Starting phenix.real_space_refine on Fri Jun 27 01:07:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8f_29848/06_2025/8g8f_29848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8f_29848/06_2025/8g8f_29848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g8f_29848/06_2025/8g8f_29848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8f_29848/06_2025/8g8f_29848.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8f_29848/06_2025/8g8f_29848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8f_29848/06_2025/8g8f_29848.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.280 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 168 5.16 5 C 19248 2.51 5 N 5328 2.21 5 O 6096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30912 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "B" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "C" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "D" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "E" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "F" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "G" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "H" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 19.02, per 1000 atoms: 0.62 Number of scatterers: 30912 At special positions: 0 Unit cell: (160.17, 161.856, 133.194, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 72 15.00 O 6096 8.00 N 5328 7.00 C 19248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.74 Conformation dependent library (CDL) restraints added in 4.1 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: 4.40 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: 13.20 Time building geometry restraints manager: 10.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5168 1.31 - 1.44: 7697 1.44 - 1.57: 18191 1.57 - 1.70: 120 1.70 - 1.82: 272 Bond restraints: 31448 Sorted by residual: bond pdb=" C4 ATP A 602 " pdb=" C5 ATP A 602 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.98e+01 bond pdb=" C4 ATP D 602 " pdb=" C5 ATP D 602 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.94e+01 bond pdb=" C4 ATP G 602 " pdb=" C5 ATP G 602 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 bond pdb=" C4 ATP E 602 " pdb=" C5 ATP E 602 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 bond pdb=" C4 ATP H 602 " pdb=" C5 ATP H 602 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.91e+01 ... (remaining 31443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 42242 4.28 - 8.56: 310 8.56 - 12.84: 43 12.84 - 17.12: 19 17.12 - 21.40: 18 Bond angle restraints: 42632 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 120.43 19.44 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.78e+02 ... (remaining 42627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 18646 35.33 - 70.67: 824 70.67 - 106.00: 70 106.00 - 141.34: 3 141.34 - 176.67: 1 Dihedral angle restraints: 19544 sinusoidal: 8376 harmonic: 11168 Sorted by residual: dihedral pdb=" C5' IMP A 603 " pdb=" O5' IMP A 603 " pdb=" P IMP A 603 " pdb=" O2P IMP A 603 " ideal model delta sinusoidal sigma weight residual -168.07 8.61 -176.67 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' IMP H 603 " pdb=" O5' IMP H 603 " pdb=" P IMP H 603 " pdb=" O2P IMP H 603 " ideal model delta sinusoidal sigma weight residual -168.07 -30.70 -137.37 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" C5' IMP G 603 " pdb=" O5' IMP G 603 " pdb=" P IMP G 603 " pdb=" O2P IMP G 603 " ideal model delta sinusoidal sigma weight residual -168.07 -43.27 -124.80 1 2.00e+01 2.50e-03 3.77e+01 ... (remaining 19541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3909 0.057 - 0.113: 823 0.113 - 0.170: 90 0.170 - 0.227: 33 0.227 - 0.284: 1 Chirality restraints: 4856 Sorted by residual: chirality pdb=" CA MET G 179 " pdb=" N MET G 179 " pdb=" C MET G 179 " pdb=" CB MET G 179 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ILE B 178 " pdb=" N ILE B 178 " pdb=" C ILE B 178 " pdb=" CB ILE B 178 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" C3D NAD H 604 " pdb=" C2D NAD H 604 " pdb=" C4D NAD H 604 " pdb=" O3D NAD H 604 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.94e-01 ... (remaining 4853 not shown) Planarity restraints: 5352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 13 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C VAL C 13 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL C 13 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO C 14 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 170 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" CD GLU H 170 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU H 170 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU H 170 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 13 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C VAL E 13 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL E 13 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO E 14 " 0.011 2.00e-02 2.50e+03 ... (remaining 5349 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1300 2.72 - 3.26: 31100 3.26 - 3.81: 51702 3.81 - 4.35: 66138 4.35 - 4.90: 108290 Nonbonded interactions: 258530 Sorted by model distance: nonbonded pdb=" O ARG F 182 " pdb=" NH1 ARG F 182 " model vdw 2.173 3.120 nonbonded pdb=" OD2 ASP A 364 " pdb=" O2' IMP A 603 " model vdw 2.178 3.040 nonbonded pdb=" OD2 ASP C 364 " pdb=" O2' IMP C 603 " model vdw 2.194 3.040 nonbonded pdb=" OD2 ASP B 364 " pdb=" O2' IMP B 603 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP E 364 " pdb=" O2' IMP E 603 " model vdw 2.198 3.040 ... (remaining 258525 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 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: 0.050 Extract box with map and model: 1.280 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 75.700 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:14.