Starting phenix.real_space_refine on Sat Jun 6 16:55:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8o_42026/06_2026/8u8o_42026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8o_42026/06_2026/8u8o_42026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u8o_42026/06_2026/8u8o_42026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8o_42026/06_2026/8u8o_42026.map" model { file = "/net/cci-nas-00/data/ceres_data/8u8o_42026/06_2026/8u8o_42026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8o_42026/06_2026/8u8o_42026.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.074 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 192 5.16 5 C 18760 2.51 5 N 5136 2.21 5 O 5920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30080 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "B" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "C" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "D" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "E" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "F" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "G" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "H" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 6.32, per 1000 atoms: 0.21 Number of scatterers: 30080 At special positions: 0 Unit cell: (159.327, 159.327, 134.037, 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 192 16.00 P 72 15.00 O 5920 8.00 N 5136 7.00 C 18760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.4 seconds 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6944 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 48 sheets defined 41.7% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 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 109 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.630A pdb=" N LYS A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.601A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.736A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) 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 417 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 486 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'B' and resid 19 through 24 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 109 Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 224 through 229 removed outlier: 3.638A pdb=" N LYS B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.602A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.737A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.623A 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 417 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 486 Processing helix chain 'B' and resid 494 through 501 Processing helix chain 'C' and resid 19 through 24 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 109 Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 159 through 164 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 229 removed outlier: 3.633A pdb=" N LYS C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.612A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.738A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.623A 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 417 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 486 Processing helix chain 'C' and resid 494 through 501 Processing helix chain 'D' and resid 19 through 24 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 109 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 159 through 164 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 224 through 229 removed outlier: 3.629A pdb=" N LYS D 229 " --> pdb=" O THR D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.589A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.737A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) 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 417 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 486 Processing helix chain 'D' and resid 494 through 501 Processing helix chain 'E' and resid 19 through 24 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 109 Processing helix chain 'E' and resid 126 through 138 Processing helix chain 'E' and resid 159 through 164 Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 224 through 229 removed outlier: 3.638A pdb=" N LYS E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.602A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 3.736A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.623A 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 417 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 486 Processing helix chain 'E' and resid 494 through 501 Processing helix chain 'F' and resid 19 through 24 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 109 Processing helix chain 'F' and resid 126 through 138 Processing helix chain 'F' and resid 159 through 164 Processing helix chain 'F' and resid 183 through 185 No H-bonds generated for 'chain 'F' and resid 183 through 185' Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 224 through 229 removed outlier: 3.636A pdb=" N LYS F 229 " --> pdb=" O THR F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.612A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.737A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.623A 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 417 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 486 Processing helix chain 'F' and resid 494 through 501 Processing helix chain 'G' and resid 19 through 24 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 109 Processing helix chain 'G' and resid 126 through 138 Processing helix chain 'G' and resid 159 through 164 Processing helix chain 'G' and resid 183 through 185 No H-bonds generated for 'chain 'G' and resid 183 through 185' Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 224 through 229 removed outlier: 3.634A pdb=" N LYS G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 266 removed outlier: 3.594A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 3.736A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.624A 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 417 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 