Starting phenix.real_space_refine on Sun Jul 5 23:38:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g8f_29848/07_2026/8g8f_29848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8f_29848/07_2026/8g8f_29848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8g8f_29848/07_2026/8g8f_29848.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g8f_29848/07_2026/8g8f_29848.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g8f_29848/07_2026/8g8f_29848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8f_29848/07_2026/8g8f_29848.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8f_29848/07_2026/8g8f_29848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8f_29848/07_2026/8g8f_29848.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.280 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: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 168 5.16 5 C 19248 2.51 5 N 5328 2.21 5 O 6096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30912 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "B" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "C" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "D" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "E" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "F" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "G" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "H" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 7.07, per 1000 atoms: 0.23 Number of scatterers: 30912 At special positions: 0 Unit cell: (160.17, 161.856, 133.194, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 72 15.00 O 6096 8.00 N 5328 7.00 C 19248 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.4 seconds 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7136 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 48 sheets defined 39.6% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 19 through 26 removed outlier: 3.791A pdb=" N CYS A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 96 through 110 removed outlier: 3.683A pdb=" N TYR A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 193 through 205 removed outlier: 3.936A pdb=" N ARG A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.895A pdb=" N TYR A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 316 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'B' and resid 19 through 26 removed outlier: 3.853A pdb=" N CYS B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 96 through 110 removed outlier: 3.639A pdb=" N TYR B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 135 removed outlier: 4.275A pdb=" N PHE B 131 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU B 132 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS B 134 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.685A pdb=" N ARG B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 254 through 267 removed outlier: 3.955A pdb=" N TYR B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.703A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'C' and resid 19 through 25 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 96 through 110 removed outlier: 3.682A pdb=" N TYR C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 132 removed outlier: 3.751A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 193 through 205 removed outlier: 3.505A pdb=" N ARG C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 254 through 267 removed outlier: 4.026A pdb=" N TYR C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.702A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid 19 through 26 removed outlier: 3.804A pdb=" N CYS D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 96 through 110 removed outlier: 3.662A pdb=" N TYR D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 135 removed outlier: 4.597A pdb=" N PHE D 131 " --> pdb=" O ARG D 128 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLU D 132 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS D 134 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 193 through 205 removed outlier: 3.685A pdb=" N ARG D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 254 through 267 removed outlier: 4.037A pdb=" N TYR D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 316 Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'E' and resid 19 through 26 removed outlier: 3.806A pdb=" N CYS E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 96 through 110 removed outlier: 3.722A pdb=" N TYR E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 193 through 205 removed outlier: 3.762A pdb=" N ARG E 203 " --> pdb=" O GLU E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 254 through 267 removed outlier: 4.084A pdb=" N TYR E 258 " --> pdb=" O GLU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 316 removed outlier: 3.722A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'F' and resid 19 through 26 removed outlier: 3.756A pdb=" N CYS F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 96 through 110 removed outlier: 3.657A pdb=" N TYR F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 removed outlier: 3.545A pdb=" N GLU F 132 " --> pdb=" O ARG F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 135 No H-bonds generated for 'chain 'F' and resid 133 through 135' Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 224 through 229 Processing helix chain 'F' and resid 254 through 267 removed outlier: 4.056A pdb=" N TYR F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.676A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid 19 through 26 removed outlier: 3.837A pdb=" N CYS G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 96 through 110 removed outlier: 3.641A pdb=" N TYR G 110 " --> pdb=" O LYS G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 removed outlier: 4.018A pdb=" N GLU G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 135 No H-bonds generated for 'chain 'G' and resid 133 through 135' Processing helix chain 'G' and resid 193 through 205 removed outlier: 3.786A pdb=" N ARG G 203 " --> pdb=" O GLU G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 229 