Starting phenix.real_space_refine on Wed May 28 21:20:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8f_29848/05_2025/8g8f_29848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8f_29848/05_2025/8g8f_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g8f_29848/05_2025/8g8f_29848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8f_29848/05_2025/8g8f_29848.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8f_29848/05_2025/8g8f_29848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8f_29848/05_2025/8g8f_29848.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.280 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 17.38, per 1000 atoms: 0.56 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: 8.92 Conformation dependent library (CDL) restraints added in 4.8 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: 4.34 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: 12.68 Time building geometry restraints manager: 9.91 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: 18646 35.33 - 70.67: 824 70.67 - 106.00: 70 106.00 - 141.34: 3 141.34 - 176.67: 1 Dihedral angle restraints: 19544 sinusoidal: 8376 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 19541 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.280 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 71.950 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.170 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 18.177 176.675 12408 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.58 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (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 HIS 0.003 0.001 HIS A 454 PHE 0.017 0.001 PHE G 165 TYR 0.012 0.001 TYR E 348 ARG 0.011 0.000 ARG E 182 Details of bonding type rmsd hydrogen bonds : bond 0.13789 ( 1137) hydrogen bonds : angle 6.29641 ( 3192) covalent geometry : bond 0.00697 (31448) covalent geometry : angle 1.02024 (42632) Misc. bond : bond 0.45805 ( 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 : 3.478 Fit side-chains 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: 0.9095 (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: 49 residues processed: 424 average time/residue: 1.2928 time to fit residues: 655.4887 Evaluate side-chains 411 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 361 time to evaluate : 3.469 ------------------------------------------------------------------------------- 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 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 331 optimal weight: 5.9990 chunk 297 optimal weight: 2.9990 chunk 164 optimal weight: 30.0000 chunk 101 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 158 optimal weight: 20.0000 chunk 307 optimal weight: 4.9990 chunk 118 optimal weight: 0.0870 chunk 186 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 chunk 355 optimal weight: 7.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 277 GLN A 343 GLN A 368 GLN A 441 GLN A 466 HIS A 478 GLN B 21 GLN B 93 HIS B 253 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 466 HIS 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: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.188174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.134947 restraints weight = 33027.795| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.83 r_work: 0.3197 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 31460 Z= 0.196 Angle : 0.649 12.980 42632 Z= 0.338 Chirality : 0.047 0.203 4856 Planarity : 0.005 0.041 5352 Dihedral : 14.475 163.016 5371 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.34 % Favored : 94.22 % Rotamer: Outliers : 3.93 % Allowed : 15.24 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 3896 helix: 0.64 (0.14), residues: 1488 sheet: -0.35 (0.20), residues: 528 loop : -0.94 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 454 PHE 0.014 0.002 PHE H 456 TYR 0.016 0.002 TYR E 348 ARG 0.007 0.001 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 1137) hydrogen bonds : angle 5.20544 ( 3192) covalent geometry : bond 0.00459 (31448) covalent geometry : angle 0.64921 (42632) Misc. bond : bond 0.00214 ( 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 504 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 378 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.5739 (OUTLIER) cc_final: 0.5529 (ptpp) REVERT: B 399 GLU cc_start: 0.7144 (pp20) cc_final: 0.6938 (pp20) REVERT: C 255 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6660 (p0) REVERT: C 277 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: D 277 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.6605 (tm-30) REVERT: E 179 MET cc_start: 0.5919 (mmm) cc_final: 0.4837 (tmm) REVERT: F 206 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6674 (pmmt) REVERT: F 277 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.7006 (tm-30) REVERT: F 438 LYS cc_start: 0.7423 (mttm) cc_final: 0.7210 (mttm) REVERT: F 456 PHE cc_start: 0.7984 (t80) cc_final: 0.7770 (t80) REVERT: G 277 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.6824 (tm-30) REVERT: G 438 LYS cc_start: 0.7505 (mtmt) cc_final: 0.7061 (mmmt) REVERT: H 277 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.6613 (tm-30) outliers start: 126 outliers final: 64 residues processed: 485 average time/residue: 1.2358 time to fit residues: 722.7413 Evaluate