt) REVERT: A 293 MET cc_start: 0.5269 (tmm) cc_final: 0.4891 (tmm) REVERT: B 22 PHE cc_start: 0.8244 (m-80) cc_final: 0.7908 (m-80) REVERT: B 57 PHE cc_start: 0.8496 (m-80) cc_final: 0.8148 (m-80) REVERT: B 76 MET cc_start: 0.8170 (mmt) cc_final: 0.7403 (mmt) REVERT: B 113 ASN cc_start: 0.9210 (t0) cc_final: 0.8939 (m-40) REVERT: B 133 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9052 (tt) REVERT: B 309 MET cc_start: 0.7557 (mpp) cc_final: 0.7296 (mpp) REVERT: C 76 MET cc_start: 0.8320 (mmt) cc_final: 0.7385 (mmt) REVERT: C 112 GLU cc_start: 0.8609 (tp30) cc_final: 0.7993 (tp30) REVERT: C 144 LYS cc_start: 0.7582 (tptp) cc_final: 0.7015 (tppt) REVERT: C 260 LEU cc_start: 0.8692 (mt) cc_final: 0.8380 (mp) REVERT: C 309 MET cc_start: 0.7793 (mpp) cc_final: 0.7216 (mpp) REVERT: D 57 PHE cc_start: 0.8678 (m-80) cc_final: 0.8087 (m-80) REVERT: D 76 MET cc_start: 0.8206 (mmt) cc_final: 0.7915 (mpp) REVERT: D 104 ARG cc_start: 0.9014 (tpp80) cc_final: 0.8599 (tpp80) REVERT: D 112 GLU cc_start: 0.8688 (tp30) cc_final: 0.8320 (tp30) REVERT: D 144 LYS cc_start: 0.7877 (tppt) cc_final: 0.7189 (tppt) REVERT: D 195 LYS cc_start: 0.9149 (ptpp) cc_final: 0.8766 (mtmt) REVERT: D 287 ARG cc_start: 0.8534 (ttp80) cc_final: 0.7988 (mmt90) REVERT: D 293 MET cc_start: 0.5640 (OUTLIER) cc_final: 0.3971 (ttt) REVERT: E 1 MET cc_start: 0.4762 (mmp) cc_final: 0.4151 (mpp) REVERT: E 60 ARG cc_start: 0.8667 (ttm110) cc_final: 0.8035 (ttp-110) REVERT: E 76 MET cc_start: 0.8366 (mmt) cc_final: 0.7806 (mmt) REVERT: E 104 ARG cc_start: 0.9289 (ttm-80) cc_final: 0.8889 (tpp80) REVERT: E 122 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8752 (mm-40) REVERT: E 144 LYS cc_start: 0.7412 (tppt) cc_final: 0.6634 (tppt) REVERT: E 147 GLU cc_start: 0.8235 (tt0) cc_final: 0.7930 (tt0) REVERT: E 287 ARG cc_start: 0.8991 (ttp-170) cc_final: 0.8401 (mmt90) REVERT: E 309 MET cc_start: 0.7855 (mpp) cc_final: 0.7173 (mpp) REVERT: F 22 PHE cc_start: 0.8706 (m-80) cc_final: 0.8260 (m-80) REVERT: F 44 TYR cc_start: 0.8146 (t80) cc_final: 0.7849 (t80) REVERT: F 76 MET cc_start: 0.8214 (mmt) cc_final: 0.7477 (mmt) REVERT: F 82 MET cc_start: 0.7561 (tpt) cc_final: 0.7175 (tpt) REVERT: F 144 LYS cc_start: 0.8008 (tppt) cc_final: 0.7526 (tppt) REVERT: F 309 MET cc_start: 0.7547 (mpp) cc_final: 0.7026 (mpp) REVERT: G 22 PHE cc_start: 0.8247 (m-80) cc_final: 0.8039 (m-80) REVERT: G 57 PHE cc_start: 0.8607 (m-10) cc_final: 0.7739 (m-80) REVERT: G 58 LYS cc_start: 0.9305 (ttpt) cc_final: 0.9036 (tttp) REVERT: G 66 ASN cc_start: 0.8446 (p0) cc_final: 0.8238 (p0) REVERT: G 76 MET cc_start: 0.8296 (mmt) cc_final: 0.7538 (mmt) REVERT: G 82 MET cc_start: 0.7204 (tpt) cc_final: 0.6858 (tpt) REVERT: G 144 LYS cc_start: 0.7760 (tppt) cc_final: 0.7277 (tppt) REVERT: G 195 LYS cc_start: 0.9116 (ptpp) cc_final: 0.8767 (mtmt) REVERT: G 212 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8656 (tm-30) REVERT: G 309 MET cc_start: 0.7584 (mpp) cc_final: 0.7027 (mpp) REVERT: U 57 PHE cc_start: 0.8677 (m-80) cc_final: 0.8067 (m-80) REVERT: U 66 ASN cc_start: 0.7126 (t0) cc_final: 0.6856 (t0) REVERT: U 76 MET cc_start: 0.8227 (mmt) cc_final: 0.7265 (mmt) REVERT: U 104 ARG cc_start: 0.9227 (tpp80) cc_final: 0.8831 (tpp80) REVERT: U 144 LYS cc_start: 0.8111 (tppt) cc_final: 0.7555 (tppt) REVERT: U 183 ASN cc_start: 0.8839 (t0) cc_final: 0.8420 (t0) REVERT: U 287 ARG cc_start: 0.7938 (mmt90) cc_final: 0.7735 (mmt90) REVERT: U 309 MET cc_start: 0.7817 (mpp) cc_final: 0.7463 (mpp) outliers start: 88 outliers final: 77 residues processed: 471 average time/residue: 0.1396 time to fit residues: 100.7220 Evaluate side-chains 504 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 424 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 212 GLN Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain U residue 27 ILE Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 303 LEU Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 3 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 223 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN G 212 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.145606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113649 restraints weight = 34941.