Processing helix chain 'G' and resid 254 through 267 removed outlier: 3.915A pdb=" N TYR G 258 " --> pdb=" O GLU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 316 removed outlier: 3.722A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 356 through 358 No H-bonds generated for 'chain 'G' and resid 356 through 358' Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 416 through 421 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.803A pdb=" N CYS H 26 " --> pdb=" O GLN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 96 through 110 removed outlier: 3.751A pdb=" N TYR H 110 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'H' and resid 193 through 205 removed outlier: 3.638A pdb=" N ARG H 203 " --> pdb=" O GLU H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 229 Processing helix chain 'H' and resid 254 through 267 removed outlier: 4.024A pdb=" N TYR H 258 " --> pdb=" O GLU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 3.554A pdb=" N GLY H 317 " --> pdb=" O LEU H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 355 Processing helix chain 'H' and resid 356 through 358 No H-bonds generated for 'chain 'H' and resid 356 through 358' Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 416 through 421 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.514A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 299 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 145 removed outlier: 3.548A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.168A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.877A pdb=" N SER A 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.716A pdb=" N SER D 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.584A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 299 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.709A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 188 through 189 removed outlier: 6.256A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 401 through 403 removed outlier: 3.689A pdb=" N SER B 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.533A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C 299 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.641A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.123A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 401 through 403 removed outlier: 3.748A pdb=" N SER C 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER D 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.535A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL D 299 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.672A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.010A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.532A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL E 299 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 143 through 145 Processing sheet with id=AD2, first strand: chain 'E' and resid 188 through 189 removed outlier: 6.048A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.822A pdb=" N SER E 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.686A pdb=" N SER H 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.442A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL F 299 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ARG F 322 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.667A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.068A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 401 through 403 removed outlier: 3.667A pdb=" N SER F 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.543A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL G 299 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 143 through 145 Processing sheet with id=AE6, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.191A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 401 through 403 removed outlier: 3.811A pdb=" N SER G 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE9, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AF1, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.502A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL H 299 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.520A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 188 through 189 removed outlier: 6.214A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 1137 hydrogen bonds defined for protein. 3192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.54 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5168 1.31 - 1.44: 7697 1.44 - 1.57: 18191 1.57 - 1.70: 120 1.70 - 1.82: 272 Bond restraints: 31448 Sorted by residual: bond pdb=" C4 ATP A 602 " pdb=" C5 ATP A 602 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.98e+01 bond pdb=" C4 ATP D 602 " pdb=" C5 ATP D 602 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.94e+01 bond pdb=" C4 ATP G 602 " pdb=" C5 ATP G 602 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 bond pdb=" C4 ATP E 602 " pdb=" C5 ATP E 602 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 bond pdb=" C4 ATP H 602 " pdb=" C5 ATP H 602 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.91e+01 ... (remaining 31443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 42242 4.28 - 8.56: 310 8.56 - 12.84: 43 12.84 - 17.12: 19 17.12 - 21.40: 18 Bond angle restraints: 42632 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 120.43 19.44 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.78e+02 ... (remaining 42627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 18052 35.33 - 70.67: 548 70.67 - 106.00: 44 106.00 - 141.34: 3 141.34 - 176.67: 1 Dihedral angle restraints: 18648 sinusoidal: 7480 harmonic: 11168 Sorted by residual: dihedral pdb=" C5' IMP A 603 " pdb=" O5' IMP A 603 " pdb=" P IMP A 603 " pdb=" O2P IMP A 603 " ideal model delta sinusoidal sigma weight residual -168.07 8.61 -176.67 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' IMP H 603 " pdb=" O5' IMP H 603 " pdb=" P IMP H 603 " pdb=" O2P IMP H 603 " ideal model delta sinusoidal sigma weight residual -168.07 -30.70 -137.37 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" C5' IMP