Starting phenix.real_space_refine on Sat Aug 8 23:40:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g8f_29848/08_2026/8g8f_29848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8f_29848/08_2026/8g8f_29848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g8f_29848/08_2026/8g8f_29848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8f_29848/08_2026/8g8f_29848.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g8f_29848/08_2026/8g8f_29848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8f_29848/08_2026/8g8f_29848.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8g8f_29848/08_2026/8g8f_29848.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g8f_29848/08_2026/8g8f_29848.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.280 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 168 5.16 5 C 19248 2.51 5 N 5328 2.21 5 O 6096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30912 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "B" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "C" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "D" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "E" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "F" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "G" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "H" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 5.64, per 1000 atoms: 0.18 Number of scatterers: 30912 At special positions: 0 Unit cell: (160.17, 161.856, 133.194, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 72 15.00 O 6096 8.00 N 5328 7.00 C 19248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.1 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: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 19 through 26 removed outlier: 3.791A pdb=" N CYS A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 96 through 110 removed outlier: 3.683A pdb=" N TYR A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 193 through 205 removed outlier: 3.936A pdb=" N ARG A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.895A pdb=" N TYR A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 316 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'B' and resid 19 through 26 removed outlier: 3.853A pdb=" N CYS B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 96 through 110 removed outlier: 3.639A pdb=" N TYR B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 135 removed outlier: 4.275A pdb=" N PHE B 131 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU B 132 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS B 134 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.685A pdb=" N ARG B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 254 through 267 removed outlier: 3.955A pdb=" N TYR B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.703A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'C' and resid 19 through 25 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 96 through 110 removed outlier: 3.682A pdb=" N TYR C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 132 removed outlier: 3.751A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 193 through 205 removed outlier: 3.505A pdb=" N ARG C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 254 through 267 removed outlier: 4.026A pdb=" N TYR C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.702A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid 19 through 26 removed outlier: 3.804A pdb=" N CYS D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 96 through 110 removed outlier: 3.662A pdb=" N TYR D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 135 removed outlier: 4.597A pdb=" N PHE D 131 " --> pdb=" O ARG D 128 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLU D 132 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS D 134 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 193 through 205 removed outlier: 3.685A pdb=" N ARG D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 254 through 267 removed outlier: 4.037A pdb=" N TYR D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 316 Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'E' and resid 19 through 26 removed outlier: 3.806A pdb=" N CYS E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 96 through 110 removed outlier: 3.722A pdb=" N TYR E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 193 through 205 removed outlier: 3.762A pdb=" N ARG E 203 " --> pdb=" O GLU E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 254 through 267 removed outlier: 4.084A pdb=" N TYR E 258 " --> pdb=" O GLU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 316 removed outlier: 3.722A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'F' and resid 19 through 26 removed outlier: 3.756A pdb=" N CYS F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 96 through 110 removed outlier: 3.657A pdb=" N TYR F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 removed outlier: 3.545A pdb=" N GLU F 132 " --> pdb=" O ARG F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 135 No H-bonds generated for 'chain 'F' and resid 133 through 135' Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 224 through 229 Processing helix chain 'F' and resid 254 through 267 removed outlier: 4.056A pdb=" N TYR F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.676A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid 19 through 26 removed outlier: 3.837A pdb=" N CYS G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 96 through 110 removed outlier: 3.641A pdb=" N TYR G 110 " --> pdb=" O LYS G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 removed outlier: 4.018A pdb=" N GLU G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 135 No H-bonds generated for 'chain 'G' and resid 133 through 135' Processing helix chain 'G' and resid 193 through 205 removed outlier: 3.786A pdb=" N ARG G 203 " --> pdb=" O GLU G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 229 Processing helix chain 'G' and resid 254 through 267 removed outlier: 3.915A pdb=" N TYR G 258 " --> pdb=" O GLU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 316 removed outlier: 3.722A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 356 through 358 No H-bonds generated for 'chain 'G' and resid 356 through 358' Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 416 through 421 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.803A pdb=" N CYS H 26 " --> pdb=" O GLN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 96 through 110 removed