Starting phenix.real_space_refine on Sat Aug 8 20:20:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8u8o_42026/08_2026/8u8o_42026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8o_42026/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8u8o_42026/08_2026/8u8o_42026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8o_42026/08_2026/8u8o_42026.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8u8o_42026/08_2026/8u8o_42026.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8u8o_42026/08_2026/8u8o_42026.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u8o_42026/08_2026/8u8o_42026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8o_42026/08_2026/8u8o_42026.map" } 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-2.2rc3-6140/lib/python3.11/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, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 6.10, per 1000 atoms: 0.20 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: 2.56 Conformation dependent library (CDL) restraints added in 1.2 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: 1.32 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: 6.73 Time building geometry restraints manager: 3.40 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=" C5 IMP A 603 " pdb=" C6 IMP A 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C5 IMP H 603 " pdb=" C6 IMP H 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C5 IMP D 603 " pdb=" C6 IMP D 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C5 IMP E 603 " pdb=" C6 IMP E 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C5 IMP G 603 " pdb=" C6 IMP G 603 " ideal model delta sigma weight residual 1.390 1.533 -0.143 2.00e-02 2.50e+03 5.15e+01 ... (remaining 30587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 40175 1.93 - 3.86: 1113 3.86 - 5.79: 175 5.79 - 7.72: 43 7.72 - 9.65: 30 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 - 31.18: 17766 31.18 - 62.37: 1042 62.37 - 93.55: 92 93.55 - 124.73: 0 124.73 - 155.92: 4 Dihedral angle restraints: 18904 sinusoidal: 8016 harmonic: 10888 Sorted by residual: dihedral pdb=" C5' IMP G 603 " pdb=" O5' IMP G 603 " pdb=" P IMP G 603 " pdb=" O2P IMP G 603 " ideal model delta sinusoidal sigma weight residual -168.07 -12.15 -155.92 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' IMP H 603 " pdb=" O5' IMP H 603 " pdb=" P IMP H 603 " pdb=" O2P IMP H 603 " ideal model delta sinusoidal sigma weight residual -168.07 -12.17 -155.90 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' IMP E 603 " pdb=" O5' IMP E 603 " pdb=" P IMP E 603 " pdb=" O2P IMP E 603 " ideal model delta sinusoidal sigma weight residual -168.07 -12.27 -155.80 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 18901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3617 0.051 - 0.101: 974 0.101 - 0.152: 241 0.152 - 0.203: 0 0.203 - 0.254: 8 Chirality restraints: 4840 Sorted by residual: chirality pdb=" C2' IMP B 603 " pdb=" C1' IMP B 603 " pdb=" C3' IMP B 603 " pdb=" O2' IMP B 603 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C2' IMP A 603 " pdb=" C1' IMP A 603 " pdb=" C3' IMP A 603 " pdb=" O2' IMP A 603 " both_signs ideal model delta sigma weight residual False -2.47 -2.72 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C2' IMP F 603 " pdb=" C1' IMP F 603 " pdb=" C3' IMP F 603 " pdb=" O2' IMP F 603 " both_signs ideal model delta sigma weight residual False -2.47 -2.72 0.25 2.00e-01 2.50e+01 1.57e+00 ... (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: 0.14 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: 6.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.670 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.006 0.144 30592 Z= 0.315 Angle : 0.816 9.652 41536 Z= 0.449 Chirality : 0.047 0.254 4840 Planarity : 0.005 0.049 5160 Dihedral : 18.028 155.916 11960 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 0.00647 / 0.31 (30592) covalent geometry : angle 0.81648 / 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 : 1.176 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: 0.6910 time to fit residues: 700.9947 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 : 0.806 ------------------------------------------------------------------------------- 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: 7.