G 603 " pdb=" O5' IMP G 603 " pdb=" P IMP G 603 " pdb=" O2P IMP G 603 " ideal model delta sinusoidal sigma weight residual -168.07 -43.27 -124.80 1 2.00e+01 2.50e-03 3.77e+01 ... (remaining 18645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3909 0.057 - 0.113: 823 0.113 - 0.170: 90 0.170 - 0.227: 33 0.227 - 0.284: 1 Chirality restraints: 4856 Sorted by residual: chirality pdb=" CA MET G 179 " pdb=" N MET G 179 " pdb=" C MET G 179 " pdb=" CB MET G 179 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ILE B 178 " pdb=" N ILE B 178 " pdb=" C ILE B 178 " pdb=" CB ILE B 178 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" C3D NAD H 604 " pdb=" C2D NAD H 604 " pdb=" C4D NAD H 604 " pdb=" O3D NAD H 604 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.94e-01 ... (remaining 4853 not shown) Planarity restraints: 5352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 13 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C VAL C 13 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL C 13 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO C 14 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 170 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" CD GLU H 170 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU H 170 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU H 170 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 13 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C VAL E 13 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL E 13 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO E 14 " 0.011 2.00e-02 2.50e+03 ... (remaining 5349 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1300 2.72 - 3.26: 31100 3.26 - 3.81: 51702 3.81 - 4.35: 66138 4.35 - 4.90: 108290 Nonbonded interactions: 258530 Sorted by model distance: nonbonded pdb=" O ARG F 182 " pdb=" NH1 ARG F 182 " model vdw 2.173 3.120 nonbonded pdb=" OD2 ASP A 364 " pdb=" O2' IMP A 603 " model vdw 2.178 3.040 nonbonded pdb=" OD2 ASP C 364 " pdb=" O2' IMP C 603 " model vdw 2.194 3.040 nonbonded pdb=" OD2 ASP B 364 " pdb=" O2' IMP B 603 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP E 364 " pdb=" O2' IMP E 603 " model vdw 2.198 3.040 ... (remaining 258525 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.790 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 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 : 0.011 0.822 31460 Z= 0.999 Angle : 1.020 21.396 42632 Z= 0.704 Chirality : 0.048 0.284 4856 Planarity : 0.004 0.050 5352 Dihedral : 16.392 176.675 11512 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.98 % Favored : 93.61 % Rotamer: Outliers : 1.87 % Allowed : 17.36 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 are not related in a simple way. whole: -0.22 (0.14), residues: 3896 helix: 0.74 (0.14), residues: 1488 sheet: 0.15 (0.22), residues: 472 loop : -0.91 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 182 TYR 0.012 0.001 TYR E 348 PHE 0.017 0.001 PHE G 165 HIS 0.003 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.44 (31448) covalent geometry : angle 1.02024 / 0.70 (42632) hydrogen bonds : bond 0.13789 / 9.45 ( 1137) hydrogen bonds : angle 6.29641 / 4.51 ( 3192) Misc. bond : bond 0.45805 / 32.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 368 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ASP cc_start: 0.7411 (m-30) cc_final: 0.7093 (m-30) REVERT: B 277 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: D 303 ASN cc_start: 0.9094 (m110) cc_final: 0.8894 (m-40) REVERT: E 179 MET cc_start: 0.5510 (tmm) cc_final: 0.4750 (tmm) REVERT: F 438 LYS cc_start: 0.7332 (mttm) cc_final: 0.7032 (mtmt) outliers start: 60 outliers final: 50 residues processed: 424 average time/residue: 0.6397 time to fit residues: 324.5367 Evaluate side-chains 412 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 361 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 318 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 0.2980 chunk 183 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 HIS ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 368 GLN A 441 GLN A 466 HIS A 478 GLN B 21 GLN B 93 HIS B 343 GLN B 368 GLN B 478 GLN C 93 HIS C 343 GLN C 368 GLN C 441 GLN C 466 HIS C 478 GLN D 93 HIS D 303 ASN D 343 GLN D 368 GLN D 441 GLN D 478 GLN E 93 HIS E 343 GLN E 368 GLN E 478 GLN F 93 HIS F 343 GLN F 368 GLN F 466 HIS F 478 GLN G 93 HIS G 343 GLN G 368 GLN G 466 HIS G 478 GLN H 93 HIS H 102 ASN H 343 GLN H 368 GLN H 441 GLN H 466 HIS H 478 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.189981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137093 restraints weight = 33316.644| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.85 r_work: 0.3230 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31460 Z= 0.142 Angle : 0.611 12.809 42632 Z= 0.316 Chirality : 0.045 0.198 4856 Planarity : 0.004 0.038 5352 Dihedral : 10.212 167.338 4479 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.98 % Favored : 94.58 % Rotamer: Outliers : 3.68 % Allowed : 15.12 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 are not related in a simple way. whole: -0.12 (0.14), residues: 3896 helix: 0.83 (0.14), residues: 1488 sheet: 0.05 (0.22), residues: 472 loop : -0.80 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 161 TYR 0.013 0.001 TYR E 348 PHE 0.014 0.001 PHE H 456 HIS 0.004 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (31448) covalent geometry : angle 0.61115 / 0.32 (42632) hydrogen bonds : bond 0.03870 / 2.61 ( 1137) hydrogen bonds : angle 5.15432 / 3.70 ( 3192) Misc. bond : bond 0.00198 / 0.