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.822 31460 Z= 0.999 Angle : 1.020 21.396 42632 Z= 0.704 Chirality : 0.048 0.284 4856 Planarity : 0.004 0.050 5352 Dihedral : 18.177 176.675 12408 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.98 % Favored : 93.61 % Rotamer: Outliers : 1.87 % Allowed : 17.36 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3896 helix: 0.74 (0.14), residues: 1488 sheet: 0.15 (0.22), residues: 472 loop : -0.91 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 454 PHE 0.017 0.001 PHE G 165 TYR 0.012 0.001 TYR E 348 ARG 0.011 0.000 ARG E 182 Details of bonding type rmsd hydrogen bonds : bond 0.13789 ( 1137) hydrogen bonds : angle 6.29641 ( 3192) covalent geometry : bond 0.00697 (31448) covalent geometry : angle 1.02024 (42632) Misc. bond : bond 0.45805 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 368 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ASP cc_start: 0.7411 (m-30) cc_final: 0.7093 (m-30) REVERT: B 277 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: D 303 ASN cc_start: 0.9095 (m110) cc_final: 0.8894 (m-40) REVERT: E 179 MET cc_start: 0.5510 (tmm) cc_final: 0.4750 (tmm) REVERT: F 438 LYS cc_start: 0.7332 (mttm) cc_final: 0.7032 (mtmt) outliers start: 60 outliers final: 49 residues processed: 424 average time/residue: 1.3173 time to fit residues: 666.8327 Evaluate side-chains 411 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 361 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 318 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 5.9990 chunk 297 optimal weight: 2.9990 chunk 164 optimal weight: 30.0000 chunk 101 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 158 optimal weight: 20.0000 chunk 307 optimal weight: 4.9990 chunk 118 optimal weight: 0.0870 chunk 186 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 chunk 355 optimal weight: 7.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 277 GLN A 343 GLN A 368 GLN A 441 GLN A 466 HIS A 478 GLN B 21 GLN B 93 HIS B 253 HIS B 343 GLN B 368 GLN B 478 GLN C 93 HIS C 343 GLN C 368 GLN C 441 GLN C 466 HIS C 478 GLN D 93 HIS D 303 ASN D 343 GLN D 368 GLN D 441 GLN D 466 HIS D 478 GLN E 93 HIS E 343 GLN E 368 GLN E 478 GLN F 93 HIS F 343 GLN F 368 GLN F 466 HIS F 478 GLN G 93 HIS G 343 GLN G 368 GLN G 466 HIS G 478 GLN H 93 HIS H 102 ASN H 343 GLN H 368 GLN H 441 GLN H 466 HIS H 478 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.188171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.134930 restraints weight = 33027.149| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.83 r_work: 0.3197 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 31460 Z= 0.196 Angle : 0.649 12.980 42632 Z= 0.338 Chirality : 0.047 0.203 4856 Planarity : 0.005 0.041 5352 Dihedral : 14.475 163.020 5371 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.34 % Favored : 94.22 % Rotamer: Outliers : 3.93 % Allowed : 15.24 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 3896 helix: 0.64 (0.14), residues: 1488 sheet: -0.35 (0.20), residues: 528 loop : -0.94 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 454 PHE 0.014 0.002 PHE H 456 TYR 0.016 0.002 TYR E 348 ARG 0.007 0.001 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 1137) hydrogen bonds : angle 5.20547 ( 3192) covalent geometry : bond 0.00459 (31448) covalent geometry : angle 0.64922 (42632) Misc. bond : bond 0.00214 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 378 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.5746 (OUTLIER) cc_final: 0.5536 (ptpp) REVERT: B 399 GLU cc_start: 0.7140 (pp20) cc_final: 0.6934 (pp20) REVERT: C 255 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.6661 (p0) REVERT: C 277 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: D 277 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.6603 (tm-30) REVERT: E 179 MET cc_start: 0.5923 (mmm) cc_final: 0.4840 (tmm) REVERT: F 206 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6678 (pmmt) REVERT: F 277 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.7005 (tm-30) REVERT: F 438 LYS cc_start: 0.7427 (mttm) cc_final: 0.7214 (mttm) REVERT: F 456 PHE cc_start: 0.7985 (t80) cc_final: 0.7771 (t80) REVERT: G 277 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.6824 (tm-30) REVERT: G 438 LYS cc_start: 0.7505 (mtmt) cc_final: 0.7061 (mmmt) REVERT: H 277 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.6614 (tm-30) outliers start: 126 outliers final: 64 residues processed: 485 average time/residue: 1.2846 time to fit residues: 751.0924 Evaluate side-chains 437 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 365 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 6 optimal weight: 4.9990 chunk 227 optimal weight: 0.7980 chunk 244 optimal weight: 0.0040 chunk 79 optimal weight: 3.9990 chunk 346 optimal weight: 2.9990 chunk 304 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 251 optimal weight: 0.6980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 478 GLN B 21 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 478 GLN E 368 GLN E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 441 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.190115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.137130 