side-chains 437 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 365 time to evaluate : 3.114 ------------------------------------------------------------------------------- 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 417 LEU Chi-restraints excluded: chain A residue 420 MET 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 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 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 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 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 255 ASP 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 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 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 6 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 346 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 251 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 478 GLN B 21 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 441 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 = 0.4063 r_free = 0.4063 target = 0.188792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135452 restraints weight = 33320.037| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.85 r_work: 0.3228 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31460 Z= 0.151 Angle : 0.586 12.847 42632 Z= 0.304 Chirality : 0.045 0.212 4856 Planarity : 0.004 0.041 5352 Dihedral : 13.690 123.188 5361 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.11 % Favored : 94.46 % Rotamer: Outliers : 4.11 % Allowed : 15.84 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.13), residues: 3896 helix: 0.81 (0.14), residues: 1488 sheet: 0.57 (0.24), residues: 376 loop : -0.91 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 454 PHE 0.011 0.001 PHE A 456 TYR 0.012 0.001 TYR E 348 ARG 0.003 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 1137) hydrogen bonds : angle 5.00200 ( 3192) covalent geometry : bond 0.00347 (31448) covalent geometry : angle 0.58578 (42632) Misc. bond : bond 0.00162 ( 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 516 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 384 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7193 (m-30) cc_final: 0.6861 (m-30) REVERT: A 296 ASN cc_start: 0.8124 (m110) cc_final: 0.7633 (p0) REVERT: A 455 LYS cc_start: 0.7534 (mtpp) cc_final: 0.7159 (ptpt) REVERT: B 455 LYS cc_start: 0.7661 (mtpp) cc_final: 0.7335 (ptpt) REVERT: C 255 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6659 (p0) REVERT: C 277 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: C 399 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6926 (pp20) REVERT: D 255 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6708 (p0) REVERT: D 399 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6945 (pp20) REVERT: E 179 MET cc_start: 0.6128 (mmm) cc_final: 0.5404 (tmm) REVERT: E 277 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: F 277 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.6921 (tm-30) REVERT: F 438 LYS cc_start: 0.7420 (mttm) cc_final: 0.6921 (mtmp) REVERT: F 456 PHE cc_start: 0.8031 (t80) cc_final: 0.7830 (t80) REVERT: G 277 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.6830 (tm-30) outliers start: 132 outliers final: 77 residues processed: 483 average time/residue: 1.2057 time to fit residues: 705.4821 Evaluate side-chains 449 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 364 time to evaluate : 3.173 ------------------------------------------------------------------------------- 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 292 ASP 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 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 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 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 410 LYS 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 185 LEU 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 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 410 LYS 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 255 ASP Chi-restraints excluded: chain G residue 277 GLN 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 292 ASP 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 11 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 278 optimal weight: 0.5980 chunk 304 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 320 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.188858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.135598 restraints weight = 33205.535| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.86 r_work: 0.3227 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31460 Z= 0.146 Angle : 0.575 12.678 42632 Z= 0.297 Chirality : 0.045 0.216 4856 Planarity : 0.004 0.038 5352 Dihedral : 12.948 89.282 5349 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.90 % Favored : 94.66 % Rotamer: Outliers : 4.58 % Allowed : 16.