486 Processing helix chain 'G' and resid 494 through 501 Processing helix chain 'H' and resid 19 through 24 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 109 Processing helix chain 'H' and resid 126 through 138 Processing helix chain 'H' and resid 159 through 164 Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 224 through 229 removed outlier: 3.634A pdb=" N LYS H 229 " --> pdb=" O THR H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 266 removed outlier: 3.595A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 3.736A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (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 417 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 486 Processing helix chain 'H' and resid 494 through 501 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: 3.630A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N MET A 385 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.652A pdb=" N ILE A 157 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.357A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 4.116A pdb=" N SER A 444 " --> pdb=" O THR D 510 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER D 508 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.940A pdb=" N SER A 508 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 444 " --> pdb=" O THR 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: 3.621A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N MET B 385 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.652A pdb=" N ILE B 157 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 188 through 189 removed outlier: 6.361A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.967A pdb=" N SER B 508 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER C 444 " --> pdb=" O THR B 510 " (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: 3.617A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N MET C 385 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.653A pdb=" N ILE C 157 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.375A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.966A pdb=" N SER C 508 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER D 444 " --> pdb=" O THR C 510 " (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: 3.631A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET D 385 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.652A pdb=" N ILE D 157 " --> pdb=" O THR D 180 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.375A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (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: 3.619A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N MET E 385 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.651A pdb=" N ILE E 157 " --> pdb=" O THR E 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 188 through 189 removed outlier: 6.359A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 401 through 402 removed outlier: 4.112A pdb=" N SER E 444 " --> pdb=" O THR H 510 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER H 508 " --> pdb=" O SER E 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.917A pdb=" N SER E 508 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER F 444 " --> pdb=" O THR 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: 3.620A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N MET F 385 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.653A pdb=" N ILE F 157 " --> pdb=" O THR F 180 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.370A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.902A pdb=" N SER F 508 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER G 444 " --> pdb=" O THR F 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: 3.622A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.653A pdb=" N ILE G 157 " --> pdb=" O THR G 180 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.369A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.974A pdb=" N SER G 508 " --> pdb=" O SER H 446 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER H 444 " --> pdb=" O THR G 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: 3.631A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.651A pdb=" N ILE H 157 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 188 through 189 removed outlier: 6.374A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) 1169 hydrogen bonds defined for protein. 3267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.85 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4969 1.30 - 1.43: 7402 1.43 - 1.56: 17765 1.56 - 1.69: 128 1.69 - 1.82: 328 Bond restraints: 30592 Sorted by residual: bond pdb=" C2 IMP F 603 " pdb=" N3 IMP F 603 " ideal model delta sigma weight residual 1.301 1.456 -0.155 2.00e-02 2.50e+03 5.97e+01 bond pdb=" C2 IMP G 603 " pdb=" N3 IMP G 603 " ideal model delta sigma weight residual 1.301 1.455 -0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" C2 IMP B 603 " pdb=" N3 IMP B 603 " ideal model delta sigma weight residual 1.301 1.455 -0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" C2 IMP C 603 " pdb=" N3 IMP C 603 " ideal model delta sigma weight residual 1.301 1.455 -0.154 2.00e-02 2.50e+03 5.92e+01 bond pdb=" C2 IMP D 603 " pdb=" N3 IMP D 603 " ideal model delta sigma weight residual 1.301 1.455 -0.154 2.00e-02 2.50e+03 5.92e+01 ... (remaining 30587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 40055 1.91 - 3.82: 1188 3.82 - 5.74: 179 5.74 - 7.65: 86 7.65 - 9.56: 28 Bond angle restraints: 41536 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 130.93 8.94 1.00e+00 1.00e+00 7.99e+01 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 131.00 8.87 1.00e+00 1.00e+00 7.86e+01 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 131.03 8.84 1.00e+00 1.00e+00 7.81e+01 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 131.06 8.81 1.00e+00 1.00e+00 7.77e+01 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 131.87 8.00 1.00e+00 1.00e+00 6.40e+01 ... (remaining 41531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16412 17.98 - 35.97: 1758 35.97 - 53.95: 657 53.95 - 71.93: 148 71.93 - 89.91: 