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 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 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.092314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.080905 restraints weight = 54792.058| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.99 r_work: 0.3126 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.2419 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= 0.157 Angle : 0.603 7.927 41536 Z= 0.312 Chirality : 0.044 0.150 4840 Planarity : 0.004 0.044 5160 Dihedral : 12.885 174.996 5178 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.33 % Allowed : 17.06 % Favored : 80.61 % 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: 0.68 (0.13), residues: 3808 helix: 1.47 (0.14), residues: 1472 sheet: 0.28 (0.24), residues: 448 loop : -0.27 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 136 TYR 0.011 0.001 TYR C 353 PHE 0.009 0.002 PHE D 114 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (30592) covalent geometry : angle 0.60283 / 0.31 (41536) hydrogen bonds : bond 0.04421 / 2.98 ( 1169) hydrogen bonds : angle 5.50311 / 3.85 ( 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 762 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 689 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8127 (tmm-80) REVERT: A 352 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8717 (tp30) REVERT: A 447 ILE cc_start: 0.8979 (mm) cc_final: 0.8773 (mt) REVERT: B 438 LYS cc_start: 0.8777 (ptmt) cc_final: 0.8549 (mtmm) REVERT: B 447 ILE cc_start: 0.8923 (mm) cc_final: 0.8687 (mt) REVERT: C 136 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8085 (ttp80) REVERT: C 491 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8529 (tp30) REVERT: D 136 ARG cc_start: 0.8489 (ttp80) cc_final: 0.8080 (ttp80) REVERT: D 410 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8244 (ttpp) REVERT: E 136 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7731 (tmm-80) REVERT: E 410 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8306 (ttpp) REVERT: F 136 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7341 (ttp80) REVERT: F 137 HIS cc_start: 0.8381 (m170) cc_final: 0.8146 (m-70) REVERT: F 410 LYS cc_start: 0.8581 (mtpp) cc_final: 0.8341 (ttpp) REVERT: G 136 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7491 (ttp80) REVERT: H 303 ASN cc_start: 0.8251 (m-40) cc_final: 0.8045 (m-40) REVERT: H 352 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8528 (tp30) REVERT: H 410 LYS cc_start: 0.8520 (mtpp) cc_final: 0.8210 (ttpp) outliers start: 73 outliers final: 22 residues processed: 729 average time/residue: 0.7607 time to fit residues: 639.6993 Evaluate side-chains 674 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 651 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER 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 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 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 339 CYS Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 178 optimal weight: 0.6980 chunk 179 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 297 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 chunk 294 optimal weight: 0.7980 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: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 368 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS E 368 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN F 441 GLN ** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.091432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.080382 restraints weight = 55136.673| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.94 r_work: 0.3127 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30592 Z= 0.129 Angle : 0.548 7.486 41536 Z= 0.287 Chirality : 0.043 0.153 4840 Planarity : 0.004 0.040 5160 Dihedral : 12.126 173.224 5160 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.74 % Allowed : 17.44 % Favored : 79.82 % 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: 0.92 (0.14), residues: 3808 helix: 1.60 (0.14), residues: 1520 sheet: 0.65 (0.26), residues: 352 loop : -0.14 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 136 TYR 0.011 0.001 TYR F 353 PHE 0.008 0.001 PHE D 114 HIS 0.006 0.001 HIS G 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (30592) covalent geometry : angle 0.54815 / 0.29 (41536) hydrogen bonds : bond 0.03865 / 2.61 ( 1169) hydrogen bonds : angle 5.30732 / 3.71 ( 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 754 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 668 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7602 (tm-30) REVERT: A 447 ILE cc_start: 0.9077 (mm) cc_final: 0.8863 (OUTLIER) REVERT: B 132 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7801 (tp30) REVERT: B 136 ARG cc_start: 0.8371 (ttp80) cc_final: 0.7787 (mtm110) REVERT: B 438 LYS cc_start: 0.8711 (ptmt) cc_final: 0.8479 (mtmm) REVERT: B 447 ILE cc_start: 0.8985 (mm) cc_final: 0.8748 (OUTLIER) REVERT: C 132 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 228 LYS cc_start: 0.9007 (mtpt) cc_final: 0.8778 (mtmt) REVERT: C 491 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8491 (tp30) REVERT: D 132 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7733 (tm-30) REVERT: D 410 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8399 (ttpp) REVERT: E 352 GLU cc_start: 0.8726 (tp30) cc_final: 0.8474 (tp30) REVERT: E 410 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8430 (ttpp) REVERT: E 487 GLU cc_start: 0.5482 (mm-30) cc_final: 0.3816 (mm-30) REVERT: F 203 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7721 (mtm110) REVERT: F 410 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8446 (ttpp) REVERT: F 487 GLU cc_start: 0.5745 (mm-30) cc_final: 0.3695 (mm-30) REVERT: G 132 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7561 (tm-30) REVERT: G 495 MET cc_start: 0.8590 (tpp) cc_final: 0.8368 (tpp) REVERT: H 352 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8495 (tp30) REVERT: H 410 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8378 (ttpp) REVERT: H 487 GLU cc_start: 0.5526 (mm-30) cc_final: 0.4862 (mm-30) outliers start: 86 outliers final: 27 residues processed: 714 average time/residue: 0.7769 time to fit residues: 639.5806 Evaluate side-chains 675 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 649 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 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 C residue 140 SER Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain E residue 65 LEU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 24 optimal weight: 4.9990 chunk 178 optimal weight: 0.0870 chunk 83 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 319 optimal weight: 6.9990 chunk 334 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 338 optimal weight: 0.9980 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 368 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 D 441 GLN ** 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 202 GLN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.077829 restraints weight = 55344.270| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.92 r_work: 0.3081 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30592 Z= 0.176 Angle : 0.591 7.540 41536 Z= 0.306 Chirality : 0.044 0.156 4840 Planarity : 0.004 0.038 5160 Dihedral : 11.505 132.815 5160 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.97 % Allowed : 18.43 % Favored : 78.60 % 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: 0.99 (0.14), residues: 3808 helix: 1.80 (0.14), residues: 1464 sheet: 0.54 (0.27), residues: 352 loop : -0.15 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 203 TYR 0.011 0.001 TYR B 353 PHE 0.011 0.002 PHE D 114 HIS 0.004 0.001 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (30592) covalent geometry : angle 0.59064 / 0.31 (41536) hydrogen bonds : bond 0.04393 / 2.96 ( 1169) hydrogen bonds : angle 5.26113 / 3.68 ( 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 745 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 652 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 447 ILE cc_start: 0.9114 (mm) cc_final: 0.8904 (mt) REVERT: B 132 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7958 (tp30) REVERT: B 136 ARG cc_start: 0.8480 (ttp80) cc_final: 0.8069 (mtm110) REVERT: B 149 THR cc_start: 0.8681 (t) cc_final: 0.8443 (p) REVERT: B 447 ILE cc_start: 0.9066 (mm) cc_final: 0.8840 (OUTLIER) REVERT: C 132 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7687 (tm-30) REVERT: C 149 THR cc_start: 0.8664 (t) cc_final: 0.8370 (p) REVERT: C 303 ASN cc_start: 0.8408 (m-40) cc_final: 0.8197 (m-40) REVERT: C 491 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8518 (tp30) REVERT: D 132 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7575 (tm-30) REVERT: D 410 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8539 (ttpp) REVERT: E 487 GLU cc_start: 0.5851 (mm-30) cc_final: 0.3812 (mm-30) REVERT: F 149 THR cc_start: 0.8661 (t) cc_final: 0.8370 (p) REVERT: F 487 GLU cc_start: 0.6019 (mm-30) cc_final: 0.3745 (mm-30) REVERT: G 132 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7523 (tm-30) REVERT: G 136 ARG cc_start: 0.8398 (ttp80) cc_final: 0.8138 (ttp80) REVERT: G 487 GLU cc_start: 0.6145 (mm-30) cc_final: 0.3927 (mm-30) REVERT: G 495 MET cc_start: 0.8671 (tpp) cc_final: 0.8419 (tpp) REVERT: H 132 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7559 (tm-30) REVERT: H 352 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8509 (tp30) REVERT: H 410 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8521 (ttpp) REVERT: H 487 GLU cc_start: 0.5879 (mm-30) cc_final: 0.5211 (mm-30) outliers start: 93 outliers final: 42 residues processed: 697 average time/residue: 0.7559 time to fit residues: 609.5556 Evaluate side-chains 675 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 633 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 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 65 LEU 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 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 C residue 491 GLU Chi-restraints excluded: chain D residue 65 LEU 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 65 LEU 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 G residue 418 ASP 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 455 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 104 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 