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3896 helix: 0.96 (0.14), residues: 1472 sheet: 0.64 (0.24), residues: 376 loop : -0.77 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 454 PHE 0.010 0.001 PHE H 456 TYR 0.013 0.001 TYR E 348 ARG 0.003 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 1137) hydrogen bonds : angle 4.91753 ( 3192) covalent geometry : bond 0.00334 (31448) covalent geometry : angle 0.57536 (42632) Misc. bond : bond 0.00154 ( 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 523 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 376 time to evaluate : 3.412 Fit side-chains revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7235 (m-30) cc_final: 0.6887 (m-30) REVERT: A 296 ASN cc_start: 0.8131 (m110) cc_final: 0.7636 (p0) REVERT: A 399 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6864 (pp20) REVERT: A 438 LYS cc_start: 0.7317 (mmpt) cc_final: 0.6744 (mtmt) REVERT: A 455 LYS cc_start: 0.7532 (mtpp) cc_final: 0.7094 (ttmm) REVERT: B 206 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6460 (ptpp) REVERT: B 255 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6671 (p0) REVERT: B 399 GLU cc_start: 0.7153 (pp20) cc_final: 0.6919 (pp20) REVERT: B 438 LYS cc_start: 0.7433 (mmtt) cc_final: 0.6874 (mtmt) REVERT: B 455 LYS cc_start: 0.7543 (mtpp) cc_final: 0.7108 (ttmm) REVERT: C 255 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6675 (p0) REVERT: C 277 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.6940 (tm-30) REVERT: C 399 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6940 (pp20) REVERT: D 243 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7571 (mt0) REVERT: D 277 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.6621 (tm-30) REVERT: D 399 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7012 (pp20) REVERT: E 162 ASP cc_start: 0.7206 (m-30) cc_final: 0.6888 (m-30) REVERT: E 179 MET cc_start: 0.6366 (mmm) cc_final: 0.5653 (tmm) REVERT: E 277 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: F 206 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6602 (pmmt) REVERT: F 277 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: F 438 LYS cc_start: 0.7450 (mttm) cc_final: 0.7232 (mttm) REVERT: F 455 LYS cc_start: 0.7472 (mttm) cc_final: 0.6980 (ttmm) REVERT: F 456 PHE cc_start: 0.8053 (t80) cc_final: 0.7828 (t80) REVERT: G 255 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.6730 (p0) REVERT: G 277 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.6828 (tm-30) REVERT: G 455 LYS cc_start: 0.7518 (mtpp) cc_final: 0.7125 (ptpt) REVERT: H 455 LYS cc_start: 0.7592 (mtpp) cc_final: 0.7251 (ptpt) outliers start: 147 outliers final: 78 residues processed: 488 average time/residue: 1.2174 time to fit residues: 721.8107 Evaluate side-chains 462 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 370 time to evaluate : 3.625 ------------------------------------------------------------------------------- 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 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 292 ASP 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 182 ARG Chi-restraints excluded: chain D residue 243 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 361 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 410 LYS 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 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 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 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 410 LYS 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 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 229 optimal weight: 0.5980 chunk 342 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 296 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 250 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 308 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN 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 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 = 0.4063 r_free = 0.4063 target = 0.188766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135413 restraints weight = 33062.694| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.83 r_work: 0.3230 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31460 Z= 0.143 Angle : 0.570 12.157 42632 Z= 0.296 Chirality : 0.045 0.222 4856 Planarity : 0.004 0.038 5352 Dihedral : 12.613 89.002 5345 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.95 % Favored : 94.61 % Rotamer: Outliers : 4.46 % Allowed : 16.86 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3896 helix: 1.02 (0.14), residues: 1472 sheet: 0.67 (0.24), residues: 376 loop : -0.75 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 454 PHE 0.010 0.001 PHE F 24 TYR 0.013 0.001 TYR F 348 ARG 0.003 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 1137) hydrogen bonds : angle 4.88358 ( 3192) covalent geometry : bond 0.00328 (31448) covalent geometry : angle 0.57033 (42632) Misc. bond : bond 0.00148 ( 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 526 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 383 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7193 (m-30) cc_final: 0.6868 (m-30) REVERT: A 296 ASN cc_start: 0.8121 (m110) cc_final: 0.7635 (p0) REVERT: A 399 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6860 (pp20) REVERT: A 455 LYS cc_start: 0.7514 (mtpp) cc_final: 0.7093 (ttmm) REVERT: B 206 LYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6409 (ptpp) REVERT: B 255 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6659 (p0) REVERT: B 399 GLU cc_start: 0.7154 (pp20) cc_final: 0.6929 (pp20) REVERT: B 438 LYS cc_start: 0.7403 (mmtt) cc_final: 0.6866 (mtmt) REVERT: B 455 LYS cc_start: 0.7534 (mtpp) cc_final: 0.7129 (ttmm) REVERT: C 255 