restraints weight = 33369.280| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.87 r_work: 0.3248 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 31460 Z= 0.121 Angle : 0.566 12.745 42632 Z= 0.293 Chirality : 0.044 0.202 4856 Planarity : 0.004 0.045 5352 Dihedral : 13.684 131.056 5361 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.90 % Favored : 94.66 % Rotamer: Outliers : 3.93 % Allowed : 15.80 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3896 helix: 0.92 (0.14), residues: 1488 sheet: 0.62 (0.24), residues: 376 loop : -0.84 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 466 PHE 0.010 0.001 PHE A 456 TYR 0.012 0.001 TYR A 353 ARG 0.004 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 1137) hydrogen bonds : angle 4.95291 ( 3192) covalent geometry : bond 0.00270 (31448) covalent geometry : angle 0.56620 (42632) Misc. bond : bond 0.00128 ( 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: 126 poor density : 381 time to evaluate : 3.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7154 (m-30) cc_final: 0.6809 (m-30) REVERT: A 455 LYS cc_start: 0.7485 (mtpp) cc_final: 0.7035 (ttmm) REVERT: B 455 LYS cc_start: 0.7517 (mtpp) cc_final: 0.7084 (ttmm) REVERT: C 255 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6669 (p0) REVERT: C 277 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: C 399 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6905 (pp20) REVERT: D 399 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6945 (pp20) REVERT: E 179 MET cc_start: 0.6053 (mmm) cc_final: 0.5231 (tmm) REVERT: E 277 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: F 277 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: G 277 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.6849 (tm-30) outliers start: 126 outliers final: 67 residues processed: 482 average time/residue: 1.6223 time to fit residues: 943.8635 Evaluate side-chains 441 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 367 time to evaluate : 3.371 ------------------------------------------------------------------------------- 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 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 154 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 F residue 510 GLU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 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 270 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 11 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 278 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 320 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 478 GLN B 368 GLN B 466 HIS B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 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 = 0.189173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.135859 restraints weight = 33206.562| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.85 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: 0.8518 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31460 Z= 0.144 Angle : 0.574 12.782 42632 Z= 0.296 Chirality : 0.044 0.220 4856 Planarity : 0.004 0.039 5352 Dihedral : 13.075 97.481 5348 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.18 % Favored : 94.38 % Rotamer: Outliers : 4.11 % Allowed : 16.43 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.13), residues: 3896 helix: 0.95 (0.14), residues: 1488 sheet: 0.64 (0.24), residues: 376 loop : -0.86 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 454 PHE 0.010 0.001 PHE H 456 TYR 0.013 0.001 TYR E 348 ARG 0.003 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 1137) hydrogen bonds : angle 4.89556 ( 3192) covalent geometry : bond 0.00330 (31448) covalent geometry : angle 0.57445 (42632) Misc. bond : bond 0.00151 ( 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 502 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 370 time to evaluate : 3.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7224 (m-30) cc_final: 0.6873 (m-30) REVERT: A 399 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6866 (pp20) REVERT: A 438 LYS cc_start: 0.7321 (mmmt) cc_final: 0.6808 (mtmt) REVERT: A 455 LYS cc_start: 0.7505 (mtpp) cc_final: 0.7076 (ttmm) REVERT: B 206 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6392 (ptpp) REVERT: B 399 GLU cc_start: 0.7156 (pp20) cc_final: 0.6943 (pp20) REVERT: B 455 LYS cc_start: 0.7544 (mtpp) cc_final: 0.7109 (ttmm) REVERT: C 255 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.6678 (p0) REVERT: C 277 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.6933 (tm-30) REVERT: C 399 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6891 (pp20) REVERT: D 255 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6683 (p0) REVERT: D 277 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.6653 (tm-30) REVERT: D 399 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6991 (pp20) REVERT: E 162 ASP cc_start: 0.7086 (m-30) cc_final: 0.6772 (m-30) REVERT: E 179 MET cc_start: 0.6221 (mmm) cc_final: 0.5590 (tmm) REVERT: E 277 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: F 277 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.6940 (tm-30) REVERT: F 438 LYS cc_start: 0.7433 (mttm) cc_final: 0.6983 (mtmp) REVERT: G 277 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.6788 (tm-30) REVERT: G 455 LYS cc_start: 0.7466 (mtpp) cc_final: 0.7035 (ptpt) REVERT: H 277 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: H 455 LYS cc_start: 0.7582 (mtpp) cc_final: 0.7187 (ptpt) outliers start: 132 outliers final: 74 residues processed: 471 average time/residue: 1.2666 time to fit residues: 722.9675 Evaluate side-chains 455 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 369 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 420 MET 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 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain 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 410 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 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 181 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 229 optimal weight: 0.5980 chunk 342 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 228 optimal weight: 0.5980 chunk 296 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 250 optimal weight: 0.1980 chunk 130 optimal weight: 0.9980 chunk 308 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 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 = 0.4080 r_free = 0.4080 target = 0.190394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137384 restraints weight = 33134.316| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.86 r_work: 0.3254 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31460 Z= 0.116 Angle : 0.549 12.335 42632 Z= 0.283 Chirality : 0.044 0.234 4856 Planarity : 0.004 0.038 5352 Dihedral : 12.565 88.834 5344 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.59 % Favored : 94.97 % Rotamer: Outliers : 3.99 % Allowed : 16.96 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3896 helix: 1.11 (0.14), residues: 1488 sheet: 0.71 (0.23), residues: 376 loop : -0.79 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 454 PHE 0.009 0.001 PHE E 456 TYR 0.012 0.001 TYR A 353 ARG 0.002 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 1137) hydrogen bonds : angle 4.78727 ( 3192) covalent geometry : bond 0.00255 (31448) covalent geometry : angle 0.54860 (42632) Misc. bond : bond 0.00120 ( 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 514 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 386 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7149 (m-30) cc_final: 0.6847 (m-30) REVERT: A 399 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6868 (pp20) REVERT: A 438 LYS cc_start: 0.7343 (mmmt) cc_final: 0.6838 (mtmt) REVERT: A 455 LYS cc_start: 0.7459 (mtpp) cc_final: 0.7060 (ttmm) REVERT: B 206 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6311 (ptpp) REVERT: B 399 GLU cc_start: 0.7158 (pp20) cc_final: 0.6944 (pp20) REVERT: B 438 LYS cc_start: 0.7447 (mmtt) cc_final: 0.6943 (mtmt) REVERT: B 455 LYS cc_start: 0.7438 (mtpp) cc_final: 0.7090 (ttmm) REVERT: C 255 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6640 (p0) REVERT: C 277 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: C 399 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6878 (pp20) REVERT: C 455 LYS cc_start: 0.7324 (mttm) cc_final: 0.7008 (ttmm) REVERT: D 243 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7494 (mt0) REVERT: D 277 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.6601 (tm-30) REVERT: D 399 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6945 (pp20) REVERT: D 455 LYS cc_start: 0.7363 (mtpp) cc_final: 0.6956 (ttmm) REVERT: E 162 ASP cc_start: 0.7152 (m-30) cc_final: 0.6839 (m-30) REVERT: E 179 MET cc_start: 0.6370 (mmm) cc_final: 0.5633 (tmm) REVERT: E 277 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.7040 (tm-30) REVERT: E 455 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7455 (ptmm) REVERT: F 277 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.6915 (tm-30) REVERT: F 438 LYS cc_start: 0.7426 (mttm) cc_final: 0.6962 (mtmp) REVERT: F 455 LYS cc_start: 0.7327 (mttm) cc_final: 0.6876 (ttmm) REVERT: G 277 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.6858 (tm-30) REVERT: G 455 LYS cc_start: 0.7321 (mtpp) cc_final: 0.6968 (ptpt) REVERT: H 277 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.6632 (tm-30) REVERT: H 455 LYS cc_start: 0.7513 (mtpp) cc_final: 0.7119 (ttmm) outliers start: 128 outliers final: 75 residues processed: 488 average time/residue: 1.2167 time to fit residues: 715.4703 Evaluate side-chains 460 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 372 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 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 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 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 E residue 154 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 145 THR 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 292 ASP Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 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 181 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 93 optimal weight: 1.9990 chunk 356 optimal weight: 9.9990 chunk 330 optimal weight: 0.9990 chunk 354 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 286 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN A 368 GLN A 466 HIS A 478 GLN B 368 GLN B 466 HIS B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 466 HIS D 478 GLN E 368 GLN E 466 HIS E 478 GLN F 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.187799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.134481 restraints weight = 33152.112| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.87 r_work: 0.3198 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31460 Z= 0.191 Angle : 0.602 11.755 42632 Z= 0.311 Chirality : 0.046 0.230 4856 