201 optimal weight: 0.7980 chunk 379 optimal weight: 0.7980 chunk 312 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 181 optimal weight: 0.3980 chunk 12 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 137 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 202 GLN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.079688 restraints weight = 55666.552| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.93 r_work: 0.3118 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30592 Z= 0.115 Angle : 0.555 7.357 41536 Z= 0.287 Chirality : 0.042 0.150 4840 Planarity : 0.004 0.040 5160 Dihedral : 10.961 94.156 5160 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.49 % Allowed : 19.58 % Favored : 77.93 % 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: 1.12 (0.14), residues: 3808 helix: 1.82 (0.14), residues: 1520 sheet: 0.97 (0.29), residues: 272 loop : -0.07 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 203 TYR 0.010 0.001 TYR F 353 PHE 0.007 0.001 PHE E 139 HIS 0.009 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (30592) covalent geometry : angle 0.55545 / 0.29 (41536) hydrogen bonds : bond 0.03448 / 2.32 ( 1169) hydrogen bonds : angle 5.14461 / 3.60 ( 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 731 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 653 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7586 (tm-30) REVERT: A 203 ARG cc_start: 0.8169 (mtm110) cc_final: 0.7937 (mtm110) REVERT: B 132 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7945 (tp30) REVERT: B 136 ARG cc_start: 0.8555 (ttp80) cc_final: 0.8152 (mtm110) REVERT: B 153 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8294 (tppt) REVERT: B 196 GLU cc_start: 0.8294 (mp0) cc_final: 0.8040 (mp0) REVERT: B 447 ILE cc_start: 0.9048 (mm) cc_final: 0.8814 (OUTLIER) REVERT: C 132 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 149 THR cc_start: 0.8671 (t) cc_final: 0.8423 (p) REVERT: C 491 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8511 (tp30) REVERT: D 132 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7528 (tm-30) REVERT: D 199 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7460 (tm-30) REVERT: E 487 GLU cc_start: 0.5619 (mm-30) cc_final: 0.3704 (mm-30) REVERT: F 149 THR cc_start: 0.8602 (t) cc_final: 0.8363 (p) REVERT: F 196 GLU cc_start: 0.8350 (mp0) cc_final: 0.8123 (mp0) REVERT: F 487 GLU cc_start: 0.5886 (mm-30) cc_final: 0.3596 (mm-30) REVERT: G 109 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8291 (mptm) REVERT: G 132 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7661 (tm-30) REVERT: G 410 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8508 (ttpp) REVERT: G 487 GLU cc_start: 0.6038 (mm-30) cc_final: 0.4279 (mm-30) REVERT: G 495 MET cc_start: 0.8646 (tpp) cc_final: 0.8386 (tpp) REVERT: H 132 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7449 (tm-30) REVERT: H 153 LYS cc_start: 0.7843 (tppt) cc_final: 0.7485 (tppt) REVERT: H 196 GLU cc_start: 0.8296 (mp0) cc_final: 0.8039 (mp0) REVERT: H 352 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8505 (tp30) REVERT: H 410 LYS cc_start: 0.8744 (mtpp) cc_final: 0.8515 (ttpp) REVERT: H 487 GLU cc_start: 0.5643 (mm-30) cc_final: 0.5399 (mm-30) outliers start: 78 outliers final: 31 residues processed: 696 average time/residue: 0.7665 time to fit residues: 616.5112 Evaluate side-chains 676 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 643 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 339 CYS 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 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 339 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 65 LEU 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 F residue 140 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain G residue 109 LYS 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 410 LYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 162 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 184 optimal weight: 7.9990 chunk 301 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 317 optimal weight: 0.7980 chunk 245 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** 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** F 198 ASN ** F 202 GLN ** 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 = 0.3403 r_free = 0.3403 target = 0.089306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.078542 restraints weight = 55289.069| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.92 r_work: 0.3096 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30592 Z= 0.141 Angle : 0.576 7.931 41536 Z= 0.297 Chirality : 0.042 0.144 4840 Planarity : 0.004 0.041 5160 Dihedral : 10.852 87.326 5160 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.87 % Allowed : 19.83 % Favored : 77.30 % 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: 1.17 (0.14), residues: 3808 helix: 2.01 (0.14), residues: 1472 sheet: 