57 Dihedral angle restraints: 19032 sinusoidal: 8144 harmonic: 10888 Sorted by residual: dihedral pdb=" CA THR F 74 " pdb=" C THR F 74 " pdb=" N GLU F 75 " pdb=" CA GLU F 75 " ideal model delta harmonic sigma weight residual 180.00 158.85 21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA THR C 74 " pdb=" C THR C 74 " pdb=" N GLU C 75 " pdb=" CA GLU C 75 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA THR E 74 " pdb=" C THR E 74 " pdb=" N GLU E 75 " pdb=" CA GLU E 75 " ideal model delta harmonic sigma weight residual 180.00 158.90 21.10 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 19029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2674 0.031 - 0.062: 1321 0.062 - 0.093: 509 0.093 - 0.124: 281 0.124 - 0.155: 55 Chirality restraints: 4840 Sorted by residual: chirality pdb=" C3' IMP H 603 " pdb=" C2' IMP H 603 " pdb=" C4' IMP H 603 " pdb=" O3' IMP H 603 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" C3' IMP F 603 " pdb=" C2' IMP F 603 " pdb=" C4' IMP F 603 " pdb=" O3' IMP F 603 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" C3' IMP B 603 " pdb=" C2' IMP B 603 " pdb=" C4' IMP B 603 " pdb=" O3' IMP B 603 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 4837 not shown) Planarity restraints: 5160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 63 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO G 64 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 64 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 64 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 63 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO C 64 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 63 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO D 64 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " 0.027 5.00e-02 4.00e+02 ... (remaining 5157 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6185 2.79 - 3.31: 28229 3.31 - 3.84: 51888 3.84 - 4.37: 63870 4.37 - 4.90: 102765 Nonbonded interactions: 252937 Sorted by model distance: nonbonded pdb=" O ALA G 396 " pdb=" NZ LYS G 409 " model vdw 2.256 3.120 nonbonded pdb=" O ALA F 396 " pdb=" NZ LYS F 409 " model vdw 2.261 3.120 nonbonded pdb=" O ALA E 396 " pdb=" NZ LYS E 409 " model vdw 2.264 3.120 nonbonded pdb=" O ALA B 396 " pdb=" NZ LYS B 409 " model vdw 2.264 3.120 nonbonded pdb=" O ALA C 396 " pdb=" NZ LYS C 409 " model vdw 2.265 3.120 ... (remaining 252932 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: 0.10 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.100 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 0.007 0.155 30592 Z= 0.334 Angle : 0.842 9.562 41536 Z= 0.454 Chirality : 0.047 0.155 4840 Planarity : 0.005 0.049 5160 Dihedral : 17.878 89.914 12088 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.24 % Allowed : 12.15 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.13), residues: 3808 helix: 0.80 (0.13), residues: 1464 sheet: 0.15 (0.25), residues: 448 loop : -0.44 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 57 TYR 0.012 0.002 TYR H 353 PHE 0.014 0.002 PHE C 357 HIS 0.005 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.33 (30592) covalent geometry : angle 0.84217 / 0.45 (41536) hydrogen bonds : bond 0.15353 / 10.36 ( 1169) hydrogen bonds : angle 6.30070 / 4.47 ( 3267) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 855 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 11 residues processed: 875 average time/residue: 0.7622 time to fit residues: 768.3271 Evaluate side-chains 664 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 653 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 GLN A 368 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 368 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN C 441 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN D 368 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN F 368 GLN F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN G 368 GLN ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.092325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.080916 restraints weight = 54772.536| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.99 r_work: 0.3127 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 30592 Z= 0.154 Angle : 0.581 6.527 41536 Z= 0.308 Chirality : 0.044 0.150 4840 Planarity : 0.004 0.044 5160 Dihedral : 12.431 85.663 5306 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.39 % Allowed : 16.80 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.13), residues: 3808 helix: 1.52 (0.14), residues: 1464 sheet: 0.30 (0.24), residues: 448 loop : -0.28 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 136 TYR 0.011 0.001 TYR C 353 PHE 0.009 0.002 PHE D 114 HIS 0.007 0.001 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 (30592) covalent geometry : angle 0.58148 / 0.31 (41536) hydrogen bonds : bond 0.04173 / 2.82 ( 1169) hydrogen bonds : angle 5.48015 / 3.83 ( 3267) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 690 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.8473 (ttp80) cc_final: 0.8154 (tmm-80) REVERT: A 352 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8703 (tp30) REVERT: A 447 ILE cc_start: 0.8981 (mm) cc_final: 0.8777 (mt) REVERT: A 491 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8546 (tp30) REVERT: B 438 LYS cc_start: 0.8775 (ptmt) cc_final: 0.8545 (mtmm) REVERT: B 447 ILE cc_start: 0.8921 (mm) cc_final: 0.8676 (mt) REVERT: B 491 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8568 (tp30) REVERT: C 136 ARG cc_start: 0.8491 (ttp80) cc_final: 0.8083 (ttp80) REVERT: C 153 LYS cc_start: 0.8636 (mmmm) cc_final: 0.8431 (tppp) REVERT: C 491 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8532 (tp30) REVERT: D 136 ARG cc_start: 0.8494 (ttp80) cc_final: 0.8088 (ttp80) REVERT: D 410 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8248 (ttpp) REVERT: E 410 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8286 (ttpp) REVERT: F 136 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7312 (ttp80) REVERT: F 137 HIS cc_start: 0.8396 (m170) cc_final: 0.8154 (m-70) REVERT: F 153 LYS cc_start: 0.8708 (mmmm) cc_final: 0.8076 (mmmm) REVERT: F 410 