Planarity : 0.004 0.039 5352 Dihedral : 12.570 88.968 5340 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.21 % Favored : 94.35 % Rotamer: Outliers : 3.87 % Allowed : 17.64 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 3896 helix: 0.99 (0.14), residues: 1472 sheet: -0.17 (0.20), residues: 528 loop : -0.75 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 466 PHE 0.012 0.002 PHE F 24 TYR 0.015 0.002 TYR A 348 ARG 0.003 0.000 ARG B 259 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 1137) hydrogen bonds : angle 4.93577 ( 3192) covalent geometry : bond 0.00449 (31448) covalent geometry : angle 0.60230 (42632) Misc. bond : bond 0.00175 ( 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 501 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 377 time to evaluate : 3.106 Fit side-chains revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7221 (m-30) cc_final: 0.6888 (m-30) REVERT: A 296 ASN cc_start: 0.8111 (m110) cc_final: 0.7613 (p0) REVERT: A 399 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6898 (pp20) REVERT: A 438 LYS cc_start: 0.7409 (mmtt) cc_final: 0.6886 (mtmp) REVERT: A 455 LYS cc_start: 0.7568 (mtpp) cc_final: 0.7205 (ptpt) REVERT: B 206 LYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6402 (ptpp) REVERT: B 255 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.6653 (p0) REVERT: B 399 GLU cc_start: 0.7170 (pp20) cc_final: 0.6948 (pp20) REVERT: B 438 LYS cc_start: 0.7462 (mmtt) cc_final: 0.6959 (mtmt) REVERT: B 455 LYS cc_start: 0.7590 (mtpp) cc_final: 0.7285 (ptpt) REVERT: C 255 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.6667 (p0) REVERT: C 399 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6954 (pp20) REVERT: C 455 LYS cc_start: 0.7480 (mttm) cc_final: 0.7144 (ttmm) REVERT: D 243 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7432 (mt0) REVERT: D 255 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.6706 (p0) REVERT: D 277 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.6671 (tm-30) REVERT: D 399 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7009 (pp20) REVERT: D 455 LYS cc_start: 0.7610 (mtpp) cc_final: 0.7161 (ttmm) REVERT: E 162 ASP cc_start: 0.7199 (m-30) cc_final: 0.6848 (m-30) REVERT: E 179 MET cc_start: 0.6563 (mmm) cc_final: 0.5710 (tmm) REVERT: E 455 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7615 (ptmm) REVERT: F 277 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.6997 (tm-30) REVERT: F 438 LYS cc_start: 0.7479 (mttm) cc_final: 0.7279 (mttm) REVERT: F 455 LYS cc_start: 0.7590 (mttm) cc_final: 0.7135 (ttmm) REVERT: G 277 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.6810 (tm-30) REVERT: G 455 LYS cc_start: 0.7495 (mtpp) cc_final: 0.7057 (ptpt) REVERT: H 277 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.6616 (tm-30) REVERT: H 399 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6966 (pp20) REVERT: H 455 LYS cc_start: 0.7641 (mtpp) cc_final: 0.7233 (ptpt) outliers start: 124 outliers final: 77 residues processed: 474 average time/residue: 1.3735 time to fit residues: 798.9532 Evaluate side-chains 460 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 369 time to evaluate : 3.778 ------------------------------------------------------------------------------- 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 165 PHE Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 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 292 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 189 optimal weight: 0.4980 chunk 42 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 387 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 244 optimal weight: 0.0770 chunk 247 optimal weight: 0.5980 chunk 291 optimal weight: 2.9990 chunk 338 optimal weight: 2.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 478 GLN E 368 GLN E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.188834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.135101 restraints weight = 33051.646| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.85 r_work: 0.3207 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 31460 Z= 0.157 Angle : 0.582 10.394 42632 Z= 0.301 Chirality : 0.045 0.238 4856 Planarity : 0.004 0.038 5352 Dihedral : 12.320 89.695 5336 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.98 % Favored : 94.58 % Rotamer: Outliers : 3.90 % Allowed : 17.89 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3896 helix: 1.02 (0.14), residues: 1472 sheet: 0.22 (0.22), residues: 472 loop : -0.73 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 466 PHE 0.011 0.002 PHE H 456 TYR 0.014 0.002 TYR E 348 ARG 0.004 0.000 ARG D 182 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 1137) hydrogen bonds : angle 4.88899 ( 3192) covalent geometry : bond 0.00362 (31448) covalent geometry : angle 0.58211 (42632) Misc. bond : bond 0.00142 ( 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 503 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 378 time to evaluate : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ASN cc_start: 0.8121 (m110) cc_final: 0.7612 (p0) REVERT: A 399 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6873 (pp20) REVERT: A 438 LYS cc_start: 0.7326 (mmtt) cc_final: 0.6837 (mtmp) REVERT: A 455 LYS cc_start: 0.7546 (mtpp) cc_final: 0.7159 (ptpt) REVERT: A 512 ARG cc_start: 0.7134 (ttp80) cc_final: 0.6918 (ttp80) REVERT: B 255 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.6643 (p0) REVERT: B 399 GLU cc_start: 0.7189 (pp20) cc_final: 0.6920 (pp20) REVERT: B 438 LYS cc_start: 0.7420 (mmtt) cc_final: 0.6856 (mtmt) REVERT: B 455 LYS cc_start: 0.7553 (mtpp) cc_final: 0.7247 (ptpt) REVERT: C 255 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.6636 (p0) REVERT: C 277 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: C 399 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6889 (pp20) REVERT: C 455 LYS cc_start: 0.7401 (mttm) cc_final: 0.7079 (ttmm) REVERT: D 255 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.6665 (p0) REVERT: D 277 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.6684 (tm-30) REVERT: D 399 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6933 (pp20) REVERT: D 455 LYS cc_start: 0.7494 (mtpp) cc_final: 0.7073 (ttmm) REVERT: E 162 ASP cc_start: 0.7179 (m-30) cc_final: 0.6834 (m-30) REVERT: E 179 MET cc_start: 0.6693 (mmm) cc_final: 0.5810 (tmm) REVERT: E 455 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7598 (ptmm) REVERT: F 206 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6770 (pmmt) REVERT: F 277 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: F 438 LYS cc_start: 0.7455 (mttm) cc_final: 0.7249 (mttm) REVERT: F 455 LYS cc_start: 0.7525 (mttm) cc_final: 0.7091 (ttmm) REVERT: G 255 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6681 (p0) REVERT: G 277 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.6840 (tm-30) REVERT: G 455 LYS cc_start: 0.7427 (mtpp) cc_final: 0.6984 (ptpt) REVERT: H 399 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6908 (pp20) REVERT: H 455 LYS cc_start: 0.7584 (mtpp) cc_final: 0.7174 (ptpt) outliers start: 125 outliers final: 81 residues processed: 477 average time/residue: 1.2537 time to fit residues: 721.8925 Evaluate side-chains 474 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 379 time to evaluate : 3.160 ------------------------------------------------------------------------------- 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 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 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 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 399 GLU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 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 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 270 VAL Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 251 optimal weight: 0.8980 chunk 177 optimal weight: 0.5980 chunk 174 optimal weight: 0.9980 chunk 363 optimal weight: 0.5980 chunk 339 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 130 optimal weight: 0.3980 chunk 228 optimal weight: 0.7980 chunk 201 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 312 ASN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 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 = 0.4082 r_free = 0.4082 target = 0.190512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137460 restraints weight = 33249.174| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.84 r_work: 0.3247 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 31460 Z= 0.110 Angle : 0.545 10.196 42632 Z= 0.280 Chirality : 0.043 0.232 4856 Planarity : 0.004 0.036 5352 Dihedral : 11.877 89.801 5336 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.26 % Favored : 95.30 % Rotamer: Outliers : 3.49 % Allowed : 18.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3896 helix: 1.23 (0.14), residues: 1472 sheet: 0.31 (0.22), residues: 472 loop : -0.60 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 466 PHE 0.010 0.001 PHE H 456 TYR 0.013 0.001 TYR A 353 ARG 0.003 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 1137) hydrogen bonds : angle 4.73871 ( 3192) covalent geometry : bond 0.00238 (31448) covalent geometry : angle 0.54541 (42632) Misc. bond : bond 0.00101 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 394 time to evaluate : 3.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6891 (pp20) REVERT: A 438 LYS cc_start: 0.7340 (mmtt) cc_final: 0.6876 (mtmp) REVERT: A 455 LYS cc_start: 0.7468 (mtpp) cc_final: 0.7065 (ttmm) REVERT: A 512 ARG cc_start: 0.7165 (ttp80) cc_final: 0.6949 (ttp80) REVERT: B 206 LYS cc_start: 0.6796 (OUTLIER) cc_final: 0.6469 (ptpp) REVERT: B 255 ASP cc_start: 0.7319 (p0) cc_final: 0.6642 (p0) REVERT: B 399 GLU cc_start: 0.7198 (pp20) cc_final: 0.6910 (pp20) REVERT: B 438 LYS cc_start: 0.7415 (mmtt) cc_final: 0.6850 (mtmt) REVERT: B 455 LYS cc_start: 0.7463 (mtpp) cc_final: 0.7093 (ttmm) REVERT: C 255 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6620 (p0) REVERT: C 277 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: C 399 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6902 (pp20) REVERT: C 455 LYS cc_start: 0.7292 (mttm) cc_final: 0.7018 (ttmm) REVERT: D 255 ASP cc_start: 0.7362 (p0) cc_final: 0.6684 (p0) REVERT: D 277 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.6617 (tm-30) REVERT: D 399 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6940 (pp20) REVERT: D 455 LYS cc_start: 0.7439 (mtpp) cc_final: 0.7062 (ttmm) REVERT: E 162 ASP cc_start: 0.7145 (m-30) cc_final: 0.6812 (m-30) REVERT: E 179 MET cc_start: 0.6697 (mmm) cc_final: 0.5816 (tmm) REVERT: E 455 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7573 (ptmm) REVERT: F 204 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.8012 (t) REVERT: F 206 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6868 (pmmt) REVERT: F 277 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.6880 (tm-30) REVERT: F 438 LYS cc_start: 0.7410 (mttm) cc_final: 0.6904 (mtmp) REVERT: F 455 LYS cc_start: 0.7309 (mttm) cc_final: 0.6936 (ttmm) REVERT: G 277 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.6883 (tm-30) REVERT: G 303 ASN cc_start: 0.8887 (m-40) cc_final: 0.8681 (m-40) REVERT: G 455 LYS cc_start: 0.7365 (mtpp) cc_final: 0.6985 (ptpt) REVERT: H 399 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6922 (pp20) REVERT: H 455 LYS cc_start: 0.7495 (mtpp) cc_final: 0.7122 (ttmm) outliers start: 112 outliers final: 67 residues processed: 484 average time/residue: 1.2875 time to fit residues: 748.9448 Evaluate side-chains 463 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 383 time to evaluate : 3.