outlier: 3.751A pdb=" N TYR H 110 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'H' and resid 193 through 205 removed outlier: 3.638A pdb=" N ARG H 203 " --> pdb=" O GLU H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 229 Processing helix chain 'H' and resid 254 through 267 removed outlier: 4.024A pdb=" N TYR H 258 " --> pdb=" O GLU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 3.554A pdb=" N GLY H 317 " --> pdb=" O LEU H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 355 Processing helix chain 'H' and resid 356 through 358 No H-bonds generated for 'chain 'H' and resid 356 through 358' Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 416 through 421 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.514A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 299 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 145 removed outlier: 3.548A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.168A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.877A pdb=" N SER A 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.716A pdb=" N SER D 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.584A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 299 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.709A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 188 through 189 removed outlier: 6.256A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 401 through 403 removed outlier: 3.689A pdb=" N SER B 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.533A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C 299 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.641A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.123A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 401 through 403 removed outlier: 3.748A pdb=" N SER C 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER D 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.535A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL D 299 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.672A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.010A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.532A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL E 299 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 143 through 145 Processing sheet with id=AD2, first strand: chain 'E' and resid 188 through 189 removed outlier: 6.048A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.822A pdb=" N SER E 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.686A pdb=" N SER H 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.442A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL F 299 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ARG F 322 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.667A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.068A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 401 through 403 removed outlier: 3.667A pdb=" N SER F 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.543A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL G 299 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 143 through 145 Processing sheet with id=AE6, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.191A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 401 through 403 removed outlier: 3.811A pdb=" N SER G 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE9, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AF1, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.502A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL H 299 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.520A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 188 through 189 removed outlier: 6.214A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 1137 hydrogen bonds defined for protein. 3192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.65 Time building geometry restraints manager: 2.98 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: 42210 4.28 - 8.56: 334 8.56 - 12.84: 51 12.84 - 17.12: 19 17.12 - 21.40: 18 Bond angle restraints: 42632 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 120.43 19.44 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.78e+02 ... (remaining 42627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 18052 35.33 - 70.67: 548 70.67 - 106.00: 44 106.00 - 141.34: 3 141.34 - 176.67: 1 Dihedral angle restraints: 18648 sinusoidal: 7480 harmonic: 11168 Sorted by residual: dihedral pdb=" C5' IMP A 603 " pdb=" O5' IMP A 603 " pdb=" P IMP A 603 " pdb=" O2P IMP A 603 " ideal model delta sinusoidal sigma weight residual -168.07 8.61 -176.67 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' IMP H 603 " pdb=" O5' IMP H 603 " pdb=" P IMP H 603 " pdb=" O2P IMP H 603 " ideal model delta sinusoidal sigma weight residual -168.07 -30.70 -137.37 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" C5' IMP G 603 " pdb=" O5' IMP G 603 " pdb=" P IMP G 603 " pdb=" O2P IMP G 603 " ideal model delta sinusoidal sigma weight residual -168.07 -43.27 -124.80 1 2.00e+01 2.50e-03 3.77e+01 ... (remaining 18645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3901 0.057 - 0.113: 823 0.113 - 0.170: 90 0.170 - 0.227: 33 0.227 - 0.284: 9 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=" C2' IMP A 603 " pdb=" C1' IMP A 603 " pdb=" C3' IMP A 603 " pdb=" O2' IMP A 603 " both_signs ideal model delta sigma weight residual False -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C2' IMP F 603 " pdb=" C1' IMP F 603 " pdb=" C3' IMP F 603 " pdb=" O2' IMP F 603 " both_signs ideal model delta sigma weight residual False -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.90e+00 ... (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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain '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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 24.800 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.822 31460 Z= 0.999 Angle : 1.044 21.396 42632 Z= 0.707 Chirality : 0.049 0.284 4856 Planarity : 0.004 0.050 5352 Dihedral : 16.393 176.675 11512 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.98 % Favored : 93.61 % Rotamer: Outliers : 1.87 % Allowed : 17.36 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3896 helix: 0.74 (0.14), residues: 1488 sheet: 0.15 (0.22), residues: 472 loop : -0.91 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 182 TYR 0.012 0.001 TYR E 348 PHE 0.017 0.001 PHE G 165 HIS 0.003 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.45 (31448) covalent geometry : angle 1.04379 / 0.71 (42632) hydrogen bonds : bond 0.13789 / 9.45 ( 1137) hydrogen bonds : angle 6.29641 / 4.51 ( 3192) Misc. bond : bond 0.45805 / 32.