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 377 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 277 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.6716 (tm-30) REVERT: B 455 LYS cc_start: 0.7528 (mtpp) cc_final: 0.7062 (ttmm) REVERT: C 255 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.6673 (p0) REVERT: C 277 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.6940 (tm-30) REVERT: D 277 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.6578 (tm-30) REVERT: E 179 MET cc_start: 0.5775 (mmm) cc_final: 0.5009 (tmm) REVERT: F 277 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.6908 (tm-30) REVERT: F 438 LYS cc_start: 0.7405 (mttm) cc_final: 0.6986 (mtmt) REVERT: G 277 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.6880 (tm-30) REVERT: G 512 ARG cc_start: 0.7293 (ttp80) cc_final: 0.7030 (ttt-90) REVERT: H 277 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.6583 (tm-30) outliers start: 118 outliers final: 59 residues processed: 480 average time/residue: 0.6176 time to fit residues: 356.8529 Evaluate side-chains 435 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 369 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 0.4980 chunk 81 optimal weight: 0.3980 chunk 116 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 390 optimal weight: 0.9980 chunk 361 optimal weight: 3.9990 chunk 317 optimal weight: 7.9990 chunk 213 optimal weight: 20.0000 chunk 319 optimal weight: 4.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 298 GLN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 466 HIS D 478 GLN E 368 GLN E 478 GLN F 298 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.186508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.133107 restraints weight = 33300.757| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.84 r_work: 0.3178 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 31460 Z= 0.245 Angle : 0.667 13.186 42632 Z= 0.344 Chirality : 0.049 0.241 4856 Planarity : 0.005 0.048 5352 Dihedral : 10.022 122.624 4470 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.42 % Favored : 94.15 % Rotamer: Outliers : 4.24 % Allowed : 15.77 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 are not related in a simple way. whole: -0.35 (0.13), residues: 3896 helix: 0.60 (0.14), residues: 1472 sheet: 0.08 (0.22), residues: 440 loop : -0.92 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 356 TYR 0.018 0.002 TYR E 348 PHE 0.013 0.002 PHE D 24 HIS 0.005 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.24 (31448) covalent geometry : angle 0.66678 / 0.34 (42632) hydrogen bonds : bond 0.05076 / 3.47 ( 1137) hydrogen bonds : angle 5.18845 / 3.70 ( 3192) Misc. bond : bond 0.00172 / 0.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 373 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7317 (m-30) cc_final: 0.6954 (m-30) REVERT: A 296 ASN cc_start: 0.8118 (m110) cc_final: 0.7652 (p0) REVERT: A 438 LYS cc_start: 0.7320 (mmmt) cc_final: 0.6749 (mtmt) REVERT: B 438 LYS cc_start: 0.7430 (mmtt) cc_final: 0.6902 (mtmt) REVERT: C 255 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6651 (p0) REVERT: C 399 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6962 (pp20) REVERT: D 243 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7592 (mt0) REVERT: D 399 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7090 (pp20) REVERT: D 456 PHE cc_start: 0.8039 (t80) cc_final: 0.7831 (t80) REVERT: E 179 MET cc_start: 0.6287 (mmm) cc_final: 0.5513 (tmm) REVERT: F 206 LYS cc_start: 0.6553 (OUTLIER) cc_final: 0.5938 (ptpp) REVERT: F 456 PHE cc_start: 0.8067 (t80) cc_final: 0.7866 (t80) REVERT: G 65 LEU cc_start: 0.9095 (mm) cc_final: 0.8877 (mm) REVERT: G 277 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: H 65 LEU cc_start: 0.9091 (mm) cc_final: 0.8872 (mm) REVERT: H 277 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.6752 (tm-30) outliers start: 136 outliers final: 84 residues processed: 475 average time/residue: 0.5851 time to fit residues: 336.6710 Evaluate side-chains 457 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 366 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 285 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 212 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 282 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 368 GLN A 478 GLN B 368 GLN B 466 HIS B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 478 GLN E 368 GLN E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.189013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.136038 restraints weight = 33061.669| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.86 r_work: 0.3213 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31460 Z= 0.130 Angle : 0.564 12.605 42632 Z= 0.290 Chirality : 0.044 0.203 4856 Planarity : 0.004 0.037 5352 Dihedral : 9.357 93.021 4461 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.70 % Favored : 94.87 % Rotamer: Outliers : 4.30 % Allowed : 16.43 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 are not related in a simple way. whole: 0.01 (0.14), residues: 3896 helix: 0.92 (0.14), residues: 1472 sheet: 0.64 (0.24), residues: 376 loop : -0.78 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.012 0.001 TYR A 353 PHE 0.009 0.001 PHE H 456 HIS 0.003 0.001 HIS D 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (31448) covalent geometry : angle 0.56411 / 0.29 (42632) hydrogen bonds : bond 0.03679 / 2.50 ( 1137) hydrogen bonds : angle 4.94136 / 3.53 ( 3192) Misc. bond : bond 0.00097 / 0.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 384 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8059 (tp30) cc_final: 0.7175 (mp0) REVERT: A 162 ASP cc_start: 0.7212 (m-30) cc_final: 0.6847 (m-30) REVERT: A 296 ASN cc_start: 0.8138 (m110) cc_final: 0.7634 (p0) REVERT: A 399 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6862 (pp20) REVERT: A 438 LYS cc_start: 0.7286 (mmmt) cc_final: 0.6781 (mtmt) REVERT: A 455 LYS cc_start: 0.7539 (mtpp) cc_final: 0.7159 (ptpt) REVERT: B 255 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6650 (p0) REVERT: B 438 LYS cc_start: 0.7368 (mmtt) cc_final: 0.6802 (mtmt) REVERT: B 455 LYS cc_start: 0.7570 (mtpp) cc_final: 0.7237 (ptpt) REVERT: C 255 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6659 (p0) REVERT: C 277 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: C 399 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6942 (pp20) REVERT: C 455 LYS cc_start: 0.7455 (mttm) cc_final: 0.7122 (ttmm) REVERT: D 243 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: D 277 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.6605 (tm-30) REVERT: D 399 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6967 (pp20) REVERT: E 179 MET cc_start: 0.6381 (mmm) cc_final: 0.5643 (tmm) REVERT: E 277 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: F 277 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: F 438 LYS cc_start: 0.7462 (mttm) cc_final: 0.6993 (mtmp) REVERT: G 255 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.6732 (p0) REVERT: G 277 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.6812 (tm-30) REVERT: G 455 LYS cc_start: 0.7543 (mtpp) cc_final: 0.7056 (ptpt) outliers start: 138 outliers final: 76 residues processed: 494 average time/residue: 0.5874 time to fit residues: 352.0609 Evaluate side-chains 460 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 372 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 203 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 308 optimal weight: 9.9990 chunk 227 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 50 optimal weight: 0.0050 chunk 135 optimal weight: 1.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 478 GLN E 368 GLN E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.187873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.134652 restraints weight = 33195.905| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.85 r_work: 0.3214 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31460 Z= 0.163 Angle : 0.588 12.486 42632 Z= 0.302 Chirality : 0.045 0.224 4856 Planarity : 0.004 0.039 5352 Dihedral : 9.266 89.718 4458 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.21 % Favored : 94.35 % Rotamer: Outliers : 4.24 % Allowed : 17.02 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 are not related in a simple way. whole: -0.02 (0.13), residues: 3896 helix: 0.92 (0.14), residues: 1472 sheet: 0.65 (0.24), residues: 376 loop : -0.82 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.014 0.002 TYR G 348 PHE 0.010 0.002 PHE F 24 HIS 0.003 0.001 HIS H 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (31448) covalent geometry : angle 0.58835 / 0.30 (42632) hydrogen bonds : bond 0.04126 / 2.80 ( 1137) hydrogen bonds : angle 4.95122 / 3.54 ( 3192) Misc. bond : bond 0.00123 / 0.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 380 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7272 (m-30) cc_final: 0.6933 (m-30) REVERT: A 277 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8312 (tt0) REVERT: A 296 ASN cc_start: 0.8128 (m110) cc_final: 0.7630 (p0) REVERT: A 399 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6904 (pp20) REVERT: A 438 LYS cc_start: 0.7310 (mmmt) cc_final: 0.6814 (mtmp) REVERT: A 455 LYS cc_start: 0.7559 (mtpp) cc_final: 0.7182 (ptpt) REVERT: B 255 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6619 (p0) REVERT: B 455 LYS cc_start: 0.7583 (mtpp) cc_final: 0.7268 (ptpt) REVERT: C 255 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6678 (p0) REVERT: C 277 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.7640 (tm-30) REVERT: C 399 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6963 (pp20) REVERT: C 455 LYS cc_start: 0.7478 (mttm) cc_final: 0.7153 (ttmm) REVERT: D 243 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: D 255 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6663 (p0) REVERT: D 277 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.6701 (tm-30) REVERT: D 399 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6962 (pp20) REVERT: E 162 ASP cc_start: 0.7161 (m-30) cc_final: 0.6832 (m-30) REVERT: E 179 MET cc_start: 0.6610 (mmm) cc_final: 0.5752 (tmm) REVERT: E 455 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7579 (ptmm) REVERT: F 206 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.5878 (ptpp) REVERT: F 277 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: G 255 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.6738 (p0) REVERT: G 277 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.6820 (tm-30) REVERT: G 455 LYS cc_start: 0.7535 (mtpp) cc_final: 0.7047 (ptpt) REVERT: H 455 LYS cc_start: 0.7640 (mtpp) cc_final: 0.7215 (ptpt) outliers start: 136 outliers final: 83 residues processed: 487 average time/residue: 0.6144 time to fit residues: 360.6817 Evaluate side-chains 473 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 375 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 269 optimal weight: 2.9990 chunk 370 optimal weight: 0.8980 chunk 237 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 309 optimal weight: 5.9990 chunk 152 optimal weight: 0.0370 chunk 271 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 312 ASN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 478 GLN E 368 GLN E 466 HIS E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 312 ASN H 368 GLN H 478 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.187294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.134214 restraints weight = 33070.252| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.84 r_work: 0.3191 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31460 Z= 0.186 Angle : 0.603 11.907 42632 Z= 0.311 Chirality : 0.046 0.227 4856 Planarity : 0.004 0.039 5352 Dihedral : 9.242 87.356 4452 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.93 % Favored : 94.64 % Rotamer: Outliers : 4.30 % Allowed : 17.46 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 are not related in a simple way. whole: -0.17 (0.13), residues: 3896 helix: 0.88 (0.14), residues: 1472 sheet: -0.22 (0.20), residues: 528 loop : -0.83 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 356 TYR 0.015 0.002 TYR B 348 PHE 0.011 0.002 PHE F 24 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (31448) covalent geometry : angle 0.60335 / 0.31 (42632) hydrogen bonds : bond 0.04332 / 2.95 ( 1137) hydrogen bonds : angle 4.98498 / 3.56 ( 3192) Misc. bond : bond 0.00124 / 0.