0.65 (0.26), residues: 352 loop : -0.10 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 203 TYR 0.011 0.001 TYR C 353 PHE 0.009 0.001 PHE C 114 HIS 0.004 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (30592) covalent geometry : angle 0.57592 / 0.30 (41536) hydrogen bonds : bond 0.03866 / 2.61 ( 1169) hydrogen bonds : angle 5.11680 / 3.59 ( 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 759 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 669 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7261 (tm-30) REVERT: A 136 ARG cc_start: 0.8428 (mtm110) cc_final: 0.8090 (ttm-80) REVERT: A 303 ASN cc_start: 0.8285 (m-40) cc_final: 0.8066 (m-40) REVERT: B 132 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7975 (tp30) REVERT: B 136 ARG cc_start: 0.8582 (ttp80) cc_final: 0.8221 (mtm110) REVERT: B 196 GLU cc_start: 0.8348 (mp0) cc_final: 0.8046 (mp0) REVERT: C 132 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7660 (tm-30) REVERT: C 149 THR cc_start: 0.8686 (t) cc_final: 0.8478 (p) REVERT: C 216 ASP cc_start: 0.6982 (t0) cc_final: 0.6741 (t0) REVERT: C 491 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8528 (tp30) REVERT: D 132 GLU cc_start: 0.7999 (tm-30) cc_final: 0.6978 (tm-30) REVERT: D 136 ARG cc_start: 0.8407 (mtm110) cc_final: 0.8029 (ttm-80) REVERT: D 206 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8676 (mptp) REVERT: E 487 GLU cc_start: 0.5715 (mm-30) cc_final: 0.3740 (mm-30) REVERT: F 149 THR cc_start: 0.8606 (t) cc_final: 0.8396 (p) REVERT: F 487 GLU cc_start: 0.5967 (mm-30) cc_final: 0.3682 (mm-30) REVERT: G 132 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7713 (tm-30) REVERT: G 149 THR cc_start: 0.8735 (t) cc_final: 0.8509 (p) REVERT: G 410 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8527 (ttpp) REVERT: G 487 GLU cc_start: 0.6190 (mm-30) cc_final: 0.5757 (mm-30) REVERT: G 495 MET cc_start: 0.8686 (tpp) cc_final: 0.8399 (tpp) REVERT: H 132 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7374 (tm-30) REVERT: H 136 ARG cc_start: 0.8335 (mtm110) cc_final: 0.8060 (mtm110) REVERT: H 196 GLU cc_start: 0.8409 (mp0) cc_final: 0.8091 (mp0) REVERT: H 410 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8569 (ttpp) REVERT: H 487 GLU cc_start: 0.5672 (mm-30) cc_final: 0.3917 (mm-30) outliers start: 90 outliers final: 46 residues processed: 717 average time/residue: 0.7558 time to fit residues: 626.5768 Evaluate side-chains 687 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 639 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 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 C residue 491 GLU Chi-restraints excluded: chain D residue 65 LEU 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 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 163 ILE 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 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 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 455 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 86 optimal weight: 1.9990 chunk 320 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 250 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 367 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 271 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 242 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** F 202 GLN ** 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 = 0.3390 r_free = 0.3390 target = 0.088487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.077776 restraints weight = 55317.577| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.91 r_work: 0.3083 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30592 Z= 0.159 Angle : 0.612 8.828 41536 Z= 0.315 Chirality : 0.043 0.222 4840 Planarity : 0.004 0.049 5160 Dihedral : 10.863 87.098 5160 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.71 % Allowed : 20.63 % Favored : 76.66 % 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: 1.12 (0.14), residues: 3808 helix: 2.00 (0.14), residues: 1464 sheet: 0.63 (0.26), residues: 352 loop : -0.14 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 203 TYR 0.012 0.001 TYR B 353 PHE 0.010 0.002 PHE D 114 HIS 0.003 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (30592) covalent geometry : angle 0.61162 / 0.31 (41536) hydrogen bonds : bond 0.03996 / 2.70 ( 1169) hydrogen bonds : angle 5.13613 / 3.60 ( 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 731 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 646 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7137 (tm-30) REVERT: A 136 ARG cc_start: 0.8424 (mtm110) cc_final: 0.8032 (ttm-80) REVERT: A 196 GLU cc_start: 0.8225 (mp0) cc_final: 0.8017 (pm20) REVERT: A 303 ASN cc_start: 0.8295 (m-40) cc_final: 0.8064 (m-40) REVERT: B 132 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7961 (tp30) REVERT: B 136 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8276 (mtm110) REVERT: B 196 GLU