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 368 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ASP cc_start: 0.7411 (m-30) cc_final: 0.7093 (m-30) REVERT: B 277 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: D 303 ASN cc_start: 0.9094 (m110) cc_final: 0.8894 (m-40) REVERT: E 179 MET cc_start: 0.5510 (tmm) cc_final: 0.4750 (tmm) REVERT: F 438 LYS cc_start: 0.7332 (mttm) cc_final: 0.7032 (mtmt) outliers start: 60 outliers final: 50 residues processed: 424 average time/residue: 0.5659 time to fit residues: 287.3825 Evaluate side-chains 412 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 361 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 318 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 0.2980 chunk 183 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 HIS A 343 GLN A 368 GLN A 441 GLN A 466 HIS A 478 GLN B 21 GLN B 93 HIS B 343 GLN B 368 GLN B 466 HIS 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: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.189639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135745 restraints weight = 33143.204| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.86 r_work: 0.3218 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31460 Z= 0.141 Angle : 0.631 12.812 42632 Z= 0.321 Chirality : 0.046 0.197 4856 Planarity : 0.004 0.039 5352 Dihedral : 10.373 175.772 4479 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.08 % Favored : 94.48 % Rotamer: Outliers : 3.40 % Allowed : 15.43 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3896 helix: 0.83 (0.14), residues: 1488 sheet: 0.05 (0.22), residues: 472 loop : -0.82 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 161 TYR 0.013 0.001 TYR E 348 PHE 0.013 0.001 PHE H 456 HIS 0.004 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (31448) covalent geometry : angle 0.63121 / 0.32 (42632) hydrogen bonds : bond 0.03982 / 2.69 ( 1137) hydrogen bonds : angle 5.22706 / 3.75 ( 3192) Misc. bond : bond 0.00190 / 0.12 ( 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 481 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 372 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 277 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.6709 (tm-30) REVERT: B 399 GLU cc_start: 0.7079 (pp20) cc_final: 0.6871 (pp20) REVERT: C 255 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.6703 (p0) REVERT: C 277 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.6944 (tm-30) REVERT: D 277 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.6566 (tm-30) REVERT: E 179 MET cc_start: 0.5706 (mmm) cc_final: 0.4965 (tmm) REVERT: F 277 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: F 438 LYS cc_start: 0.7400 (mttm) cc_final: 0.6981 (mtmt) REVERT: G 277 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.6858 (tm-30) REVERT: H 277 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.6578 (tm-30) outliers start: 109 outliers final: 56 residues processed: 469 average time/residue: 0.5489 time to fit residues: 310.8412 Evaluate side-chains 428 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 365 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 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 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 277 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 0.0570 chunk 81 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 390 optimal weight: 1.9990 chunk 361 optimal weight: 8.9990 chunk 317 optimal weight: 0.7980 chunk 213 optimal weight: 10.0000 chunk 319 optimal weight: 3.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 368 GLN A 478 GLN B 253 HIS B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 478 GLN E 368 GLN E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.187552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134153 restraints weight = 33239.188| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.85 r_work: 0.3192 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31460 Z= 0.192 Angle : 0.642 13.028 42632 Z= 0.326 Chirality : 0.047 0.227 4856 Planarity : 0.005 0.048 5352 Dihedral : 9.883 135.242 4465 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.31 % Favored : 94.25 % Rotamer: Outliers : 4.08 % Allowed : 15.52 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.13), residues: 3896 helix: 0.68 (0.14), residues: 1488 sheet: 0.51 (0.24), residues: 376 loop : -0.94 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.016 0.002 TYR G 348 PHE 0.013 0.002 PHE H 456 HIS 0.004 0.001 HIS H 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (31448) covalent geometry : angle 0.64180 / 0.33 (42632) hydrogen bonds : bond 0.04580 / 3.12 ( 1137) hydrogen bonds : angle 5.08555 / 3.62 ( 3192) Misc. bond : bond 0.00151 / 0.11 ( 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 507 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 376 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7301 (m-30) cc_final: 0.6943 (m-30) REVERT: A 296 ASN cc_start: 0.8106 (m110) cc_final: 0.7605 (p0) REVERT: A 438 LYS cc_start: 0.7331 (mmmt) cc_final: 0.6797 (mtmt) REVERT: B 399 GLU cc_start: 0.7181 (pp20) cc_final: 0.6965 (pp20) REVERT: B 438 LYS cc_start: 0.7402 (mmtt) cc_final: 0.6772 (mtmt) REVERT: B 455 LYS cc_start: 0.7684 (mtpp) cc_final: 0.7327 (ptpt) REVERT: C 255 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.6688 (p0) REVERT: C 399 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6951 (pp20) REVERT: D 456 PHE cc_start: 0.8003 (t80) cc_final: 0.7803 (t80) REVERT: E 65 LEU cc_start: 0.9077 (mm) cc_final: 0.8854 (mm) REVERT: E 179 MET cc_start: 0.6220 (mmm) cc_final: 0.5471 (tmm) REVERT: F 438 LYS cc_start: 0.7427 (mttm) cc_final: 0.7203 (mttm) REVERT: G 277 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.6783 (tm-30) REVERT: H 65 LEU cc_start: 0.9085 (mm) cc_final: 0.8880 (mm) outliers start: 131 outliers final: 77 residues processed: 478 average time/residue: 0.5113 time to fit residues: 296.1879 Evaluate side-chains 444 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 364 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 270 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 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 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 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 