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6682 (p0) REVERT: C 277 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: C 399 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6905 (pp20) REVERT: C 455 LYS cc_start: 0.7431 (mttm) cc_final: 0.7117 (ttmm) REVERT: D 255 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.6662 (p0) REVERT: D 277 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.6641 (tm-30) REVERT: D 399 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6960 (pp20) REVERT: E 162 ASP cc_start: 0.7206 (m-30) cc_final: 0.6870 (m-30) REVERT: E 179 MET cc_start: 0.6599 (mmm) cc_final: 0.5768 (tmm) REVERT: E 277 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: E 455 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7532 (ptmm) REVERT: F 277 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: F 438 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.6944 (mtmp) REVERT: F 455 LYS cc_start: 0.7442 (mttm) cc_final: 0.6968 (ttmm) REVERT: G 277 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.6842 (tm-30) REVERT: G 455 LYS cc_start: 0.7480 (mtpp) cc_final: 0.7123 (ptpt) REVERT: H 277 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: H 399 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6978 (pp20) REVERT: H 455 LYS cc_start: 0.7581 (mtpp) cc_final: 0.7172 (ttmm) outliers start: 143 outliers final: 79 residues processed: 492 average time/residue: 1.2436 time to fit residues: 737.4457 Evaluate side-chains 466 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 371 time to evaluate : 3.642 ------------------------------------------------------------------------------- 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 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 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 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 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 496 SER 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 182 ARG Chi-restraints excluded: chain D residue 255 ASP 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 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 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 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 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 410 LYS Chi-restraints excluded: chain F residue 438 LYS 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 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 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 399 GLU 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 93 optimal weight: 0.9990 chunk 356 optimal weight: 8.9990 chunk 330 optimal weight: 3.9990 chunk 354 optimal weight: 0.9990 chunk 243 optimal weight: 0.0050 chunk 59 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 286 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 298 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 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 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.188851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.135603 restraints weight = 33143.604| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.84 r_work: 0.3211 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31460 Z= 0.140 Angle : 0.569 11.230 42632 Z= 0.294 Chirality : 0.044 0.228 4856 Planarity : 0.004 0.038 5352 Dihedral : 12.356 89.372 5342 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.80 % Favored : 94.76 % Rotamer: Outliers : 4.08 % Allowed : 17.30 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3896 helix: 1.06 (0.14), residues: 1472 sheet: 0.68 (0.24), residues: 376 loop : -0.73 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 454 PHE 0.010 0.001 PHE E 456 TYR 0.013 0.001 TYR E 348 ARG 0.002 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1137) hydrogen bonds : angle 4.85324 ( 3192) covalent geometry : bond 0.00319 (31448) covalent geometry : angle 0.56905 (42632) Misc. bond : bond 0.00137 ( 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 519 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 388 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6705 (p0) REVERT: A 296 ASN cc_start: 0.8130 (m110) cc_final: 0.7638 (p0) REVERT: A 399 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6862 (pp20) REVERT: A 438 LYS cc_start: 0.7444 (mmtt) cc_final: 0.6878 (mtmt) REVERT: A 455 LYS cc_start: 0.7494 (mtpp) cc_final: 0.7077 (ttmm) REVERT: A 512 ARG cc_start: 0.7138 (ttp80) cc_final: 0.6922 (ttp80) REVERT: B 206 LYS cc_start: 0.6818 (OUTLIER) cc_final: 0.6435 (ptpp) REVERT: B 399 GLU cc_start: 0.7185 (pp20) cc_final: 0.6957 (pp20) REVERT: B 438 LYS cc_start: 0.7452 (mmtt) cc_final: 0.6908 (mtmt) REVERT: B 455 LYS cc_start: 0.7499 (mtpp) cc_final: 0.7114 (ttmm) REVERT: C 255 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.6664 (p0) REVERT: C 277 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: C 399 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6887 (pp20) REVERT: C 455 LYS cc_start: 0.7330 (mttm) cc_final: 0.7026 (ttmm) REVERT: D 182 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6762 (tpt90) REVERT: D 255 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.6649 (p0) REVERT: D 277 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.6645 (tm-30) REVERT: D 399 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6955 (pp20) REVERT: D 455 LYS cc_start: 0.7493 (mtpp) cc_final: 0.7049 (ttmm) REVERT: E 162 ASP cc_start: 0.7189 (m-30) cc_final: 0.6851 (m-30) REVERT: E 179 MET cc_start: 0.6595 (mmm) cc_final: 0.5751 (tmm) REVERT: E 277 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: E 455 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7578 (ptmm) REVERT: F 206 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6635 (pmmt) REVERT: F 277 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.6946 (tm-30) REVERT: F 438 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6891 (mtmp) REVERT: F 455 LYS cc_start: 0.7430 (mttm) cc_final: 0.6974 (ttmm) REVERT: G 255 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.6709 (p0) REVERT: G 277 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: G 455 LYS cc_start: 0.7462 (mtpp) cc_final: 0.7054 (ptpt) REVERT: H 255 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6709 (p0) REVERT: H 399 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6925 (pp20) REVERT: H 455 LYS cc_start: 0.7578 (mtpp) cc_final: 0.7164 (ttmm) outliers start: 131 outliers final: 80 residues processed: 489 average time/residue: 1.2658 time to fit residues: 753.7546 Evaluate side-chains 479 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 380 time to evaluate : 3.195 ------------------------------------------------------------------------------- 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 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 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 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 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 182 ARG Chi-restraints excluded: chain D residue 255 ASP 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 312 ASN Chi-restraints excluded: chain D residue 318 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 E residue 154 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 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 383 THR Chi-restraints excluded: chain F residue 410 LYS Chi-restraints excluded: chain F residue 438 LYS 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 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 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 189 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 387 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 247 optimal weight: 0.6980 chunk 291 optimal weight: 2.9990 chunk 338 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 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 = 0.4050 r_free = 0.4050 target = 0.187460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.134348 restraints weight = 33215.260| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.88 r_work: 0.3191 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 31460 Z= 0.185 Angle : 0.608 9.989 42632 Z= 0.314 Chirality : 0.046 0.218 4856 Planarity : 0.004 0.040 5352 Dihedral : 12.368 89.873 5341 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.88 % Favored : 94.69 % Rotamer: Outliers : 3.99 % Allowed : 17.99 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.13), residues: 3896 helix: 0.92 (0.14), residues: 1472 sheet: -0.21 (0.20), residues: 528 loop : -0.79 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 507 PHE 0.012 0.002 PHE F 24 TYR 0.015 0.002 TYR B 348 ARG 0.002 0.000 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 1137) hydrogen bonds : angle 4.96448 ( 3192) covalent geometry : bond 0.00431 (31448) covalent geometry : angle 0.60784 (42632) Misc. bond : bond 0.00147 ( 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 510 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 382 time to evaluate : 3.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.5674 (OUTLIER) cc_final: 0.5378 (mmm160) REVERT: A 296 ASN cc_start: 0.8125 (m110) cc_final: 0.7617 (p0) REVERT: A 455 LYS cc_start: 0.7572 (mtpp) cc_final: 0.7205 (ptpt) REVERT: B 255 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6667 (p0) REVERT: B 399 GLU cc_start: 0.7214 (pp20) cc_final: 0.6926 (pp20) REVERT: B 455 LYS cc_start: 0.7600 (mtpp) cc_final: 0.7282 (ptpt) REVERT: C 255 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.6670 (p0) REVERT: C 399 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6916 (pp20) REVERT: C 455 LYS cc_start: 0.7578 (mttm) cc_final: 0.7276 (ttmm) REVERT: D 255 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.6667 (p0) REVERT: D 277 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.6679 (tm-30) REVERT: E 162 ASP cc_start: 0.7239 (m-30) cc_final: 0.6878 (m-30) REVERT: E 179 MET cc_start: 0.6813 (mmm) cc_final: 0.5918 (tmm) REVERT: E 455 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7632 (ptmm) REVERT: F 206 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6894 (pmmt) REVERT: F 277 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.6938 (tm-30) REVERT: F 438 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6922 (mtmp) REVERT: F 455 LYS cc_start: 0.7595 (mttm) cc_final: 0.7143 (ttmm) REVERT: G 255 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.6696 (p0) REVERT: G 277 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.6820 (tm-30) REVERT: G 455 LYS cc_start: 0.7481 (mtpp) cc_final: 0.7039 (ptpt) REVERT: H 399 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6928 (pp20) REVERT: H 455 LYS