cc_start: 0.8421 (mp0) cc_final: 0.8156 (mp0) REVERT: C 132 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7051 (tm-30) REVERT: C 136 ARG cc_start: 0.8453 (ttp80) cc_final: 0.8117 (ttm-80) REVERT: C 216 ASP cc_start: 0.7095 (t0) cc_final: 0.6801 (t0) REVERT: D 132 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7530 (tm-30) REVERT: E 132 GLU cc_start: 0.7933 (tp30) cc_final: 0.7177 (tp30) REVERT: E 136 ARG cc_start: 0.8127 (tmm-80) cc_final: 0.7860 (mtm110) REVERT: E 487 GLU cc_start: 0.5795 (mm-30) cc_final: 0.3756 (mm-30) REVERT: F 487 GLU cc_start: 0.6060 (mm-30) cc_final: 0.3612 (mm-30) REVERT: G 132 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7700 (tm-30) REVERT: G 495 MET cc_start: 0.8714 (tpp) cc_final: 0.8422 (tpp) REVERT: H 132 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7326 (tm-30) REVERT: H 136 ARG cc_start: 0.8358 (mtm110) cc_final: 0.7949 (mtm110) REVERT: H 196 GLU cc_start: 0.8439 (mp0) cc_final: 0.8141 (mp0) REVERT: H 303 ASN cc_start: 0.8102 (m-40) cc_final: 0.7874 (m-40) REVERT: H 410 LYS cc_start: 0.8806 (mtpp) cc_final: 0.8599 (ttpp) REVERT: H 487 GLU cc_start: 0.5766 (mm-30) cc_final: 0.3793 (mm-30) outliers start: 85 outliers final: 45 residues processed: 693 average time/residue: 0.7441 time to fit residues: 596.9721 Evaluate side-chains 693 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 648 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 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 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 255 ASP Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue 65 LEU 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 E residue 140 SER 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 163 ILE 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 455 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 455 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 364 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 260 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 264 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 241 optimal weight: 0.1980 chunk 308 optimal weight: 4.9990 chunk 322 optimal weight: 0.5980 chunk 365 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** 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** ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** 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 303 ASN H 441 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.088944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.078267 restraints weight = 55529.196| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.92 r_work: 0.3094 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.3700 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= 0.138 Angle : 0.607 8.780 41536 Z= 0.312 Chirality : 0.042 0.145 4840 Planarity : 0.004 0.057 5160 Dihedral : 10.738 87.605 5160 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.20 % Allowed : 21.36 % 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: 1.16 (0.14), residues: 3808 helix: 2.04 (0.14), residues: 1464 sheet: 0.65 (0.26), residues: 352 loop : -0.14 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 203 TYR 0.010 0.001 TYR F 353 PHE 0.008 0.001 PHE F 114 HIS 0.011 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (30592) covalent geometry : angle 0.60742 / 0.31 (41536) hydrogen bonds : bond 0.03673 / 2.48 ( 1169) hydrogen bonds : angle 5.11262 / 3.58 ( 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 723 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 654 time to evaluate : 1.175 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: 0.7981 (tm-30) cc_final: 0.6934 (tm-30) REVERT: A 136 ARG cc_start: 0.8431 (mtm110) cc_final: 0.8013 (ttm-80) REVERT: A 303 ASN cc_start: 0.8255 (m-40) cc_final: 0.8021 (m-40) REVERT: B 132 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7915 (tp30) REVERT: B 136 ARG cc_start: 0.8593 (ttp80) cc_final: 0.8227 (mtm110) REVERT: B 438 LYS cc_start: 0.8804 (ptmt) cc_final: 0.8564 (ptmt) REVERT: C 132 GLU cc_start: 0.8058 (tm-30) cc_final: 0.6984 (tm-30) REVERT: C 136 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8102 (ttm-80) REVERT: C 153 LYS cc_start: 0.8367 (tppt) cc_final: 0.7706 (tppt) REVERT: D 132 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7522 (tm-30) REVERT: E 132 GLU cc_start: 0.7908 (tp30) cc_final: 0.7154 (tp30) REVERT: E 352 GLU cc_start: 0.8835 (tp30) cc_final: 0.8618 (tm-30) REVERT: E 487 GLU cc_start: 0.5755 (mm-30) cc_final: 0.3723 (mm-30) REVERT: F 132 GLU cc_start: 0.7891 (tp30) cc_final: 0.7016 (tp30) REVERT: F 136 ARG cc_start: 0.7976 (tmm-80) cc_final: 0.7637 (ttp80) REVERT: F 487 GLU cc_start: 0.6013 (mm-30) cc_final: 0.3731 (mm-30) REVERT: G 132 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7675 (tm-30) REVERT: G 487 GLU cc_start: 0.6215 (mm-30) cc_final: 0.5934 (mm-30) REVERT: G 495 MET cc_start: 0.8723 (tpp) cc_final: 0.8425 (tpp) REVERT: H 132 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7377 (tp30) REVERT: H 136 ARG cc_start: 0.8339 (mtm110) cc_final: 0.7870 (mtm110) REVERT: H 487 GLU cc_start: 0.5740 (mm-30) cc_final: 0.4013 (mm-30) outliers start: 69 outliers final: 51 residues processed: 692 average time/residue: 0.7622 time to fit residues: 610.3373 Evaluate side-chains 684 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 633 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 193 THR 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 406 VAL 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 65 LEU 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 E residue 140 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 GLU 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 193 THR Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 510 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 196 GLU Chi-restraints excluded: chain H residue 339 CYS 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: 1.9990 chunk 105 optimal weight: 0.7980 chunk 2 optimal weight: 0.0870 chunk 98 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 326 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 355 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN 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** F 137 HIS F 202 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.079990 restraints weight = 55328.203| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.90 r_work: 0.3120 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.3832 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= 0.121 Angle : 0.627 11.583 41536 Z= 0.321 Chirality : 0.042 0.172 4840 Planarity : 0.004 0.062 5160 Dihedral : 10.453 88.261 5160 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.66 % Allowed : 22.42 % Favored : 75.92 % 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: 1.30 (0.14), residues: 3808 helix: 2.25 (0.14), residues: 1424 sheet: 0.62 (0.25), residues: 352 loop : -0.07 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 203 TYR 0.009 0.001 TYR E 353 PHE 0.007 0.001 PHE H 401 HIS 0.008 0.000 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (30592) covalent geometry : angle 0.62665 / 0.32 (41536) hydrogen bonds : bond 0.03263 / 2.21 ( 1169) hydrogen bonds : angle 5.04031 / 3.53 ( 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 703 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 651 time to evaluate : 1.193 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: A 132 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7037 (tm-30) REVERT: A 136 ARG cc_start: 0.8445 (mtm110) cc_final: 0.8034 (ttm-80) REVERT: A 303 ASN cc_start: 0.8167 (m-40) cc_final: 0.7956 (m-40) REVERT: B 132 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7859 (OUTLIER) REVERT: B 136 ARG cc_start: 0.8592 (ttp80) cc_final: 0.8169 (mtm110) REVERT: B 438 LYS cc_start: 0.8798 (ptmt) cc_final: 0.8563 (ptmt) REVERT: C 132 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7052 (tm-30) REVERT: C 136 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8161 (ttm-80) REVERT: C 150 MET cc_start: 0.8264 (mmt) cc_final: 0.8024 (mtt) REVERT: D 132 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7541 (tm-30) REVERT: E 132 GLU cc_start: 0.7969 (tp30) cc_final: 0.7547 (tm-30) REVERT: E 136 ARG cc_start: 0.8445 (mtm110) cc_final: 0.8193 (mtm110) REVERT: E 352 GLU cc_start: 0.8819 (tp30) cc_final: 0.8609 (tm-30) REVERT: E 487 GLU cc_start: 0.5798 (mm-30) cc_final: 0.3816 (mm-30) REVERT: F 132 GLU cc_start: 0.7891 (tp30) cc_final: 0.7095 (tp30) REVERT: F 136 ARG cc_start: 0.8075 (tmm-80) cc_final: 0.7777 (ttp80) REVERT: F 487 GLU cc_start: 0.6019 (mm-30) cc_final: 0.3811 (mm-30) REVERT: G 132 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7620 (tm-30) REVERT: G 487 GLU cc_start: 0.6147 (mm-30) cc_final: 0.4794 (mm-30) REVERT: G 495 MET cc_start: 0.8661 (tpp) cc_final: 0.8369 (tpp) REVERT: H 132 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7371 (tp30) REVERT: H 136 ARG cc_start: 0.8363 (mtm110) cc_final: 0.7897 (mtm110) REVERT: H 487 GLU cc_start: 0.5678 (mm-30) cc_final: 0.3835 (mm-30) outliers start: 52 outliers final: 37 residues processed: 683 average time/residue: 0.7633 time to fit residues: 603.3076 Evaluate side-chains 675 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 639 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 335 GLU 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 339 CYS Chi-restraints excluded: chain D residue 65 LEU 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 E residue 140 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 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 193 THR Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 196 GLU 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: 0.8980 chunk 337 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 198 