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 285 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 212 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 282 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 478 GLN E 368 GLN E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.189154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.135989 restraints weight = 33049.136| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.86 r_work: 0.3233 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1306 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= 0.133 Angle : 0.585 12.670 42632 Z= 0.295 Chirality : 0.045 0.214 4856 Planarity : 0.004 0.038 5352 Dihedral : 9.335 101.655 4454 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.72 % Favored : 94.84 % Rotamer: Outliers : 4.40 % Allowed : 16.21 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3896 helix: 0.96 (0.14), residues: 1472 sheet: 0.61 (0.24), residues: 376 loop : -0.75 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 182 TYR 0.012 0.001 TYR A 353 PHE 0.010 0.001 PHE H 456 HIS 0.003 0.001 HIS E 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (31448) covalent geometry : angle 0.58485 / 0.29 (42632) hydrogen bonds : bond 0.03717 / 2.52 ( 1137) hydrogen bonds : angle 4.93642 / 3.53 ( 3192) Misc. bond : bond 0.00111 / 0.08 ( 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 519 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 378 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7180 (m-30) cc_final: 0.6835 (m-30) REVERT: A 296 ASN cc_start: 0.8123 (m110) cc_final: 0.7633 (p0) REVERT: A 399 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6888 (pp20) REVERT: A 438 LYS cc_start: 0.7312 (mmmt) cc_final: 0.6817 (mtmp) REVERT: A 455 LYS cc_start: 0.7551 (mtpp) cc_final: 0.7185 (ptpt) REVERT: B 255 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6667 (p0) REVERT: B 399 GLU cc_start: 0.7176 (pp20) cc_final: 0.6933 (pp20) REVERT: B 438 LYS cc_start: 0.7362 (mmtt) cc_final: 0.6826 (mtmt) REVERT: B 455 LYS cc_start: 0.7573 (mtpp) cc_final: 0.7265 (ptpt) REVERT: C 255 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.6677 (p0) REVERT: C 277 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.6943 (tm-30) REVERT: C 399 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6920 (pp20) REVERT: C 455 LYS cc_start: 0.7475 (mttm) cc_final: 0.7139 (ttmm) REVERT: D 277 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.6576 (tm-30) REVERT: E 162 ASP cc_start: 0.7090 (m-30) cc_final: 0.6762 (m-30) REVERT: E 179 MET cc_start: 0.6319 (mmm) cc_final: 0.5636 (tmm) REVERT: E 277 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: F 277 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.6932 (tm-30) REVERT: F 438 LYS cc_start: 0.7442 (mttm) cc_final: 0.7220 (mttm) REVERT: G 255 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.6754 (p0) REVERT: G 277 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: G 455 LYS cc_start: 0.7535 (mtpp) cc_final: 0.7068 (ptpt) outliers start: 141 outliers final: 78 residues processed: 488 average time/residue: 0.5065 time to fit residues: 299.2841 Evaluate side-chains 458 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 370 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 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 145 THR Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 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 47 ASP 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 F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 203 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 308 optimal weight: 10.0000 chunk 227 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 50 optimal weight: 0.0870 chunk 135 optimal weight: 4.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 478 GLN E 368 GLN E 478 GLN F 48 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.188775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.134999 restraints weight = 33042.492| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.84 r_work: 0.3216 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31460 Z= 0.155 Angle : 0.597 12.396 42632 Z= 0.301 Chirality : 0.045 0.211 4856 Planarity : 0.004 0.039 5352 Dihedral : 9.242 89.820 4451 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.93 % Favored : 94.64 % Rotamer: Outliers : 4.08 % Allowed : 16.83 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.13), residues: 3896 helix: 0.97 (0.14), residues: 1472 sheet: 0.63 (0.24), residues: 376 loop : -0.79 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 322 TYR 0.014 0.002 TYR B 348 PHE 0.010 0.002 PHE D 24 HIS 0.003 0.001 HIS E 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (31448) covalent geometry : angle 0.59734 / 0.30 (42632) hydrogen bonds : bond 0.04007 / 2.72 ( 1137) hydrogen bonds : angle 4.92196 / 3.52 ( 3192) Misc. bond : bond 0.00094 / 0.07 ( 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 506 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 375 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 ASN cc_start: 0.8123 (m110) cc_final: 0.7624 (p0) REVERT: A 399 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6895 (pp20) REVERT: A 438 LYS cc_start: 0.7302 (mmmt) cc_final: 0.6822 (mtmp) REVERT: A 455 LYS cc_start: 0.7545 (mtpp) cc_final: 0.7187 (ptpt) REVERT: B 255 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6667 (p0) REVERT: B 399 GLU cc_start: 0.7210 (pp20) cc_final: 0.6960 (pp20) REVERT: B 455 LYS cc_start: 0.7576 (mtpp) cc_final: 0.7280 (ptpt) REVERT: C 255 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6682 (p0) REVERT: C 277 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: C 399 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6926 (pp20) REVERT: C 455 LYS cc_start: 0.7455 (mttm) cc_final: 0.7139 (ttmm) REVERT: D 255 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.6668 (p0) REVERT: D 277 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.6634 (tm-30) REVERT: E 162 ASP cc_start: 0.7181 (m-30) cc_final: 0.6845 (m-30) REVERT: E 179 MET cc_start: 0.6579 (mmm) cc_final: 0.5709 (tmm) REVERT: E 455 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7569 (ptmm) REVERT: F 206 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6736 (pmmt) REVERT: F 277 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.6959 (tm-30) REVERT: F 438 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6944 (mtmp) REVERT: G 255 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.6723 (p0) REVERT: G 277 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.6827 (tm-30) REVERT: G 455 LYS cc_start: 0.7533 (mtpp) cc_final: 0.7059 (ptpt) REVERT: H 277 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.6588 (tm-30) REVERT: H 455 LYS cc_start: 0.7604 (mtpp) cc_final: 0.7271 (ptpt) outliers start: 131 outliers final: 84 residues processed: 476 average time/residue: 0.5126 time to fit residues: 295.4047 Evaluate side-chains 466 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 368 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 165 PHE 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 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 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 447 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 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 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 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 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 277 GLN Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 450 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 269 optimal weight: 1.9990 chunk 370 optimal weight: 0.9980 chunk 237 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 308 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 309 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 271 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 GLN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 478 GLN E 368 GLN E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.187743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.134595 restraints weight = 33032.892| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.84 r_work: 0.3204 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 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 : 0.004 0.044 31460 Z= 0.170 Angle : 0.607 11.379 42632 Z= 0.307 Chirality : 0.046 0.233 4856 Planarity : 0.004 0.039 5352 Dihedral : 9.212 86.443 4449 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.83 % Favored : 94.74 % Rotamer: Outliers : 4.21 % Allowed : 17.24 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.13), residues: 3896 helix: 0.95 (0.14), residues: 1472 sheet: -0.20 (0.20), residues: 528 loop : -0.78 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.014 0.002 TYR E 348 PHE 0.011 0.002 PHE F 24 HIS 0.003 0.001 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (31448) covalent geometry : angle 0.60727 / 0.31 (42632) hydrogen bonds : bond 0.04168 / 2.83 ( 1137) hydrogen bonds : angle 4.95476 / 3.55 ( 3192) Misc. bond : bond 0.00107 / 0.08 ( 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: 135 poor density : 384 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.5433 (OUTLIER) cc_final: 0.5100 (mmm160) REVERT: A 277 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.6990 (tm-30) REVERT: A 296 ASN cc_start: 0.8133 (m110) cc_final: 0.7622 (p0) REVERT: A 399 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6912 (pp20) REVERT: A 438 LYS cc_start: 0.7249 (mmmt) cc_final: 0.6781 (mtmp) REVERT: A 455 LYS cc_start: 0.7590 (mtpp) cc_final: 0.7185 (ptpt) REVERT: A 512 ARG cc_start: 0.7180 (ttp80) cc_final: 0.6958 (ttp80) REVERT: B 206 LYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5551 (ptpp) REVERT: B 255 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6595 (p0) REVERT: B 399 GLU cc_start: 0.7239 (pp20) cc_final: 0.6955 (pp20) REVERT: B 438 LYS cc_start: 0.7448 (mmtp) cc_final: 0.6911 (mtmt) REVERT: B 455 LYS cc_start: 0.7588 (mtpp) cc_final: 0.7281 (ptpt) REVERT: C 255 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6679 (p0) REVERT: C 399 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6935 (pp20) REVERT: C 455 LYS cc_start: 0.7557 (mttm) cc_final: 0.7261 (ttmm) REVERT: D 182 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6307 (tpt90) REVERT: D 255 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6651 (p0) REVERT: D 277 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.6629 (tm-30) REVERT: E 162 ASP cc_start: 0.7160 (m-30) cc_final: 0.6812 (m-30) REVERT: E 179 MET cc_start: 0.6693 (mmm) cc_final: 0.5770 (tmm) REVERT: E 455 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7545 (ptmm) REVERT: F 179 MET cc_start: 0.6912 (ppp) cc_final: 0.6630 (ppp) REVERT: F 206 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6743 (pmmt) REVERT: F 277 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.6890 (tm-30) REVERT: F 296 ASN cc_start: 0.8071 (m-40) cc_final: 0.7593 (p0) REVERT: F 438 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6965 (mtmp) REVERT: F 455 LYS cc_start: 0.7576 (mttm) cc_final: 0.7117 (ttmm) REVERT: G 255 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.6704 (p0) REVERT: G 277 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: G 441 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8569 (mt0) REVERT: G 455 LYS cc_start: 0.7531 (mtpp) cc_final: 0.7058 (ptpt) REVERT: H 399 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6990 (pp20) REVERT: H 455 LYS cc_start: 0.7635 (mtpp) cc_final: 0.7215 (ptpt) outliers start: 135 outliers final: 90 residues processed: 487 average time/residue: 0.5232 time to fit residues: 308.4564 Evaluate side-chains 487 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 379 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 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 180 THR 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 361 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 318 VAL 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 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 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 441 GLN 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 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 450 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 353 optimal weight: 4.9990 chunk 382 optimal weight: 0.9990 chunk 380 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 131 optimal weight: 0.6980 chunk 266 optimal weight: 5.9990 chunk 99 optimal weight: 0.0060 chunk 265 optimal weight: 0.2980 chunk 281 optimal weight: 2.9990 chunk 387 optimal weight: 3.