cc_start: 0.7640 (mtpp) cc_final: 0.7216 (ptpt) outliers start: 128 outliers final: 92 residues processed: 478 average time/residue: 1.2099 time to fit residues: 697.1161 Evaluate side-chains 484 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 379 time to evaluate : 3.179 ------------------------------------------------------------------------------- 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 277 GLN 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 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 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 450 LYS 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 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 D residue 496 SER Chi-restraints excluded: chain E residue 154 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 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 383 THR Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 438 LYS 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 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 292 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 251 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 363 optimal weight: 5.9990 chunk 339 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 228 optimal weight: 0.6980 chunk 201 optimal weight: 0.8980 chunk 5 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.189548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.136714 restraints weight = 33314.189| |-----------------------------------------------------------------------------| r_work (start): 0.3470 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: 3.75 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 31460 Z= 0.116 Angle : 0.554 10.759 42632 Z= 0.285 Chirality : 0.043 0.199 4856 Planarity : 0.004 0.037 5352 Dihedral : 11.996 89.421 5337 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.29 % Favored : 95.28 % Rotamer: Outliers : 3.55 % Allowed : 18.49 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3896 helix: 1.14 (0.14), residues: 1472 sheet: 0.23 (0.22), residues: 472 loop : -0.65 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 454 PHE 0.010 0.001 PHE C 456 TYR 0.012 0.001 TYR H 353 ARG 0.003 0.000 ARG D 182 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 1137) hydrogen bonds : angle 4.81370 ( 3192) covalent geometry : bond 0.00252 (31448) covalent geometry : angle 0.55421 (42632) Misc. bond : bond 0.00124 ( 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 506 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 392 time to evaluate : 3.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LYS cc_start: 0.7429 (mttm) cc_final: 0.6872 (mtmt) REVERT: A 455 LYS cc_start: 0.7508 (mtpp) cc_final: 0.7090 (ttmm) REVERT: B 103 GLU cc_start: 0.8004 (tp30) cc_final: 0.7202 (mp0) REVERT: B 255 ASP cc_start: 0.7309 (p0) cc_final: 0.6643 (p0) REVERT: B 399 GLU cc_start: 0.7221 (pp20) cc_final: 0.6998 (pp20) REVERT: B 455 LYS cc_start: 0.7509 (mtpp) cc_final: 0.7119 (ttmm) REVERT: C 255 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6622 (p0) REVERT: C 277 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: C 399 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6896 (pp20) REVERT: C 455 LYS cc_start: 0.7317 (mttm) cc_final: 0.7059 (ttmm) REVERT: D 255 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6669 (p0) REVERT: D 277 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.6648 (tm-30) REVERT: D 455 LYS cc_start: 0.7515 (mtpp) cc_final: 0.7083 (ttmm) REVERT: E 162 ASP cc_start: 0.7208 (m-30) cc_final: 0.6886 (m-30) REVERT: E 179 MET cc_start: 0.6762 (mmm) cc_final: 0.5892 (tmm) REVERT: E 277 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: E 455 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7572 (ptmm) REVERT: F 204 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.8028 (t) REVERT: F 206 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6898 (pmmt) REVERT: F 277 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.6852 (tm-30) REVERT: F 438 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6917 (mtmp) REVERT: F 455 LYS cc_start: 0.7424 (mttm) cc_final: 0.7015 (ttmm) REVERT: G 277 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: G 455 LYS cc_start: 0.7410 (mtpp) cc_final: 0.7063 (ptpt) REVERT: H 399 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6915 (pp20) REVERT: H 455 LYS cc_start: 0.7573 (mtpp) cc_final: 0.7144 (ttmm) outliers start: 114 outliers final: 76 residues processed: 484 average time/residue: 1.2259 time to fit residues: 716.4354 Evaluate side-chains 478 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 389 time to evaluate : 3.353 ------------------------------------------------------------------------------- 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 312 ASN 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 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 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 255 ASP 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 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 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 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 204 SER 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 410 LYS Chi-restraints excluded: chain F residue 438 LYS 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 