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 378 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.5485 (OUTLIER) cc_final: 0.5170 (mmm160) REVERT: A 296 ASN cc_start: 0.8125 (m110) cc_final: 0.7612 (p0) REVERT: A 399 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6913 (pp20) REVERT: A 438 LYS cc_start: 0.7277 (mmtt) cc_final: 0.6781 (mtmp) REVERT: A 512 ARG cc_start: 0.7167 (ttp80) cc_final: 0.6952 (ttp80) REVERT: B 206 LYS cc_start: 0.6833 (OUTLIER) cc_final: 0.6370 (ptpp) REVERT: B 255 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6601 (p0) REVERT: B 455 LYS cc_start: 0.7584 (mtpp) cc_final: 0.7256 (ptpt) REVERT: C 255 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.6661 (p0) REVERT: C 399 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6965 (pp20) REVERT: C 455 LYS cc_start: 0.7571 (mttm) cc_final: 0.7235 (ttmm) REVERT: D 243 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: D 255 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.6640 (p0) REVERT: D 277 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.6724 (tm-30) REVERT: E 162 ASP cc_start: 0.7203 (m-30) cc_final: 0.6870 (m-30) REVERT: E 179 MET cc_start: 0.6677 (mmm) cc_final: 0.5767 (tmm) REVERT: E 455 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7549 (ptmm) REVERT: F 277 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: F 455 LYS cc_start: 0.7585 (mttm) cc_final: 0.7095 (ttmm) REVERT: G 255 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.6726 (p0) REVERT: G 277 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.6806 (tm-30) REVERT: H 277 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: H 399 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6965 (pp20) REVERT: H 455 LYS cc_start: 0.7657 (mtpp) cc_final: 0.7204 (ptpt) outliers start: 138 outliers final: 91 residues processed: 484 average time/residue: 0.6189 time to fit residues: 360.6352 Evaluate side-chains 485 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 379 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 450 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 353 optimal weight: 2.9990 chunk 382 optimal weight: 0.8980 chunk 380 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 131 optimal weight: 0.5980 chunk 266 optimal weight: 6.9990 chunk 99 optimal weight: 0.0010 chunk 265 optimal weight: 8.9990 chunk 281 optimal weight: 2.9990 chunk 387 optimal weight: 1.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 478 GLN E 368 GLN E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.187716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.134804 restraints weight = 33253.090| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.85 r_work: 0.3207 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 31460 Z= 0.162 Angle : 0.588 10.422 42632 Z= 0.302 Chirality : 0.045 0.215 4856 Planarity : 0.004 0.038 5352 Dihedral : 9.064 81.131 4451 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.16 % Favored : 94.40 % Rotamer: Outliers : 4.08 % Allowed : 17.67 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 are not related in a simple way. whole: -0.03 (0.13), residues: 3896 helix: 0.95 (0.14), residues: 1472 sheet: 0.17 (0.22), residues: 472 loop : -0.80 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 356 TYR 0.014 0.002 TYR E 348 PHE 0.010 0.002 PHE F 24 HIS 0.003 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (31448) covalent geometry : angle 0.58804 / 0.30 (42632) hydrogen bonds : bond 0.04067 / 2.76 ( 1137) hydrogen bonds : angle 4.93172 / 3.53 ( 3192) Misc. bond : bond 0.00106 / 0.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 386 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.5662 (OUTLIER) cc_final: 0.5332 (mmm160) REVERT: A 255 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.6726 (p0) REVERT: A 296 ASN cc_start: 0.8128 (m110) cc_final: 0.7619 (p0) REVERT: A 399 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6890 (pp20) REVERT: A 438 LYS cc_start: 0.7251 (mmtt) cc_final: 0.6769 (mtmp) REVERT: A 455 LYS cc_start: 0.7587 (mtpp) cc_final: 0.7139 (ptpt) REVERT: B 255 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.6618 (p0) REVERT: B 455 LYS cc_start: 0.7571 (mtpp) cc_final: 0.7264 (ptpt) REVERT: C 255 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6672 (p0) REVERT: C 399 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6933 (pp20) REVERT: C 455 LYS cc_start: 0.7559 (mttm) cc_final: 0.7260 (ttmm) REVERT: D 243 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7542 (mt0) REVERT: D 255 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6627 (p0) REVERT: D 277 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.6730 (tm-30) REVERT: E 162 ASP cc_start: 0.7182 (m-30) cc_final: 0.6820 (m-30) REVERT: E 179 MET cc_start: 0.6808 (mmm) cc_final: 0.5880 (tmm) REVERT: E 455 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7492 (ptmm) REVERT: F 277 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.6909 (tm-30) REVERT: F 438 LYS cc_start: 0.7458 (mtpp) cc_final: 0.6984 (mtmt) REVERT: F 455 LYS cc_start: 0.7592 (mttm) cc_final: 0.7148 (ttmm) REVERT: G 255 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.6705 (p0) REVERT: G 277 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: G 455 LYS cc_start: 0.7517 (mtpp) cc_final: 0.7044 (ptpt) REVERT: H 399 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6937 (pp20) REVERT: H 455 LYS cc_start: 0.7628 (mtpp) cc_final: 0.7213 (ptpt) outliers start: 131 outliers final: 94 residues processed: 487 average time/residue: 0.6120 time to fit residues: 359.3459 Evaluate side-chains 488 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 380 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 196 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 103 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 366 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 312 ASN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 478 GLN E 368 GLN E 466 HIS E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.188997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136398 restraints weight = 33193.299| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.84 r_work: 0.3236 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31460 Z= 0.122 Angle : 0.555 9.398 42632 Z= 0.284 Chirality : 0.044 0.200 4856 Planarity : 0.004 0.037 5352 Dihedral : 8.785 77.331 4446 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.83 % Favored : 94.74 % Rotamer: Outliers : 3.71 % Allowed : 18.20 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 are not related in a simple way. whole: 0.15 (0.14), residues: 3896 helix: 1.11 (0.14), residues: 1472 sheet: 0.25 (0.22), residues: 472 loop : -0.69 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 182 TYR 0.012 0.001 TYR H 353 PHE 0.010 0.001 PHE B 401 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (31448) covalent geometry : angle 0.55495 / 0.28 (42632) hydrogen bonds : bond 0.03554 / 2.41 ( 1137) hydrogen bonds : angle 4.83439 / 3.46 ( 3192) Misc. bond : bond 0.00066 / 0.