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 312 ASN D 466 HIS D 478 GLN E 368 GLN E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 312 ASN H 368 GLN H 478 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.188527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.135497 restraints weight = 33233.360| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.87 r_work: 0.3218 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31460 Z= 0.138 Angle : 0.582 9.998 42632 Z= 0.293 Chirality : 0.045 0.226 4856 Planarity : 0.004 0.038 5352 Dihedral : 9.049 82.019 4448 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.03 % Favored : 94.53 % Rotamer: Outliers : 4.27 % Allowed : 17.58 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3896 helix: 1.07 (0.14), residues: 1472 sheet: 0.20 (0.22), residues: 472 loop : -0.71 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.013 0.001 TYR A 353 PHE 0.009 0.001 PHE F 24 HIS 0.003 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (31448) covalent geometry : angle 0.58246 / 0.29 (42632) hydrogen bonds : bond 0.03789 / 2.57 ( 1137) hydrogen bonds : angle 4.87621 / 3.49 ( 3192) Misc. bond : bond 0.00083 / 0.06 ( 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 530 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 393 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.5659 (OUTLIER) cc_final: 0.5352 (mmm160) REVERT: A 255 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6699 (p0) REVERT: A 296 ASN cc_start: 0.8128 (m110) cc_final: 0.7629 (p0) REVERT: A 399 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6887 (pp20) REVERT: A 438 LYS cc_start: 0.7282 (mmmt) cc_final: 0.6808 (mtmp) REVERT: A 455 LYS cc_start: 0.7563 (mtpp) cc_final: 0.7167 (ptpt) REVERT: B 206 LYS cc_start: 0.6056 (OUTLIER) cc_final: 0.5540 (ptpp) REVERT: B 255 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6683 (p0) REVERT: B 399 GLU cc_start: 0.7222 (pp20) cc_final: 0.6934 (pp20) REVERT: B 455 LYS cc_start: 0.7546 (mtpp) cc_final: 0.7247 (ptpt) REVERT: C 255 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.6681 (p0) REVERT: C 277 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.6993 (tm-30) REVERT: C 399 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6921 (pp20) REVERT: C 455 LYS cc_start: 0.7442 (mttm) cc_final: 0.7182 (ttmm) REVERT: D 255 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6633 (p0) REVERT: D 277 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.6644 (tm-30) REVERT: D 399 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6931 (pp20) REVERT: E 162 ASP cc_start: 0.7181 (m-30) cc_final: 0.6849 (m-30) REVERT: E 179 MET cc_start: 0.6761 (mmm) cc_final: 0.5840 (tmm) REVERT: E 277 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: E 455 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7455 (ptmm) REVERT: F 179 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6570 (ppp) REVERT: F 206 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6709 (pmmt) REVERT: F 277 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.6926 (tm-30) REVERT: F 438 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6926 (mtmp) REVERT: F 455 LYS cc_start: 0.7468 (mttm) cc_final: 0.7038 (ttmm) REVERT: G 277 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.6835 (tm-30) REVERT: G 441 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8539 (mt0) REVERT: G 455 LYS cc_start: 0.7476 (mtpp) cc_final: 0.7041 (ptpt) REVERT: H 399 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6912 (pp20) REVERT: H 455 LYS cc_start: 0.7603 (mtpp) cc_final: 0.7191 (ptpt) outliers start: 137 outliers final: 88 residues processed: 500 average time/residue: 0.5450 time to fit residues: 328.4488 Evaluate side-chains 494 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 386 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 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 15 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 180 THR 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 361 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 47 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 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 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 179 MET 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 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 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 441 GLN Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 196 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 103 optimal weight: 0.0170 chunk 127 optimal weight: 0.9980 chunk 233 optimal weight: 0.8980 chunk 1 optimal weight: 0.0070 chunk 51 optimal weight: 0.9980 chunk 264 optimal weight: 0.4980 chunk 366 optimal weight: 0.4980 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 312 ASN 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 478 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.191727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139260 restraints weight = 33246.071| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.85 r_work: 0.3282 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31460 Z= 0.097 Angle : 0.548 11.135 42632 Z= 0.272 Chirality : 0.043 0.231 4856 Planarity : 0.004 0.036 5352 Dihedral : 8.617 79.226 4443 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.18 % Favored : 95.38 % Rotamer: Outliers : 3.05 % Allowed : 18.77 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3896 helix: 1.26 (0.14), residues: 1472 sheet: 0.31 (0.22), residues: 472 loop : -0.52 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 182 TYR 0.010 0.001 TYR H 353 PHE 0.010 0.001 PHE E 456 HIS 0.003 0.001 HIS H 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (31448) covalent geometry : angle 0.54811 / 0.27 (42632) hydrogen bonds : bond 0.02929 / 1.99 ( 1137) hydrogen bonds : angle 4.70189 / 3.37 ( 3192) Misc. bond : bond 0.00025 / 0.02 ( 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 501 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 403 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8001 (tp30) cc_final: 0.7116 (mp0) REVERT: A 399 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6871 (pp20) REVERT: A 438 LYS cc_start: 0.7236 (mmmt) cc_final: 0.6792 (mtmp) REVERT: A 455 LYS cc_start: 0.7341 (mtpp) cc_final: 0.7025 (ptpt) REVERT: B 255 ASP cc_start: 0.7223 (p0) cc_final: 0.6583 (p0) REVERT: B 399 GLU cc_start: 0.7227 (pp20) cc_final: 0.6940 (pp20) REVERT: B 438 LYS cc_start: 0.7356 (mmtp) cc_final: 0.6866 (mtmt) REVERT: B 455 LYS cc_start: 0.7300 (mtpp) cc_final: 0.6992 (ttmm) REVERT: C 255 ASP cc_start: 0.7355 (p0) cc_final: 0.6692 (p0) REVERT: C 399 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6920 (pp20) REVERT: C 455 LYS cc_start: 0.7243 (mttm) cc_final: 0.7038 (ttmm) REVERT: D 255 ASP cc_start: 0.7304 (p0) cc_final: 0.6611 (p0) REVERT: D 277 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.6540 (tm-30) REVERT: D 399 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6918 (pp20) REVERT: D 455 LYS cc_start: 0.7342 (mtpp) cc_final: 0.6942 (ttmm) REVERT: E 162 ASP cc_start: 0.7043 (m-30) cc_final: 0.6675 (m-30) REVERT: E 179 MET cc_start: 0.6750 (mmm) cc_final: 0.5841 (tmm) REVERT: F 179 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6547 (ppp) REVERT: F 206 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6651 (pmmt) REVERT: F 438 LYS cc_start: 0.7475 (mttm) cc_final: 0.6976 (mtmp) REVERT: F 455 LYS cc_start: 0.7256 (mttm) cc_final: 0.6892 (ttmm) REVERT: G 255 ASP cc_start: 0.7360 (p0) cc_final: 0.6708 (p0) REVERT: G 277 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: G 303 ASN cc_start: 0.8841 (m-40) cc_final: 0.8634 (m-40) REVERT: G 455 LYS cc_start: 0.7262 (mtpp) cc_final: 0.6926 (ptpt) REVERT: H 399 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6905 (pp20) REVERT: H 455 LYS cc_start: 0.7366 (mtpp) cc_final: 0.7061 (ptpt) outliers start: 98 outliers final: 65 residues processed: 482 average time/residue: 0.5395 time to fit residues: 313.7374 Evaluate side-chains 461 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 388 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 145 THR 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 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 270 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 438 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 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 439 VAL Chi-restraints excluded: chain D residue 450 LYS 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 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN 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 179 MET 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 383 THR Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 448 GLN 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 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU 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 259 optimal weight: 9.9990 chunk 362 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 326 optimal weight: 0.9990 chunk 289 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 246 optimal weight: 0.5980 chunk 291 optimal weight: 2.9990 chunk 153 optimal weight: 0.4980 chunk 213 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 GLN A 466 HIS A 478 GLN B 368 GLN B 466 HIS B 478 GLN C 368 GLN C 466 HIS D 21 GLN D 368 GLN D 466 HIS E 368 GLN E 466 HIS E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 448 GLN G 466 HIS G 478 GLN H 368 GLN H 466 HIS H 478 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.189992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137091 restraints weight = 33057.320| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.84 r_work: 0.3238 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31460 Z= 0.121 Angle : 0.571 11.809 42632 Z= 0.283 Chirality : 0.044 0.240 4856 Planarity : 0.004 0.037 5352 Dihedral : 8.630 80.642 4437 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.77 % Favored : 94.79 % Rotamer: Outliers : 2.87 % Allowed : 19.05 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3896 helix: 1.26 (0.14), residues: 1472 sheet: 0.27 (0.22), residues: 472 loop : -0.56 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 105 TYR 0.014 0.001 TYR A 353 PHE 0.012 0.001 PHE E 456 HIS 0.003 0.001 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (31448) covalent geometry : angle 0.57061 / 0.28 (42632) hydrogen bonds : bond 0.03463 / 2.34 ( 1137) hydrogen bonds : angle 4.73147 / 3.40 ( 3192) Misc. bond : bond 0.00070 / 0.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 382 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8007 (tp30) cc_final: 0.7109 (mp0) REVERT: A 277 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: A 399 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6866 (pp20) REVERT: A 438 LYS cc_start: 0.7247 (mmmt) cc_final: 0.6795 (mtmp) REVERT: A 455 LYS cc_start: 0.7354 (mtpp) cc_final: 0.6937 (ptpt) REVERT: B 255 ASP cc_start: 0.7254 (p0) cc_final: 0.6642 (p0) REVERT: B 399 GLU cc_start: 0.7202 (pp20) cc_final: 0.6925 (pp20) REVERT: B 455 LYS cc_start: 0.7347 (mtpp) cc_final: 0.7010 (ttmm) REVERT: C 255 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6675 (p0) REVERT: C 277 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.6891 (tm-30) REVERT: C 399 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6926 (pp20) REVERT: C 455 LYS cc_start: 0.7268 (mttm) cc_final: 0.7051 (ttmm) REVERT: D 255 ASP cc_start: 0.7355 (p0) cc_final: 0.6694 (p0) REVERT: D 277 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.6582 (tm-30) REVERT: D 399 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6904 (pp20) REVERT: E 162 ASP cc_start: 0.7100 (m-30) cc_final: 0.6745 (m-30) REVERT: E 179 MET cc_start: 0.6799 (mmm) cc_final: 0.5944 (tmm) REVERT: E 455 LYS cc_start: 0.7839 (ptpt) cc_final: 0.7497 (ptmm) REVERT: F 179 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6533 (ppp) REVERT: F 206 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6658 (pmmt) REVERT: F 277 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.6919 (tm-30) REVERT: F 438 LYS cc_start: 0.7424 (mttm) cc_final: 0.6902 (mtmp) REVERT: F 455 LYS cc_start: 0.7313 (mttm) cc_final: 0.6915 (ttmm) REVERT: F 510 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: G 277 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: G 455 LYS cc_start: 0.7287 (mtpp) cc_final: 0.6888 (ptpt) REVERT: H 277 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.6497 (tm-30) REVERT: H 399 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6940 (pp20) REVERT: H 455 LYS cc_start: 0.7405 (mtpp) cc_final: 0.7020 (ptpt) outliers start: 92 outliers final: 65 residues processed: 455 average time/residue: 0.5461 time to fit residues: 299.5722 Evaluate side-chains 460 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 381 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 145 THR 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 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 180 THR 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 E residue 47 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 179 MET 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 383 THR Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 448 GLN 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 