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8329 (ttpp) REVERT: F 487 GLU cc_start: 0.5550 (mm-30) cc_final: 0.5315 (mm-30) REVERT: G 136 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7482 (ttp80) REVERT: H 153 LYS cc_start: 0.8581 (mmmm) cc_final: 0.7772 (mmmm) REVERT: H 352 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8523 (tp30) REVERT: H 491 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8542 (tp30) outliers start: 75 outliers final: 28 residues processed: 731 average time/residue: 0.7664 time to fit residues: 643.4023 Evaluate side-chains 665 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 633 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 178 optimal weight: 0.0980 chunk 179 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 297 optimal weight: 2.9990 chunk 305 optimal weight: 0.0980 chunk 294 optimal weight: 0.9990 chunk 225 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 314 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 GLN A 303 ASN A 368 GLN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN C 368 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN G 303 ASN G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.092855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.081807 restraints weight = 55138.900| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.93 r_work: 0.3145 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30592 Z= 0.107 Angle : 0.508 6.925 41536 Z= 0.273 Chirality : 0.042 0.153 4840 Planarity : 0.004 0.038 5160 Dihedral : 11.129 89.963 5288 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.84 % Allowed : 17.25 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.14), residues: 3808 helix: 1.70 (0.14), residues: 1520 sheet: 0.68 (0.26), residues: 352 loop : -0.08 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 203 TYR 0.010 0.001 TYR F 353 PHE 0.006 0.001 PHE E 139 HIS 0.004 0.001 HIS G 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (30592) covalent geometry : angle 0.50761 / 0.27 (41536) hydrogen bonds : bond 0.03499 / 2.36 ( 1169) hydrogen bonds : angle 5.27937 / 3.69 ( 3267) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 655 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7610 (tm-30) REVERT: A 136 ARG cc_start: 0.8351 (ttp80) cc_final: 0.8128 (ttp80) REVERT: A 447 ILE cc_start: 0.9024 (mm) cc_final: 0.8803 (OUTLIER) REVERT: B 132 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7849 (tp30) REVERT: B 438 LYS cc_start: 0.8670 (ptmt) cc_final: 0.8419 (mtmm) REVERT: B 447 ILE cc_start: 0.8935 (mm) cc_final: 0.8704 (OUTLIER) REVERT: B 491 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8550 (tp30) REVERT: C 132 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7631 (tm-30) REVERT: C 136 ARG cc_start: 0.8347 (ttp80) cc_final: 0.8142 (ttp80) REVERT: C 491 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8500 (tp30) REVERT: D 132 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7724 (tm-30) REVERT: D 410 LYS cc_start: 0.8553 (mtpp) cc_final: 0.8292 (ttpp) REVERT: E 132 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7593 (tm-30) REVERT: E 136 ARG cc_start: 0.7948 (tmm-80) cc_final: 0.7717 (ttp80) REVERT: E 352 GLU cc_start: 0.8733 (tp30) cc_final: 0.8443 (tp30) REVERT: E 410 LYS cc_start: 0.8579 (mtpp) cc_final: 0.8345 (ttpp) REVERT: E 487 GLU cc_start: 0.5434 (mm-30) cc_final: 0.3683 (mm-30) REVERT: F 410 LYS cc_start: 0.8601 (mtpp) cc_final: 0.8372 (ttpp) REVERT: F 487 GLU cc_start: 0.5894 (mm-30) cc_final: 0.4001 (mm-30) REVERT: G 132 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7541 (tm-30) REVERT: G 495 MET cc_start: 0.8554 (tpp) cc_final: 0.8325 (tpp) REVERT: H 132 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7686 (tm-30) REVERT: H 199 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8212 (tm-30) REVERT: H 410 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8357 (ttpp) REVERT: H 487 GLU cc_start: 0.5291 (mm-30) cc_final: 0.3414 (mm-30) outliers start: 89 outliers final: 27 residues processed: 698 average time/residue: 0.7881 time to fit residues: 631.0014 Evaluate side-chains 671 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 643 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 410 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 24 optimal weight: 0.2980 chunk 178 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 241 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 319 optimal weight: 0.9990 chunk 334 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 338 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 368 GLN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.091992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.081076 restraints weight = 55061.655| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.92 r_work: 0.3142 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30592 Z= 0.113 Angle : 0.520 7.164 41536 Z= 0.276 Chirality : 0.041 0.152 4840 Planarity : 0.004 0.038 5160 Dihedral : 10.628 89.793 5288 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.30 % Allowed : 18.40 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.14), residues: 3808 helix: 1.89 (0.14), residues: 1512 sheet: 0.85 (0.29), residues: 272 loop : -0.02 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 203 TYR 0.010 0.001 TYR E 353 PHE 0.006 0.001 PHE F 114 HIS 0.004 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (30592) covalent geometry : angle 0.51980 / 0.28 (41536) hydrogen bonds : bond 0.03474 / 2.34 ( 1169) hydrogen bonds : angle 5.13754 / 3.60 ( 3267) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 651 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7484 (tm-30) REVERT: A 228 LYS cc_start: 0.9027 (mtpt) cc_final: 0.8811 (mtmt) REVERT: A 447 ILE cc_start: 0.9042 (mm) cc_final: 0.8819 (mt) REVERT: B 132 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7886 (tp30) REVERT: B 136 ARG cc_start: 0.8389 (ttp80) cc_final: 0.7948 (mtm110) REVERT: B 153 LYS cc_start: 0.8608 (mmmm) cc_final: 0.8285 (tppt) REVERT: B 447 ILE cc_start: 0.8979 (mm) cc_final: 0.8743 (OUTLIER) REVERT: B 491 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8540 (tp30) REVERT: C 132 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7364 (tm-30) REVERT: C 136 ARG cc_start: 0.8346 (ttp80) cc_final: 0.8068 (ttp80) REVERT: C 491 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8528 (tp30) REVERT: D 132 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7650 (tm-30) REVERT: D 153 LYS cc_start: 0.8598 (mmmm) cc_final: 0.8044 (tppt) REVERT: D 203 ARG cc_start: 0.8054 (mtm110) cc_final: 0.7818 (mtm110) REVERT: D 410 LYS cc_start: 0.8653 (mtpp) cc_final: 0.8411 (ttpp) REVERT: E 132 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7152 (tm-30) REVERT: E 199 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8183 (tm-30) REVERT: E 410 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8444 (ttpp) REVERT: E 487 GLU cc_start: 0.5486 (mm-30) cc_final: 0.3649 (mm-30) REVERT: F 136 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7121 (tmm-80) REVERT: F 149 THR cc_start: 0.8583 (t) cc_final: 0.8283 (p) REVERT: F 410 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8466 (ttpp) REVERT: F 487 GLU cc_start: 0.5953 (mm-30) cc_final: 0.4165 (mm-30) REVERT: G 132 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7723 (tm-30) REVERT: G 410 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8458 (ttpp) REVERT: G 487 GLU cc_start: 0.5725 (mm-30) cc_final: 0.3813 (mm-30) REVERT: G 495 MET cc_start: 0.8595 (tpp) cc_final: 0.8327 (tpp) REVERT: H 132 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7422 (tm-30) REVERT: H 136 ARG cc_start: 0.8224 (ttp80) cc_final: 0.8005 (mtm110) REVERT: H 410 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8423 (ttpp) REVERT: H 487 GLU cc_start: 0.5460 (mm-30) cc_final: 0.3555 (mm-30) outliers start: 72 outliers final: 23 residues processed: 688 average time/residue: 0.7879 time to fit residues: 622.7299 Evaluate side-chains 660 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 634 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 410 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 104 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 379 optimal weight: 3.9990 chunk 312 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 368 GLN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 ASN H 441 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.089384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.078510 restraints weight = 55401.310| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.93 r_work: 0.3093 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30592 Z= 0.158 Angle : 0.556 6.471 41536 Z= 0.295 Chirality : 0.042 0.142 4840 Planarity : 0.004 0.039 5160 Dihedral : 10.715 88.469 5288 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.81 % Allowed : 18.94 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.14), residues: 3808 helix: 1.94 (0.14), residues: 1472 sheet: 0.59 (0.27), residues: 352 loop : -0.08 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 203 TYR 0.012 0.001 TYR A 353 PHE 0.011 0.002 PHE D 114 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (30592) covalent geometry : angle 0.55590 / 0.30 (41536) hydrogen bonds : bond 0.04158 / 2.80 ( 1169) hydrogen bonds : angle 5.15957 / 3.62 ( 3267) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 658 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7565 (tm-30) REVERT: B 132 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7914 (tp30) REVERT: B 136 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8143 (mtm110) REVERT: B 149 THR cc_start: 0.8670 (t) cc_final: 0.8458 (p) REVERT: B 352 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8689 (tp30) REVERT: B 447 ILE cc_start: 0.9054 (mm) cc_final: 0.8825 (OUTLIER) REVERT: C 132 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7392 (tm-30) REVERT: C 136 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8137 (ttp80) REVERT: C 149 THR cc_start: 0.8660 (t) cc_final: 0.8384 (p) REVERT: C 206 LYS cc_start: 0.8908 (mmmt) cc_final: 0.8695 (mmtm) REVERT: D 132 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7563 (tm-30) REVERT: D 149 THR cc_start: 0.8698 (t) cc_final: 0.8396 (p) REVERT: D 410 LYS cc_start: 0.8750 (mtpp) cc_final: 0.8548 (ttpp) REVERT: E 132 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7561 (tm-30) REVERT: E 487 GLU cc_start: 0.5900 (mm-30) cc_final: 0.3782 (mm-30) REVERT: F 132 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7394 (tm-30) REVERT: F 149 THR cc_start: 0.8639 (t) cc_final: 0.8416 (p) REVERT: F 153 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8465 (tppt) REVERT: F 206 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8598 (mmtm) REVERT: F 487 GLU cc_start: 0.6103 (mm-30) cc_final: 0.3895 (mm-30) REVERT: G 132 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7606 (tm-30) REVERT: G 410 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8533 (ttpp) REVERT: G 487 GLU cc_start: 0.6020 (mm-30) cc_final: 0.4000 (mm-30) REVERT: G 495 MET cc_start: 0.8672 (tpp) cc_final: 0.8379 (tpp) REVERT: H 132 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7443 (tm-30) REVERT: H 136 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8159 (mtm110) REVERT: H 179 MET cc_start: 0.8684 (ptm) cc_final: 0.8461 (pp-130) REVERT: H 199 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7487 (tm-30) REVERT: H 203 ARG cc_start: 0.8310 (mtm110) cc_final: 0.8108 (mtm110) REVERT: H 303 ASN cc_start: 0.8136 (m-40) cc_final: 0.7911 (m-40) REVERT: H 410 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8508 (ttpp) REVERT: H 487 GLU cc_start: 0.5648 (mm-30) cc_final: 0.3765 (mm-30) outliers start: 88 outliers final: 39 residues processed: 696 average time/residue: 0.7880 time to fit residues: 630.4558 Evaluate side-chains 689 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 649 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 410 LYS Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 162 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 301 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 317 optimal weight: 0.9990 chunk 245 optimal weight: 0.0770 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 368 