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 410 LYS Chi-restraints excluded: chain F residue 439 VAL 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 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 103 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 chunk 48 optimal weight: 0.0470 chunk 17 optimal weight: 5.9990 chunk 64 optimal weight: 0.0050 chunk 348 optimal weight: 0.7980 chunk 278 optimal weight: 0.9990 chunk 365 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.5092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 312 ASN A 368 GLN A 478 GLN B 368 GLN B 466 HIS B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 478 GLN E 368 GLN E 466 HIS E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 312 ASN H 368 GLN H 466 HIS H 478 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.190978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.138016 restraints weight = 33127.982| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.83 r_work: 0.3265 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 31460 Z= 0.108 Angle : 0.546 11.565 42632 Z= 0.279 Chirality : 0.043 0.170 4856 Planarity : 0.004 0.036 5352 Dihedral : 11.639 89.190 5332 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.47 % Favored : 95.12 % Rotamer: Outliers : 2.59 % Allowed : 19.17 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.14), residues: 3896 helix: 1.26 (0.14), residues: 1472 sheet: 0.35 (0.22), residues: 472 loop : -0.53 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 466 PHE 0.012 0.001 PHE H 456 TYR 0.012 0.001 TYR D 353 ARG 0.002 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 1137) hydrogen bonds : angle 4.70000 ( 3192) covalent geometry : bond 0.00233 (31448) covalent geometry : angle 0.54627 (42632) Misc. bond : bond 0.00097 ( 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 465 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 382 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6897 (pp20) REVERT: A 438 LYS cc_start: 0.7346 (mmtt) cc_final: 0.6906 (mtmp) REVERT: A 455 LYS cc_start: 0.7429 (mtpp) cc_final: 0.7062 (ttmm) REVERT: B 206 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6512 (ptpp) REVERT: B 255 ASP cc_start: 0.7317 (p0) cc_final: 0.6634 (p0) REVERT: B 399 GLU cc_start: 0.7193 (pp20) cc_final: 0.6960 (pp20) REVERT: B 455 LYS cc_start: 0.7322 (mtpp) cc_final: 0.6969 (ttmm) REVERT: C 255 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.6687 (p0) REVERT: C 277 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: C 399 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6916 (pp20) REVERT: C 455 LYS cc_start: 0.7254 (mttm) cc_final: 0.6995 (ttmm) REVERT: D 255 ASP cc_start: 0.7362 (p0) cc_final: 0.6691 (p0) REVERT: D 277 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.6583 (tm-30) REVERT: D 399 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6958 (pp20) REVERT: D 455 LYS cc_start: 0.7342 (mtpp) cc_final: 0.6992 (ttmm) REVERT: E 162 ASP cc_start: 0.7061 (m-30) cc_final: 0.6720 (m-30) REVERT: E 179 MET cc_start: 0.6715 (mmm) cc_final: 0.5846 (tmm) REVERT: E 455 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7563 (ptmm) REVERT: F 204 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.7853 (t) REVERT: F 206 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6740 (pmmt) REVERT: F 277 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: F 438 LYS cc_start: 0.7407 (mttm) cc_final: 0.6909 (mtmp) REVERT: F 455 LYS cc_start: 0.7292 (mttm) cc_final: 0.6937 (ttmm) REVERT: F 510 GLU cc_start: 0.7172 (tp30) cc_final: 0.6612 (mp0) REVERT: G 277 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.6841 (tm-30) REVERT: G 303 ASN cc_start: 0.8878 (m-40) cc_final: 0.8671 (m-40) REVERT: G 455 LYS cc_start: 0.7275 (mtpp) cc_final: 0.6887 (ptpt) REVERT: H 399 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6937 (pp20) REVERT: H 455 LYS cc_start: 0.7474 (mtpp) cc_final: 0.7144 (ttmm) outliers start: 83 outliers final: 59 residues processed: 450 average time/residue: 1.2931 time to fit residues: 699.3122 Evaluate side-chains 449 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 377 time to evaluate : 3.152 ------------------------------------------------------------------------------- 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 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 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 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 E residue 455 LYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 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 50 optimal weight: 1.9990 chunk 351 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 309 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 237 optimal weight: 10.0000 chunk 257 optimal weight: 0.0470 chunk 199 optimal weight: 2.9990 chunk 350 optimal weight: 8.9990 chunk 185 optimal