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 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 439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 346 optimal weight: 2.9990 chunk 356 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 330 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 325 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 192 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 287 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 21 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 448 GLN G 466 HIS G 478 GLN H 312 ASN H 368 GLN H 478 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.187424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.134402 restraints weight = 33087.733| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.85 r_work: 0.3199 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 31460 Z= 0.197 Angle : 0.635 11.765 42632 Z= 0.317 Chirality : 0.047 0.181 4856 Planarity : 0.004 0.039 5352 Dihedral : 8.951 80.601 4436 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.06 % Favored : 94.53 % Rotamer: Outliers : 2.52 % Allowed : 19.58 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.13), residues: 3896 helix: 0.96 (0.14), residues: 1472 sheet: -0.13 (0.20), residues: 528 loop : -0.72 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 356 TYR 0.016 0.002 TYR E 348 PHE 0.016 0.002 PHE E 456 HIS 0.004 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (31448) covalent geometry : angle 0.63502 / 0.32 (42632) hydrogen bonds : bond 0.04445 / 3.02 ( 1137) hydrogen bonds : angle 4.93867 / 3.54 ( 3192) Misc. bond : bond 0.00131 / 0.10 ( 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 465 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 384 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8068 (tp30) cc_final: 0.7198 (mp0) REVERT: A 277 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: A 296 ASN cc_start: 0.8103 (m110) cc_final: 0.7598 (p0) REVERT: A 399 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6890 (pp20) REVERT: A 438 LYS cc_start: 0.7285 (mmmt) cc_final: 0.6811 (mtmp) REVERT: A 455 LYS cc_start: 0.7554 (mtpp) cc_final: 0.7099 (ptpt) REVERT: B 206 LYS cc_start: 0.6051 (OUTLIER) cc_final: 0.5506 (ptpp) REVERT: B 255 ASP cc_start: 0.7266 (p0) cc_final: 0.6689 (p0) REVERT: B 399 GLU cc_start: 0.7221 (pp20) cc_final: 0.6941 (pp20) REVERT: B 455 LYS cc_start: 0.7543 (mtpp) cc_final: 0.7266 (ptpt) REVERT: C 255 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.6701 (p0) REVERT: C 277 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: C 399 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6947 (pp20) REVERT: C 455 LYS cc_start: 0.7448 (mttm) cc_final: 0.7220 (ttmm) REVERT: D 255 ASP cc_start: 0.7392 (p0) cc_final: 0.6686 (p0) REVERT: D 277 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.6707 (tm-30) REVERT: D 399 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6952 (pp20) REVERT: E 103 GLU cc_start: 0.8025 (tp30) cc_final: 0.7080 (mp0) REVERT: E 162 ASP cc_start: 0.7295 (m-30) cc_final: 0.6936 (m-30) REVERT: E 455 LYS cc_start: 0.7909 (ptpt) cc_final: 0.7581 (ptmm) REVERT: F 179 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6546 (ppp) REVERT: F 206 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6797 (pmmt) REVERT: F 277 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.6860 (tm-30) REVERT: F 455 LYS cc_start: 0.7547 (mttm) cc_final: 0.7151 (ttmm) REVERT: F 510 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: G 277 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.6787 (tm-30) REVERT: G 455 LYS cc_start: 0.7473 (mtpp) cc_final: 0.7046 (ptpt) REVERT: H 277 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.6576 (tm-30) REVERT: H 399 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7015 (pp20) REVERT: H 455 LYS cc_start: 0.7598 (mtpp) cc_final: 0.7151 (ptpt) outliers start: 81 outliers final: 61 residues processed: 446 average time/residue: 0.5931 time to fit residues: 317.5025 Evaluate side-chains 458 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 382 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 145 THR 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 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 154 LEU 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 E residue 47 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN 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 179 MET 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 383 THR Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 448 GLN 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 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 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 439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 337 optimal weight: 1.9990 chunk 219 optimal weight: 8.9990 chunk 334 optimal weight: 0.7980 chunk 328 optimal weight: 0.8980 chunk 381 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 239 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 372 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN A 368 GLN A 478 GLN B 21 GLN B 368 GLN B 478 GLN C 21 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 466 HIS E 21 GLN E 368 GLN E 478 GLN F 368 GLN F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 312 ASN H 368 GLN H 478 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.189253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.136312 restraints weight = 33116.235| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.85 r_work: 0.3236 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31460 Z= 0.127 Angle : 0.580 12.218 42632 Z= 0.289 Chirality : 0.044 0.170 4856 Planarity : 0.004 0.037 5352 Dihedral : 8.708 79.469 4435 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.57 % Favored : 95.02 % Rotamer: Outliers : 2.68 % Allowed : 19.64 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.14), residues: 3896 helix: 1.10 (0.14), residues: 1472 sheet: 0.25 (0.22), residues: 472 loop : -0.63 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.013 0.001 TYR A 353 PHE 0.013 0.001 PHE C 456 HIS 0.003 0.001 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (31448) covalent geometry : angle 0.58026 / 0.29 (42632) hydrogen bonds : bond 0.03575 / 2.42 ( 1137) hydrogen bonds : angle 4.83420 / 3.47 ( 3192) Misc. bond : bond 0.00067 / 0.05 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11684.16 seconds wall clock time: 199 minutes 24.85 seconds (11964.85 seconds total)