GLN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.088736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.077970 restraints weight = 55357.594| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.92 r_work: 0.3084 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30592 Z= 0.162 Angle : 0.579 7.962 41536 Z= 0.305 Chirality : 0.043 0.152 4840 Planarity : 0.004 0.043 5160 Dihedral : 10.741 87.637 5288 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.65 % Allowed : 20.38 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.14), residues: 3808 helix: 1.90 (0.14), residues: 1464 sheet: 0.59 (0.27), residues: 352 loop : -0.14 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 203 TYR 0.011 0.001 TYR E 353 PHE 0.010 0.002 PHE D 114 HIS 0.003 0.001 HIS G 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (30592) covalent geometry : angle 0.57919 / 0.31 (41536) hydrogen bonds : bond 0.04109 / 2.77 ( 1169) hydrogen bonds : angle 5.14518 / 3.60 ( 3267) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 658 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8011 (tm-30) cc_final: 0.6924 (tm-30) REVERT: A 136 ARG cc_start: 0.8426 (mtm110) cc_final: 0.8015 (ttm-80) REVERT: A 196 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: B 132 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7908 (tp30) REVERT: B 136 ARG cc_start: 0.8576 (ttp80) cc_final: 0.8205 (mtm110) REVERT: B 196 GLU cc_start: 0.8283 (mp0) cc_final: 0.8045 (mp0) REVERT: B 447 ILE cc_start: 0.9093 (mm) cc_final: 0.8863 (OUTLIER) REVERT: C 132 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7477 (tm-30) REVERT: C 136 ARG cc_start: 0.8500 (ttp80) cc_final: 0.8222 (ttp80) REVERT: C 149 THR cc_start: 0.8697 (t) cc_final: 0.8474 (p) REVERT: D 132 GLU cc_start: 0.8034 (tm-30) cc_final: 0.6990 (tm-30) REVERT: D 136 ARG cc_start: 0.8431 (mtm110) cc_final: 0.8068 (ttm-80) REVERT: D 149 THR cc_start: 0.8674 (t) cc_final: 0.8413 (p) REVERT: D 206 LYS cc_start: 0.8889 (mmmt) cc_final: 0.8686 (mptp) REVERT: E 132 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7405 (tm-30) REVERT: E 136 ARG cc_start: 0.8390 (mtm110) cc_final: 0.7974 (mtm110) REVERT: E 487 GLU cc_start: 0.5859 (mm-30) cc_final: 0.3663 (mm-30) REVERT: F 132 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7509 (tm-30) REVERT: F 136 ARG cc_start: 0.8363 (ttp80) cc_final: 0.8161 (ttp80) REVERT: F 153 LYS cc_start: 0.8737 (mmmm) cc_final: 0.8462 (tppt) REVERT: F 196 GLU cc_start: 0.8361 (mp0) cc_final: 0.8130 (mp0) REVERT: F 487 GLU cc_start: 0.6088 (mm-30) cc_final: 0.3688 (mm-30) REVERT: G 132 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7726 (tm-30) REVERT: G 196 GLU cc_start: 0.8343 (mp0) cc_final: 0.8137 (mp0) REVERT: G 203 ARG cc_start: 0.8338 (mtm110) cc_final: 0.8055 (mtm110) REVERT: G 487 GLU cc_start: 0.6031 (mm-30) cc_final: 0.3886 (mm-30) REVERT: G 495 MET cc_start: 0.8687 (tpp) cc_final: 0.8398 (tpp) REVERT: H 132 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7459 (tm-30) REVERT: H 136 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8206 (mtm110) REVERT: H 410 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8528 (ttpp) REVERT: H 487 GLU cc_start: 0.5682 (mm-30) cc_final: 0.3598 (mm-30) outliers start: 83 outliers final: 44 residues processed: 703 average time/residue: 0.7742 time to fit residues: 627.4094 Evaluate side-chains 690 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 645 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 410 LYS Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 86 optimal weight: 0.2980 chunk 320 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 250 optimal weight: 0.9980 chunk 216 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 367 optimal weight: 8.9990 chunk 225 optimal weight: 5.9990 chunk 271 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 242 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.078996 restraints weight = 55349.358| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.91 r_work: 0.3105 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30592 Z= 0.124 Angle : 0.565 10.296 41536 Z= 0.296 Chirality : 0.041 0.147 4840 Planarity : 0.004 0.049 5160 Dihedral : 10.521 88.205 5288 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.23 % Allowed : 21.01 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.14), residues: 3808 helix: 2.05 (0.14), residues: 1464 sheet: 0.59 (0.26), residues: 352 loop : -0.07 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 203 TYR 0.010 0.001 TYR F 353 PHE 0.007 0.001 PHE C 114 HIS 0.003 0.000 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (30592) covalent geometry : angle 0.56516 / 0.30 (41536) hydrogen bonds : bond 0.03530 / 2.38 ( 1169) hydrogen bonds : angle 5.07576 / 3.55 ( 3267) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 651 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8013 (tm-30) cc_final: 0.6994 (tm-30) REVERT: A 136 ARG cc_start: 0.8412 (mtm110) cc_final: 0.7983 (ttm-80) REVERT: A 196 GLU cc_start: 0.8336 (mp0) cc_final: 0.8122 (mp0) REVERT: B 132 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7875 (tp30) REVERT: B 136 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8187 (mtm110) REVERT: B 196 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: C 132 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7699 (tm-30) REVERT: D 132 GLU cc_start: 0.8013 (tm-30) cc_final: 0.6989 (tm-30) REVERT: D 136 ARG cc_start: 0.8405 (mtm110) cc_final: 0.8064 (ttm-80) REVERT: E 132 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7401 (tm-30) REVERT: E 136 ARG cc_start: 0.8367 (mtm110) cc_final: 0.7976 (mtm110) REVERT: E 487 GLU cc_start: 0.5821 (mm-30) cc_final: 0.3733 (mm-30) REVERT: F 132 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7669 (tm-30) REVERT: F 153 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8541 (tppt) REVERT: F 196 GLU cc_start: 0.8336 (mp0) cc_final: 0.8109 (mp0) REVERT: F 487 GLU cc_start: 0.6087 (mm-30) cc_final: 0.3905 (mm-30) REVERT: G 132 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7670 (tm-30) REVERT: G 196 GLU cc_start: 0.8334 (mp0) cc_final: 0.8099 (mp0) REVERT: G 487 GLU cc_start: 0.6055 (mm-30) cc_final: 