181 LYS 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 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 103 optimal weight: 0.6980 chunk 266 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 348 optimal weight: 0.7980 chunk 278 optimal weight: 2.9990 chunk 365 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 368 GLN D 466 HIS 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 466 HIS H 478 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.189696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136946 restraints weight = 33147.620| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.87 r_work: 0.3225 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31460 Z= 0.121 Angle : 0.562 12.771 42632 Z= 0.287 Chirality : 0.043 0.219 4856 Planarity : 0.004 0.037 5352 Dihedral : 11.779 89.543 5335 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.65 % Favored : 94.92 % Rotamer: Outliers : 2.96 % Allowed : 19.20 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.14), residues: 3896 helix: 1.17 (0.14), residues: 1472 sheet: 0.26 (0.22), residues: 472 loop : -0.61 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 454 PHE 0.012 0.001 PHE C 456 TYR 0.012 0.001 TYR H 353 ARG 0.002 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 1137) hydrogen bonds : angle 4.77215 ( 3192) covalent geometry : bond 0.00269 (31448) covalent geometry : angle 0.56186 (42632) Misc. bond : bond 0.00115 ( 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 484 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 389 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8045 (tp30) cc_final: 0.7164 (mp0) REVERT: A 438 LYS cc_start: 0.7315 (mttm) cc_final: 0.7071 (mmmt) REVERT: A 455 LYS cc_start: 0.7474 (mtpp) cc_final: 0.7075 (ttmm) REVERT: B 103 GLU cc_start: 0.7988 (tp30) cc_final: 0.7155 (mp0) REVERT: B 255 ASP cc_start: 0.7309 (p0) cc_final: 0.6638 (p0) REVERT: B 399 GLU cc_start: 0.7207 (pp20) cc_final: 0.6960 (pp20) REVERT: B 438 LYS cc_start: 0.7442 (mmtp) cc_final: 0.7239 (mmtt) REVERT: B 455 LYS cc_start: 0.7441 (mtpp) cc_final: 0.7071 (ttmm) REVERT: C 255 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.6636 (p0) REVERT: C 277 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.6890 (tm-30) REVERT: C 399 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6890 (pp20) REVERT: C 455 LYS cc_start: 0.7301 (mttm) cc_final: 0.7046 (ttmm) REVERT: D 255 ASP cc_start: 0.7353 (p0) cc_final: 0.6673 (p0) REVERT: D 277 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: D 455 LYS cc_start: 0.7484 (mtpp) cc_final: 0.7066 (ttmm) REVERT: E 103 GLU cc_start: 0.8027 (tp30) cc_final: 0.7188 (mp0) REVERT: E 162 ASP cc_start: 0.7152 (m-30) cc_final: 0.6815 (m-30) REVERT: E 179 MET cc_start: 0.6758 (mmm) cc_final: 0.5870 (tmm) REVERT: E 277 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: E 455 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7617 (ptmm) REVERT: F 204 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.8004 (t) REVERT: F 206 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6910 (pmmt) REVERT: F 277 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: F 438 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6907 (mtmp) REVERT: F 455 LYS cc_start: 0.7311 (mttm) cc_final: 0.6910 (ttmm) REVERT: G 277 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: G 455 LYS cc_start: 0.7394 (mtpp) cc_final: 0.7045 (ptpt) REVERT: H 277 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.6454 (tm-30) REVERT: H 399 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6940 (pp20) REVERT: H 455 LYS cc_start: 0.7543 (mtpp) cc_final: 0.7209 (ptpt) outliers start: 95 outliers final: 68 residues processed: 463 average time/residue: 1.2525 time to fit residues: 698.4495 Evaluate side-chains 461 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 380 time to evaluate : 3.125 ------------------------------------------------------------------------------- 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 383 THR 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 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 420 MET 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 154 LEU 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 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 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 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 204 SER 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 383 THR Chi-restraints excluded: chain F residue 438 LYS 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 181 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 277 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 50 optimal weight: 0.5980 chunk 351 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 309 optimal weight: 0.9980 chunk 198 optimal weight: 0.5980 chunk 237 optimal weight: 10.0000 chunk 257 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 350 optimal weight: 5.9990 chunk 185 optimal weight: 0.0770 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 466 HIS D 478 GLN 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 = 0.4072 r_free = 0.4072 target = 0.189536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.136820 restraints weight = 33169.602| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.86 r_work: 0.3238 