weight: 0.9980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 441 GLN D 466 HIS D 478 GLN E 368 GLN E 478 GLN F 368 GLN F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 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 = 0.4075 r_free = 0.4075 target = 0.189883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136953 restraints weight = 33117.671| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.86 r_work: 0.3247 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1804 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= 0.132 Angle : 0.564 11.723 42632 Z= 0.288 Chirality : 0.044 0.222 4856 Planarity : 0.004 0.037 5352 Dihedral : 11.622 89.462 5332 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.95 % Favored : 94.64 % Rotamer: Outliers : 2.77 % Allowed : 19.17 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3896 helix: 1.20 (0.14), residues: 1472 sheet: 0.33 (0.22), residues: 472 loop : -0.59 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 454 PHE 0.018 0.001 PHE F 456 TYR 0.013 0.001 TYR B 348 ARG 0.003 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 1137) hydrogen bonds : angle 4.74700 ( 3192) covalent geometry : bond 0.00298 (31448) covalent geometry : angle 0.56376 (42632) Misc. bond : bond 0.00122 ( 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 474 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 385 time to evaluate : 3.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8037 (tp30) cc_final: 0.7186 (mp0) REVERT: A 399 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6866 (pp20) REVERT: A 438 LYS cc_start: 0.7345 (mmtt) cc_final: 0.6900 (mtmp) REVERT: A 455 LYS cc_start: 0.7476 (mtpp) cc_final: 0.7090 (ttmm) REVERT: A 512 ARG cc_start: 0.7149 (ttp80) cc_final: 0.6932 (ttp80) REVERT: B 255 ASP cc_start: 0.7312 (p0) cc_final: 0.6637 (p0) REVERT: B 399 GLU cc_start: 0.7180 (pp20) cc_final: 0.6939 (pp20) REVERT: B 455 LYS cc_start: 0.7427 (mtpp) cc_final: 0.7081 (ttmm) REVERT: C 255 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.6675 (p0) REVERT: C 277 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: C 399 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6895 (pp20) REVERT: C 455 LYS cc_start: 0.7293 (mttm) cc_final: 0.7033 (ttmm) REVERT: D 255 ASP cc_start: 0.7388 (p0) cc_final: 0.6717 (p0) REVERT: D 277 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: D 399 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6929 (pp20) REVERT: D 455 LYS cc_start: 0.7374 (mtpp) cc_final: 0.7023 (ttmm) REVERT: E 162 ASP cc_start: 0.7059 (m-30) cc_final: 0.6697 (m-30) REVERT: E 179 MET cc_start: 0.6719 (mmm) cc_final: 0.5954 (tmm) REVERT: E 277 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: E 455 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7578 (ptmm) REVERT: F 204 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7960 (t) REVERT: F 206 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6895 (pmmt) REVERT: F 277 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: F 438 LYS cc_start: 0.7432 (mttm) cc_final: 0.6927 (mtmp) REVERT: F 455 LYS cc_start: 0.7310 (mttm) cc_final: 0.6957 (ttmm) REVERT: F 510 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: G 65 LEU cc_start: 0.8895 (mt) cc_final: 0.8687 (mm) REVERT: G 277 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.6835 (tm-30) REVERT: G 455 LYS cc_start: 0.7294 (mtpp) cc_final: 0.6908 (ptpt) REVERT: H 277 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.6429 (tm-30) REVERT: H 399 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6928 (pp20) REVERT: H 455 LYS cc_start: 0.7523 (mtpp) cc_final: 0.7194 (ttmm) outliers start: 89 outliers final: 63 residues processed: 453 average time/residue: 1.2285 time to fit residues: 668.8240 Evaluate side-chains 459 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 381 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 439 VAL 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 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 417 LEU 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 365 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 287 optimal weight: 9.9990 chunk 227 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 10 optimal weight: 0.0030 chunk 310 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 466 HIS D 478 GLN E 368 GLN E 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 = 0.4087 r_free = 0.4087 target = 0.190893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.137284 restraints weight = 32811.069| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.84 r_work: 0.3252 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31460 Z= 0.120 Angle : 0.569 15.850 42632 Z= 0.288 Chirality : 0.044 0.233 4856 Planarity : 0.004 0.037 5352 Dihedral : 11.537 89.829 5332 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.65 % Favored : 94.94 % Rotamer: Outliers : 2.68 % Allowed : 19.36 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3896 helix: 1.22 (0.14), residues: 1472 sheet: 0.33 (0.22), residues: 472 loop : -0.55 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 454 PHE 0.017 0.001 PHE E 456 TYR 0.012 0.001 TYR H 353 ARG 0.002 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 1137) hydrogen bonds : angle 4.73647 ( 3192) covalent geometry : bond 0.00267 (31448) covalent geometry : angle 0.56894 (42632) Misc. bond : bond 0.00110 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29938.42 seconds wall clock time: 514 minutes 28.93 seconds (30868.93 seconds total)