0.3955 (mm-30) REVERT: G 495 MET cc_start: 0.8704 (tpp) cc_final: 0.8404 (tpp) REVERT: H 132 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7489 (tp30) REVERT: H 136 ARG cc_start: 0.8426 (ttp80) cc_final: 0.8178 (mtm110) REVERT: H 410 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8525 (ttpp) REVERT: H 487 GLU cc_start: 0.5567 (mm-30) cc_final: 0.3821 (mm-30) outliers start: 70 outliers final: 41 residues processed: 690 average time/residue: 0.7740 time to fit residues: 615.5774 Evaluate side-chains 682 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 639 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 410 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 364 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 264 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 308 optimal weight: 7.9990 chunk 322 optimal weight: 0.7980 chunk 365 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.087553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.076822 restraints weight = 55366.190| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.91 r_work: 0.3064 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30592 Z= 0.189 Angle : 0.622 9.407 41536 Z= 0.326 Chirality : 0.043 0.140 4840 Planarity : 0.005 0.056 5160 Dihedral : 10.788 85.987 5288 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.39 % Allowed : 21.17 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.13), residues: 3808 helix: 1.94 (0.14), residues: 1424 sheet: 0.49 (0.26), residues: 368 loop : -0.16 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 203 TYR 0.011 0.001 TYR A 353 PHE 0.011 0.002 PHE F 110 HIS 0.003 0.001 HIS G 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (30592) covalent geometry : angle 0.62193 / 0.33 (41536) hydrogen bonds : bond 0.04381 / 2.96 ( 1169) hydrogen bonds : angle 5.13724 / 3.59 ( 3267) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 637 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 179 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8497 (pp-130) REVERT: B 132 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7910 (tp30) REVERT: B 136 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8213 (mtm110) REVERT: B 196 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: B 352 GLU cc_start: 0.8906 (tp30) cc_final: 0.8680 (tp30) REVERT: B 438 LYS cc_start: 0.8838 (ptmt) cc_final: 0.8598 (ptmt) REVERT: B 447 ILE cc_start: 0.9137 (mm) cc_final: 0.8915 (OUTLIER) REVERT: C 132 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7731 (tm-30) REVERT: D 132 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7473 (tm-30) REVERT: D 303 ASN cc_start: 0.8335 (m-40) cc_final: 0.8117 (m-40) REVERT: E 132 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7395 (tm-30) REVERT: E 136 ARG cc_start: 0.8419 (mtm110) cc_final: 0.8187 (mtm110) REVERT: E 352 GLU cc_start: 0.8849 (tp30) cc_final: 0.8639 (tm-30) REVERT: E 487 GLU cc_start: 0.6055 (mm-30) cc_final: 0.3791 (mm-30) REVERT: F 132 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7615 (tm-30) REVERT: F 153 LYS cc_start: 0.8784 (mmmm) cc_final: 0.8535 (tppt) REVERT: F 487 GLU cc_start: 0.5979 (mm-30) cc_final: 0.3677 (mm-30) REVERT: G 132 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7034 (tm-30) REVERT: G 136 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8275 (ttm-80) REVERT: G 487 GLU cc_start: 0.6214 (mm-30) cc_final: 0.3804 (mm-30) REVERT: G 495 MET cc_start: 0.8756 (tpp) cc_final: 0.8481 (tpp) REVERT: H 132 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7594 (tp30) REVERT: H 410 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8583 (ttpp) REVERT: H 487 GLU cc_start: 0.5893 (mm-30) cc_final: 0.3946 (mm-30) outliers start: 75 outliers final: 45 residues processed: 679 average time/residue: 0.7693 time to fit residues: 602.1653 Evaluate side-chains 671 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 624 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 510 THR Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 410 LYS Chi-restraints excluded: chain H residue 437 VAL Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 91 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 326 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 355 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.089666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.078999 restraints weight = 55278.252| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.90 r_work: 0.3108 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30592 Z= 0.124 Angle : 0.613 11.852 41536 Z= 0.318 Chirality : 0.041 0.154 4840 Planarity : 0.004 0.063 5160 Dihedral : 10.504 87.078 5288 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.75 % Allowed : 22.10 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.14), residues: 3808 helix: 2.10 (0.14), residues: 1424 sheet: 0.55 (0.26), residues: 352 loop : -0.07 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 203 TYR 0.011 0.001 TYR F 353 PHE 0.007 0.001 PHE H 401 HIS 0.002 0.000 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (30592) covalent geometry : angle 0.61338 / 0.32 (41536) hydrogen bonds : bond 0.03431 / 2.32 ( 1169) hydrogen bonds : angle 5.05378 / 3.54 ( 3267) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 646 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8026 (tm-30) cc_final: 0.6956 (tm-30) REVERT: A 136 ARG cc_start: 0.8451 (mtm110) cc_final: 0.7957 (ttm-80) REVERT: A 216 ASP cc_start: 0.7843 (m-30) cc_final: 0.7631 (t0) REVERT: A 229 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8669 (ptpp) REVERT: B 132 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7872 (OUTLIER) REVERT: B 136 ARG cc_start: 0.8554 (ttp80) cc_final: 0.8188 (mtm110) REVERT: B 196 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: B 438 LYS cc_start: 0.8796 (ptmt) cc_final: 0.8560 (ptmt) REVERT: C 132 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7655 (tm-30) REVERT: C 216 ASP cc_start: 0.7112 (t0) cc_final: 0.6820 (t0) REVERT: D 132 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7596 (tm-30) REVERT: E 132 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7490 (tp30) REVERT: E 136 ARG cc_start: 0.8486 (mtm110) cc_final: 0.8034 (mtm110) REVERT: E 352 GLU cc_start: 0.8836 (tp30) cc_final: 0.8611 (tm-30) REVERT: E 487 GLU cc_start: 0.5956 (mm-30) cc_final: 0.3768 (mm-30) REVERT: F 132 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7532 (tm-30) REVERT: F 153 LYS cc_start: 0.8792 (mmmm) cc_final: 0.8564 (tppt) REVERT: F 487 GLU cc_start: 0.5985 (mm-30) cc_final: 0.3882 (mm-30) REVERT: G 132 GLU cc_start: 0.8032 (tm-30) cc_final: 0.6985 (tm-30) REVERT: G 136 ARG cc_start: 0.8496 (ttp80) cc_final: 0.8228 (ttm-80) REVERT: G 487 GLU cc_start: 0.6178 (mm-30) cc_final: 0.4081 (mm-30) REVERT: G 495 MET cc_start: 0.8698 (tpp) cc_final: 0.8397 (tpp) REVERT: H 132 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7504 (tp30) REVERT: H 410 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8546 (ttpp) REVERT: H 487 GLU cc_start: 0.5639 (mm-30) cc_final: 0.3760 (mm-30) outliers start: 55 outliers final: 38 residues processed: 683 average time/residue: 0.7683 time to fit residues: 605.0676 Evaluate side-chains 673 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 634 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 410 LYS Chi-restraints excluded: chain H residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 200 optimal weight: 0.7980 chunk 337 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 226 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.089861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079019 restraints weight = 54614.990| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.94 r_work: 0.3102 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30592 Z= 0.131 Angle : 0.626 12.115 41536 Z= 0.323 Chirality : 0.042 0.157 4840 Planarity : 0.005 0.070 5160 Dihedral : 10.354 88.106 5288 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.50 % Allowed : 22.74 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.14), residues: 3808 helix: 2.07 (0.14), residues: 1432 sheet: 0.47 (0.25), residues: 368 loop : -0.06 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 203 TYR 0.010 0.001 TYR E 353 PHE 0.021 0.001 PHE G 401 HIS 0.003 0.000 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (30592) covalent geometry : angle 0.62618 / 0.32 (41536) hydrogen bonds : bond 0.03522 / 2.38 ( 1169) hydrogen bonds : angle 5.01710 / 3.51 ( 3267) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 644 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7013 (tm-30) REVERT: A 136 ARG cc_start: 0.8464 (mtm110) cc_final: 0.8012 (ttm-80) REVERT: A 216 ASP cc_start: 0.7951 (m-30) cc_final: 0.7602 (t0) REVERT: A 229 LYS cc_start: 0.8912 (mtmm) cc_final: 0.8706 (ptpp) REVERT: B 132 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7874 (tp30) REVERT: B 136 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8190 (mtm110) REVERT: B 196 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: B 438 LYS cc_start: 0.8792 (ptmt) cc_final: 0.8563 (ptmt) REVERT: C 132 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7735 (tm-30) REVERT: C 206 LYS cc_start: 0.8831 (mmtp) cc_final: 0.8598 (mmtm) REVERT: D 132 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7537 (tm-30) REVERT: D 243 GLN cc_start: 0.8737 (mp10) cc_final: 0.8506 (mp10) REVERT: E 132 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7506 (tp30) REVERT: E 136 ARG cc_start: 0.8481 (mtm110) cc_final: 0.8060 (mtm110) REVERT: E 229 LYS cc_start: 0.8877 (mtmm) cc_final: 0.8655 (ptpp) REVERT: E 337 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8017 (mmt) REVERT: E 352 GLU cc_start: 0.8829 (tp30) cc_final: 0.8606 (tm-30) REVERT: E 487 GLU cc_start: 0.5906 (mm-30) cc_final: 0.3705 (mm-30) REVERT: F 132 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7594 (tm-30) REVERT: F 153 LYS cc_start: 0.8814 (mmmm) cc_final: 0.8583 (tppt) REVERT: F 487 GLU cc_start: 0.5955 (mm-30) cc_final: 0.3903 (mm-30) REVERT: G 132 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7646 (tm-30) REVERT: G 487 GLU cc_start: 0.6117 (mm-30) cc_final: 0.3911 (mm-30) REVERT: G 495 MET cc_start: 0.8700 (tpp) cc_final: 0.8404 (tpp) REVERT: H 132 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7597 (tp30) REVERT: H 410 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8605 (ttpp) REVERT: H 487 GLU cc_start: 0.5651 (mm-30) cc_final: 0.3458 (mm-30) outliers start: 47 outliers final: 38 residues processed: 671 average time/residue: 0.7377 time to fit residues: 570.8117 Evaluate side-chains 673 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 632 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 410 LYS Chi-restraints excluded: chain H residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 232 optimal weight: 0.0980 chunk 331 optimal weight: 0.5980 chunk 338 optimal weight: 0.5980 chunk 191 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 308 optimal weight: 7.9990 chunk 351 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 chunk 306 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 292 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 HIS G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.091298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.080036 restraints weight = 54822.795| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.99 r_work: 0.3104 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30592 Z= 0.126 Angle : 0.620 11.806 41536 Z= 0.320 Chirality : 0.042 0.170 4840 Planarity : 0.005 0.063 5160 Dihedral : 10.168 89.016 5288 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.63 % Allowed : 22.74 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.14), residues: 3808 helix: 2.10 (0.14), residues: 1432 sheet: 0.49 (0.24), residues: 368 loop : -0.09 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 203 TYR 0.010 0.001 TYR F 353 PHE 0.023 0.001 PHE G 401 HIS 0.003 0.000 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (30592) covalent geometry : angle 0.62016 / 0.32 (41536) hydrogen bonds : bond 0.03429 / 2.31 ( 1169) hydrogen bonds : angle 5.00172 / 3.50 ( 3267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14594.42 seconds wall clock time: 248 minutes 17.86 seconds (14897.86 seconds total)