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 0.031 31460 Z= 0.130 Angle : 0.567 12.007 42632 Z= 0.289 Chirality : 0.044 0.208 4856 Planarity : 0.004 0.037 5352 Dihedral : 11.738 88.909 5332 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.72 % Favored : 94.84 % Rotamer: Outliers : 2.74 % Allowed : 19.54 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3896 helix: 1.16 (0.14), residues: 1472 sheet: 0.27 (0.22), residues: 472 loop : -0.61 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 454 PHE 0.013 0.001 PHE E 456 TYR 0.013 0.001 TYR A 353 ARG 0.002 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 1137) hydrogen bonds : angle 4.77075 ( 3192) covalent geometry : bond 0.00293 (31448) covalent geometry : angle 0.56658 (42632) Misc. bond : bond 0.00121 ( 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 466 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 378 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8050 (tp30) cc_final: 0.7168 (mp0) REVERT: A 455 LYS cc_start: 0.7473 (mtpp) cc_final: 0.7074 (ttmm) REVERT: B 103 GLU cc_start: 0.8000 (tp30) cc_final: 0.7154 (mp0) REVERT: B 255 ASP cc_start: 0.7314 (p0) cc_final: 0.6644 (p0) REVERT: B 399 GLU cc_start: 0.7215 (pp20) cc_final: 0.6971 (pp20) REVERT: B 455 LYS cc_start: 0.7455 (mtpp) cc_final: 0.7084 (ttmm) REVERT: C 255 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.6645 (p0) REVERT: C 277 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: C 399 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6901 (pp20) REVERT: C 455 LYS cc_start: 0.7283 (mttm) cc_final: 0.7034 (ttmm) REVERT: D 255 ASP cc_start: 0.7355 (p0) cc_final: 0.6678 (p0) REVERT: D 277 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.6632 (tm-30) REVERT: D 455 LYS cc_start: 0.7509 (mtpp) cc_final: 0.7086 (ttmm) REVERT: E 103 GLU cc_start: 0.8026 (tp30) cc_final: 0.7175 (mp0) REVERT: E 162 ASP cc_start: 0.7148 (m-30) cc_final: 0.6807 (m-30) REVERT: E 179 MET cc_start: 0.6772 (mmm) cc_final: 0.6010 (tmm) REVERT: E 277 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.7099 (tm-30) REVERT: E 455 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7593 (ptmm) REVERT: F 204 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.7999 (t) REVERT: F 206 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6906 (pmmt) REVERT: F 277 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: F 438 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.6900 (mtmp) REVERT: F 455 LYS cc_start: 0.7315 (mttm) cc_final: 0.6913 (ttmm) REVERT: G 277 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: G 455 LYS cc_start: 0.7400 (mtpp) cc_final: 0.7050 (ptpt) REVERT: H 277 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.6472 (tm-30) REVERT: H 399 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6946 (pp20) REVERT: H 455 LYS cc_start: 0.7554 (mtpp) cc_final: 0.7213 (ptpt) outliers start: 88 outliers final: 67 residues processed: 446 average time/residue: 1.2585 time to fit residues: 673.7296 Evaluate side-chains 461 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 381 time to evaluate : 3.584 ------------------------------------------------------------------------------- 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 383 THR 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 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 420 MET 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 154 LEU 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 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 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 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 204 SER 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 383 THR Chi-restraints excluded: chain F residue 438 LYS 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 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 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 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 365 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 287 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 310 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 176 optimal weight: 0.1980 chunk 112 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.189316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.136440 restraints weight = 33043.663| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.85 r_work: 0.3227 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 31460 Z= 0.172 Angle : 0.694 59.199 42632 Z= 0.376 Chirality : 0.045 0.446 4856 Planarity : 0.004 0.037 5352 Dihedral : 11.740 88.926 5332 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.62 % Favored : 94.94 % Rotamer: Outliers : 2.71 % Allowed : 19.58 % Favored : 77.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3896 helix: 1.15 (0.14), residues: 1472 sheet: 0.26 (0.22), residues: 472 loop : -0.61 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 454 PHE 0.011 0.001 PHE E 456 TYR 0.013 0.001 TYR A 353 ARG 0.002 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 1137) hydrogen bonds : angle 4.77111 ( 3192) covalent geometry : bond 0.00381 (31448) covalent geometry : angle 0.69392 (42632) Misc. bond : bond 0.00139 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27140.69 seconds wall clock time: 466 minutes 47.47 seconds (28007.47 seconds total)