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 400 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8126 (tp30) cc_final: 0.7288 (mp0) REVERT: A 296 ASN cc_start: 0.8126 (m110) cc_final: 0.7631 (p0) REVERT: A 399 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6899 (pp20) REVERT: A 438 LYS cc_start: 0.7288 (mmtt) cc_final: 0.6803 (mtmp) REVERT: A 455 LYS cc_start: 0.7521 (mtpp) cc_final: 0.7085 (ptpt) REVERT: B 255 ASP cc_start: 0.7302 (p0) cc_final: 0.6686 (p0) REVERT: B 455 LYS cc_start: 0.7512 (mtpp) cc_final: 0.7232 (ptpt) REVERT: C 255 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.6676 (p0) REVERT: C 277 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.6909 (tm-30) REVERT: C 399 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6917 (pp20) REVERT: C 455 LYS cc_start: 0.7406 (mttm) cc_final: 0.7137 (ttmm) REVERT: D 243 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7518 (mt0) REVERT: D 255 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6642 (p0) REVERT: D 277 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.6664 (tm-30) REVERT: E 162 ASP cc_start: 0.7203 (m-30) cc_final: 0.6879 (m-30) REVERT: E 179 MET cc_start: 0.6826 (mmm) cc_final: 0.5912 (tmm) REVERT: E 277 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: E 455 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7458 (ptmm) REVERT: F 277 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.6932 (tm-30) REVERT: F 438 LYS cc_start: 0.7479 (mtpp) cc_final: 0.6981 (mtmt) REVERT: F 455 LYS cc_start: 0.7449 (mttm) cc_final: 0.7041 (ttmm) REVERT: G 277 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.6860 (tm-30) REVERT: G 455 LYS cc_start: 0.7453 (mtpp) cc_final: 0.7023 (ptpt) REVERT: H 255 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.6716 (p0) REVERT: H 399 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6930 (pp20) REVERT: H 455 LYS cc_start: 0.7542 (mtpp) cc_final: 0.7138 (ptpt) outliers start: 119 outliers final: 79 residues processed: 490 average time/residue: 0.6042 time to fit residues: 357.5397 Evaluate side-chains 478 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 386 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 450 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 259 optimal weight: 4.9990 chunk 362 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 326 optimal weight: 0.9980 chunk 289 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 246 optimal weight: 0.4980 chunk 291 optimal weight: 0.7980 chunk 153 optimal weight: 0.3980 chunk 213 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 312 ASN A 368 GLN A 466 HIS A 478 GLN B 368 GLN B 466 HIS B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 312 ASN D 368 GLN D 478 GLN E 368 GLN E 466 HIS E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 441 GLN G 466 HIS G 478 GLN H 312 ASN H 368 GLN H 466 HIS H 478 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.189518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137017 restraints weight = 33115.397| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.86 r_work: 0.3243 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31460 Z= 0.117 Angle : 0.561 13.874 42632 Z= 0.283 Chirality : 0.043 0.222 4856 Planarity : 0.004 0.036 5352 Dihedral : 8.585 77.174 4443 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.77 % Favored : 94.79 % Rotamer: Outliers : 3.12 % Allowed : 19.08 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 are not related in a simple way. whole: 0.23 (0.14), residues: 3896 helix: 1.17 (0.14), residues: 1472 sheet: 0.28 (0.22), residues: 472 loop : -0.63 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 512 TYR 0.012 0.001 TYR H 353 PHE 0.009 0.001 PHE H 456 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (31448) covalent geometry : angle 0.56124 / 0.28 (42632) hydrogen bonds : bond 0.03440 / 2.33 ( 1137) hydrogen bonds : angle 4.78139 / 3.43 ( 3192) Misc. bond : bond 0.00061 / 0.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 389 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8086 (tp30) cc_final: 0.7194 (mp0) REVERT: A 399 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6918 (pp20) REVERT: A 438 LYS cc_start: 0.7259 (mmtt) cc_final: 0.6785 (mtmp) REVERT: A 455 LYS cc_start: 0.7481 (mtpp) cc_final: 0.7070 (ptpt) REVERT: B 255 ASP cc_start: 0.7289 (p0) cc_final: 0.6636 (p0) REVERT: B 455 LYS cc_start: 0.7462 (mtpp) cc_final: 0.7109 (ttmm) REVERT: C 255 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.6664 (p0) REVERT: C 277 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: C 399 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6919 (pp20) REVERT: C 455 LYS cc_start: 0.7309 (mttm) cc_final: 0.7057 (ttmm) REVERT: D 255 ASP cc_start: 0.7347 (p0) cc_final: 0.6686 (p0) REVERT: D 277 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.6648 (tm-30) REVERT: E 162 ASP cc_start: 0.7241 (m-30) cc_final: 0.6922 (m-30) REVERT: E 179 MET cc_start: 0.6850 (mmm) cc_final: 0.5939 (tmm) REVERT: E 277 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: E 455 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7436 (ptmm) REVERT: F 277 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.6850 (tm-30) REVERT: F 438 LYS cc_start: 0.7488 (mtpp) cc_final: 0.6992 (mtmt) REVERT: F 455 LYS cc_start: 0.7327 (mttm) cc_final: 0.6912 (ttmm) REVERT: G 277 