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.088968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.078290 restraints weight = 54921.779| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.90 r_work: 0.3093 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30592 Z= 0.151 Angle : 0.657 11.430 41536 Z= 0.335 Chirality : 0.043 0.145 4840 Planarity : 0.005 0.066 5160 Dihedral : 10.518 88.166 5160 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.59 % Allowed : 22.67 % Favored : 75.73 % 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: 2.08 (0.14), residues: 1432 sheet: 0.67 (0.26), residues: 352 loop : -0.10 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 203 TYR 0.011 0.001 TYR E 353 PHE 0.023 0.001 PHE G 401 HIS 0.003 0.001 HIS G 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (30592) covalent geometry : angle 0.65668 / 0.33 (41536) hydrogen bonds : bond 0.03802 / 2.57 ( 1169) hydrogen bonds : angle 5.07676 / 3.56 ( 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: 50 poor density : 641 time to evaluate : 1.172 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: A 132 GLU cc_start: 0.8007 (tm-30) cc_final: 0.6996 (tm-30) REVERT: A 136 ARG cc_start: 0.8462 (mtm110) cc_final: 0.8002 (ttm-80) REVERT: A 303 ASN cc_start: 0.8263 (m-40) cc_final: 0.8033 (m-40) REVERT: B 132 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7892 (OUTLIER) REVERT: B 136 ARG cc_start: 0.8578 (ttp80) cc_final: 0.8185 (mtm110) REVERT: B 352 GLU cc_start: 0.8828 (tp30) cc_final: 0.8593 (tp30) REVERT: B 438 LYS cc_start: 0.8797 (ptmt) cc_final: 0.8564 (ptmt) REVERT: C 132 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7706 (tm-30) REVERT: D 132 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7566 (tm-30) REVERT: D 216 ASP cc_start: 0.7367 (t0) cc_final: 0.7116 (t0) REVERT: E 132 GLU cc_start: 0.7939 (tp30) cc_final: 0.7542 (tm-30) REVERT: E 136 ARG cc_start: 0.8432 (mtm110) cc_final: 0.8229 (mtm110) REVERT: E 229 LYS cc_start: 0.8905 (mtmm) cc_final: 0.8694 (ptpp) REVERT: E 337 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.7991 (mmt) REVERT: E 352 GLU cc_start: 0.8842 (tp30) cc_final: 0.8633 (tm-30) REVERT: E 487 GLU cc_start: 0.5810 (mm-30) cc_final: 0.3674 (mm-30) REVERT: F 132 GLU cc_start: 0.7893 (tp30) cc_final: 0.7084 (tp30) REVERT: F 136 ARG cc_start: 0.8100 (tmm-80) cc_final: 0.7766 (ttp80) REVERT: F 487 GLU cc_start: 0.6043 (mm-30) cc_final: 0.3757 (mm-30) REVERT: G 132 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7652 (tm-30) REVERT: G 487 GLU cc_start: 0.6254 (mm-30) cc_final: 0.4842 (mm-30) REVERT: G 495 MET cc_start: 0.8714 (tpp) cc_final: 0.8432 (tpp) REVERT: H 132 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7409 (tp30) REVERT: H 136 ARG cc_start: 0.8379 (mtm110) cc_final: 0.8000 (mtm110) REVERT: H 487 GLU cc_start: 0.5703 (mm-30) cc_final: 0.3846 (mm-30) outliers start: 50 outliers final: 39 residues processed: 666 average time/residue: 0.7610 time to fit residues: 586.7634 Evaluate side-chains 674 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 635 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 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 335 GLU 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 339 CYS Chi-restraints excluded: chain D residue 65 LEU 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 E residue 140 SER Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 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 437 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 196 GLU 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: 0.6980 chunk 331 optimal weight: 0.5980 chunk 338 optimal weight: 0.9980 chunk 191 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 308 optimal weight: 5.9990 chunk 351 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3410 r_free = 0.3410 target = 0.089842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.078646 restraints weight = 54909.495| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.99 r_work: 0.3085 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30592 Z= 0.146 Angle : 0.655 10.631 41536 Z= 0.334 Chirality : 0.042 0.146 4840 Planarity : 0.005 0.071 5160 Dihedral : 10.467 88.844 5160 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.47 % Allowed : 22.93 % Favored : 75.61 % 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: 1.10 (0.14), residues: 3808 helix: 2.04 (0.14), residues: 1432 sheet: 0.34 (0.23), residues: 448 loop : -0.13 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 203 TYR 0.011 0.001 TYR E 353 PHE 0.023 0.001 PHE G 401 HIS 0.003 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (30592) covalent geometry : angle 0.65535 / 0.33 (41536) hydrogen bonds : bond 0.03732 / 2.52 ( 1169) hydrogen bonds : angle 5.08156 / 3.56 ( 3267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14662.83 seconds wall clock time: 249 minutes 40.39 seconds (14980.39 seconds total)