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.117124 restraints weight = 22329.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119390 restraints weight = 17074.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120855 restraints weight = 14476.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.121821 restraints weight = 13036.408| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20800 Z= 0.133 Angle : 0.581 9.678 28088 Z= 0.293 Chirality : 0.041 0.196 3136 Planarity : 0.003 0.038 3560 Dihedral : 3.987 29.059 2688 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.65 % Allowed : 22.40 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.17), residues: 2488 helix: 1.34 (0.18), residues: 824 sheet: -1.85 (0.27), residues: 296 loop : -1.31 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 210 TYR 0.015 0.001 TYR F 61 PHE 0.019 0.001 PHE G 272 TRP 0.009 0.001 TRP F 211 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00317 (20800) covalent geometry : angle 0.58054 (28088) hydrogen bonds : bond 0.02835 ( 790) hydrogen bonds : angle 4.66170 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 424 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8406 (mmt) cc_final: 0.7673 (mmt) REVERT: A 135 SER cc_start: 0.9482 (t) cc_final: 0.9162 (p) REVERT: A 144 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8193 (tppt) REVERT: A 293 MET cc_start: 0.5278 (tmm) cc_final: 0.4897 (tmm) REVERT: B 22 PHE cc_start: 0.8291 (m-80) cc_final: 0.7943 (m-80) REVERT: B 57 PHE cc_start: 0.8527 (m-80) cc_final: 0.8150 (m-80) REVERT: B 76 MET cc_start: 0.8225 (mmt) cc_final: 0.7477 (mmt) REVERT: B 133 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9067 (tt) REVERT: B 287 ARG cc_start: 0.8324 (mpt180) cc_final: 0.7996 (mpt180) REVERT: B 309 MET cc_start: 0.7570 (mpp) cc_final: 0.6974 (mpp) REVERT: C 76 MET cc_start: 0.8347 (mmt) cc_final: 0.7405 (mmt) REVERT: C 112 GLU cc_start: 0.8632 (tp30) cc_final: 0.8023 (tp30) REVERT: C 144 LYS cc_start: 0.7582 (tptp) cc_final: 0.7037 (tppt) REVERT: C 260 LEU cc_start: 0.8716 (mt) cc_final: 0.8405 (mp) REVERT: C 293 MET cc_start: 0.5517 (tpt) cc_final: 0.3922 (mmt) REVERT: C 309 MET cc_start: 0.7719 (mpp) cc_final: 0.7173 (mpp) REVERT: D 60 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.8314 (ttp80) REVERT: D 76 MET cc_start: 0.8237 (mmt) cc_final: 0.7992 (mpp) REVERT: D 104 ARG cc_start: 0.9019 (tpp80) cc_final: 0.8615 (tpp80) REVERT: D 112 GLU cc_start: 0.8670 (tp30) cc_final: 0.8288 (tp30) REVERT: D 144 LYS cc_start: 0.7901 (tppt) cc_final: 0.7220 (tppt) REVERT: D 195 LYS cc_start: 0.9180 (ptpp) cc_final: 0.8814 (mtmt) REVERT: D 287 ARG cc_start: 0.8546 (ttp80) cc_final: 0.7998 (mmt90) REVERT: D 293 MET cc_start: 0.5457 (OUTLIER) cc_final: 0.3838 (ttt) REVERT: E 1 MET cc_start: 0.4734 (mmp) cc_final: 0.4144 (mpp) REVERT: E 60 ARG cc_start: 0.8674 (ttm110) cc_final: 0.7824 (ttp-110) REVERT: E 76 MET cc_start: 0.8420 (mmt) cc_final: 0.7821 (mmt) REVERT: E 104 ARG cc_start: 0.9328 (ttm-80) cc_final: 0.8908 (tpp80) REVERT: E 122 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8757 (mm-40) REVERT: E 144 LYS cc_start: 0.7337 (tppt) cc_final: 0.6630 (tppt) REVERT: E 147 GLU cc_start: 0.8202 (tt0) cc_final: 0.7896 (tt0) REVERT: E 287 ARG cc_start: 0.9002 (ttp-170) cc_final: 0.8435 (mmt90) REVERT: E 309 MET cc_start: 0.7903 (mpp) cc_final: 0.7229 (mpp) REVERT: F 22 PHE cc_start: 0.8702 (m-80) cc_final: 0.8277 (m-80) REVERT: F 44 TYR cc_start: 0.8163 (t80) cc_final: 0.7872 (t80) REVERT: F 76 MET cc_start: 0.8187 (mmt) cc_final: 0.7284 (mmt) REVERT: F 82 MET cc_start: 0.7564 (tpt) cc_final: 0.7182 (tpt) REVERT: F 144 LYS cc_start: 0.8005 (tppt) cc_final: 0.7517 (tppt) REVERT: G 57 PHE cc_start: 0.8615 (m-10) cc_final: 0.7745 (m-80) REVERT: G 58 LYS cc_start: 0.9305 (ttpt) cc_final: 0.9042 (tttp) REVERT: G 66 ASN cc_start: 0.8452 (p0) cc_final: 0.8241 (p0) REVERT: G 76 MET cc_start: 0.8327 (mmt) cc_final: 0.7561 (mmt) REVERT: G 82 MET cc_start: 0.7107 (tpt) cc_final: 0.6796 (tpt) REVERT: G 144 LYS cc_start: 0.7821 (tppt) cc_final: 0.7360 (tppt) REVERT: G 195 LYS cc_start: 0.9169 (ptpp) cc_final: 0.8824 (mtmt) REVERT: G 212 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8631 (tm-30) REVERT: G 309 MET cc_start: 0.7586 (mpp) cc_final: 0.7035 (mpp) REVERT: U 57 PHE cc_start: 0.8665 (m-80) cc_final: 0.8048 (m-80) REVERT: U 66 ASN cc_start: 0.7115 (t0) cc_final: 0.6861 (t0) REVERT: U 76 MET cc_start: 0.8235 (mmt) cc_final: 0.7274 (mmt) REVERT: U 104 ARG cc_start: 0.9239 (tpp80) cc_final: 0.8836 (tpp80) REVERT: U 112 GLU cc_start: 0.8658 (tp30) cc_final: 0.8112 (tp30) REVERT: U 144 LYS cc_start: 0.8112 (tppt) cc_final: 0.7561 (tppt) REVERT: U 183 ASN cc_start: 0.8805 (t0) cc_final: 0.8388 (t0) REVERT: U 195 LYS cc_start: 0.9250 (ptpp) cc_final: 0.9014 (mtmm) REVERT: U 287 ARG cc_start: 0.7897 (mmt90) cc_final: 0.7676 (mmt90) REVERT: U 293 MET cc_start: 0.6281 (ptp) cc_final: 0.5903 (ptp) REVERT: U 309 MET cc_start: 0.7828 (mpp) cc_final: 0.7476 (mpp) outliers start: 83 outliers final: 79 residues processed: 457 average time/residue: 0.1431 time to fit residues: 100.3670 Evaluate side-chains 500 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 418 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 212 GLN Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain U residue 27 ILE Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 303 LEU Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.0770 chunk 231 optimal weight: 0.0770 chunk 104 optimal weight: 2.9990 chunk 108 optimal weight: 0.0050 chunk 205 optimal weight: 2.9990 chunk 239 optimal weight: 0.1980 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 overall best weight: 0.2710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** D 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN G 183 ASN U 71 ASN U 160 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.148230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115603 restraints weight = 34574.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119413 restraints weight = 21009.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121944 restraints weight = 15623.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123604 restraints weight = 13003.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124664 restraints weight = 11563.662| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20800 Z= 0.101 Angle : 0.564 10.052 28088 Z= 0.284 Chirality : 0.040 0.189 3136 Planarity : 0.003 0.036 3560 Dihedral : 3.896 24.082 2688 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.90 % Allowed : 23.33 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.17), residues: 2488 helix: 1.46 (0.19), residues: 824 sheet: -1.77 (0.27), residues: 296 loop : -1.23 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 210 TYR 0.019 0.001 TYR G 61 PHE 0.022 0.001 PHE G 272 TRP 0.010 0.001 TRP F 211 HIS 0.002 0.000 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00232 (20800) covalent geometry : angle 0.56367 (28088) hydrogen bonds : bond 0.02583 ( 790) hydrogen bonds : angle 4.56904 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3188.33 seconds wall clock time: 56 minutes 17.94 seconds (3377.94 seconds total)