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.6868 (tm-30) REVERT: G 455 LYS cc_start: 0.7407 (mtpp) cc_final: 0.7061 (ptpt) REVERT: H 255 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6702 (p0) REVERT: H 399 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6947 (pp20) REVERT: H 455 LYS cc_start: 0.7495 (mtpp) cc_final: 0.7114 (ptpt) outliers start: 100 outliers final: 74 residues processed: 466 average time/residue: 0.6156 time to fit residues: 344.6601 Evaluate side-chains 473 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 388 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 450 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 346 optimal weight: 0.9980 chunk 356 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 chunk 330 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 325 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 287 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 312 ASN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 466 HIS E 368 GLN E 466 HIS E 478 GLN F 368 GLN F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.189076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136432 restraints weight = 33173.048| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.85 r_work: 0.3233 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 31460 Z= 0.196 Angle : 0.764 59.200 42632 Z= 0.431 Chirality : 0.047 0.435 4856 Planarity : 0.004 0.064 5352 Dihedral : 8.528 77.297 4437 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.75 % Favored : 94.82 % Rotamer: Outliers : 2.96 % Allowed : 19.39 % Favored : 77.65 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 are not related in a simple way. whole: 0.20 (0.14), residues: 3896 helix: 1.11 (0.14), residues: 1472 sheet: 0.27 (0.22), residues: 472 loop : -0.64 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 356 TYR 0.013 0.002 TYR B 348 PHE 0.008 0.001 PHE C 24 HIS 0.003 0.001 HIS H 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (31448) covalent geometry : angle 0.76427 / 0.43 (42632) hydrogen bonds : bond 0.03640 / 2.47 ( 1137) hydrogen bonds : angle 4.78089 / 3.43 ( 3192) Misc. bond : bond 0.00102 / 0.08 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 384 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8086 (tp30) cc_final: 0.7182 (mp0) REVERT: A 399 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6918 (pp20) REVERT: A 438 LYS cc_start: 0.7266 (mmtt) cc_final: 0.6792 (mtmp) REVERT: A 455 LYS cc_start: 0.7478 (mtpp) cc_final: 0.7067 (ptpt) REVERT: B 255 ASP cc_start: 0.7282 (p0) cc_final: 0.6636 (p0) REVERT: B 455 LYS cc_start: 0.7455 (mtpp) cc_final: 0.7104 (ttmm) REVERT: C 255 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6696 (p0) REVERT: C 277 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.6860 (tm-30) REVERT: C 399 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6908 (pp20) REVERT: C 455 LYS cc_start: 0.7316 (mttm) cc_final: 0.7064 (ttmm) REVERT: D 255 ASP cc_start: 0.7350 (p0) cc_final: 0.6690 (p0) REVERT: D 277 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.6648 (tm-30) REVERT: E 103 GLU cc_start: 0.8041 (tp30) cc_final: 0.7207 (mp0) REVERT: E 162 ASP cc_start: 0.7254 (m-30) cc_final: 0.6936 (m-30) REVERT: E 179 MET cc_start: 0.6865 (mmm) cc_final: 0.5951 (tmm) REVERT: E 277 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.7042 (tm-30) REVERT: E 455 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7457 (ptmm) REVERT: F 277 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.6895 (tm-30) REVERT: F 438 LYS cc_start: 0.7469 (mtpp) cc_final: 0.6989 (mtmt) REVERT: F 455 LYS cc_start: 0.7314 (mttm) cc_final: 0.6903 (ttmm) REVERT: F 510 GLU cc_start: 0.7207 (tp30) cc_final: 0.6661 (mp0) REVERT: G 277 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.6819 (tm-30) REVERT: G 455 LYS cc_start: 0.7408 (mtpp) cc_final: 0.7060 (ptpt) REVERT: H 255 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.6715 (p0) REVERT: H 277 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.6486 (tm-30) REVERT: H 399 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6934 (pp20) REVERT: H 455 LYS cc_start: 0.7498 (mtpp) cc_final: 0.7111 (ptpt) outliers start: 95 outliers final: 75 residues processed: 453 average time/residue: 0.6096 time to fit residues: 330.6444 Evaluate side-chains 469 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 382 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 450 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 337 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 334 optimal weight: 0.8980 chunk 328 optimal weight: 0.9990 chunk 381 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 372 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 312 ASN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN E 368 GLN E 478 GLN F 368 GLN F 441 GLN F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.189078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.136529 restraints weight = 33194.895| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.86 r_work: 0.3232 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 31460 Z= 0.196 Angle : 0.764 59.200 42632 Z= 0.431 Chirality : 0.047 0.435 4856 Planarity : 0.004 0.064 5352 Dihedral : 8.519 77.297 4436 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.75 % Favored : 94.82 % Rotamer: Outliers : 2.77 % Allowed : 19.58 % Favored : 77.65 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 are not related in a simple way. whole: 0.20 (0.14), residues: 3896 helix: 1.11 (0.14), residues: 1472 sheet: 0.27 (0.22), residues: 472 loop : -0.64 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 356 TYR 0.013 0.002 TYR B 348 PHE 0.008 0.001 PHE C 24 HIS 0.003 0.001 HIS H 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (31448) covalent geometry : angle 0.76427 / 0.43 (42632) hydrogen bonds : bond 0.03640 / 2.47 ( 1137) hydrogen bonds : angle 4.78089 / 3.43 ( 3192) Misc. bond : bond 0.00102 / 0.08 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13439.14 seconds wall clock time: 229 minutes 19.54 seconds (13759.54 seconds total)