Starting phenix.real_space_refine on Tue Jul 7 04:39:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rgi_24450/07_2026/7rgi_24450_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rgi_24450/07_2026/7rgi_24450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rgi_24450/07_2026/7rgi_24450_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rgi_24450/07_2026/7rgi_24450_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rgi_24450/07_2026/7rgi_24450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rgi_24450/07_2026/7rgi_24450.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.198 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 144 5.16 5 C 13776 2.51 5 N 3768 2.21 5 O 4248 1.98 5 H 21752 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 173 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43712 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "B" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "C" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "D" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "E" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "F" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "G" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "H" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 7.59, per 1000 atoms: 0.17 Number of scatterers: 43712 At special positions: 0 Unit cell: (142.68, 142.68, 107.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 24 15.00 O 4248 8.00 N 3768 7.00 C 13776 6.00 H 21752 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 1.3 seconds 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 23 sheets defined 42.6% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.741A pdb=" N PHE A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.657A pdb=" N LEU A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 4.939A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 342 through 355 removed outlier: 3.894A pdb=" N TYR A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'B' and resid 20 through 25 removed outlier: 3.707A pdb=" N PHE B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 256 through 266 removed outlier: 3.655A pdb=" N LEU B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 4.897A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.893A pdb=" N TYR B 348 " --> pdb=" O GLY B 344 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.598A pdb=" N VAL B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 455 removed outlier: 3.517A pdb=" N LYS B 455 " --> pdb=" O SER B 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 455' Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 498 Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.861A pdb=" N PHE C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) 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 77 through 85 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 266 removed outlier: 3.655A pdb=" N LEU C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 262 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 5.008A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 338 Processing helix chain 'C' and resid 342 through 355 removed outlier: 3.796A pdb=" N TYR C 348 " --> pdb=" O GLY C 344 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 495 through 499 Processing helix chain 'D' and resid 19 through 24 removed outlier: 3.690A pdb=" N LEU D 23 " --> pdb=" O THR D 19 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) No H-bonds generated for '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 77 through 85 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 266 removed outlier: 3.655A pdb=" N LEU D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 262 " --> pdb=" O TYR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 4.925A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.834A 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 removed outlier: 3.895A pdb=" N TYR D 348 " --> pdb=" O GLY D 344 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 378 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 456 through 472 Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 495 through 499 Processing helix chain 'E' and resid 20 through 24 removed outlier: 4.083A pdb=" N PHE E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 20 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 77 through 85 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 256 through 266 removed outlier: 3.654A pdb=" N LEU E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 4.914A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 342 through 355 removed outlier: 3.909A pdb=" N TYR E 348 " --> pdb=" O GLY E 344 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 380 removed outlier: 3.599A pdb=" N VAL E 373 " --> pdb=" O THR E 369 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY E 380 " --> pdb=" O ALA E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 455 removed outlier: 3.516A pdb=" N LYS E 455 " --> pdb=" O SER E 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 452 through 455' Processing helix chain 'E' and resid 456 through 472 Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 498 Processing helix chain 'F' and resid 20 through 25 removed outlier: 3.858A pdb=" N PHE F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 77 through 85 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 256 through 266 removed outlier: 3.654A pdb=" N LEU F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU F 262 " --> pdb=" O TYR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 5.013A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 Processing helix chain 'F' and resid 342 through 355 removed outlier: 3.768A pdb=" N TYR F 348 " --> pdb=" O GLY F 344 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 380 removed outlier: 3.598A pdb=" N VAL F 373 " --> pdb=" O THR F 369 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY F 380 " --> pdb=" O ALA F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 455 removed outlier: 3.517A pdb=" N LYS F 455 " --> pdb=" O SER F 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 452 through 455' Processing helix chain 'F' and resid 456 through 472 Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'G' and resid 20 through 24 removed outlier: 3.744A pdb=" N PHE G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 20 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 77 through 85 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 253 through 255 No H-bonds generated for 'chain 'G' and resid 253 through 255' Processing helix chain 'G' and resid 256 through 266 removed outlier: 3.660A pdb=" N LEU G 260 " --> pdb=" O ASP G 256 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP G 261 " --> pdb=" O LYS G 257 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU G 262 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 4.963A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 338 Processing helix chain 'G' and resid 342 through 355 removed outlier: 3.796A pdb=" N TYR G 348 " --> pdb=" O GLY G 344 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 380 removed outlier: 3.598A pdb=" N VAL G 373 " --> pdb=" O THR G 369 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY G 380 " --> pdb=" O ALA G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 455 removed outlier: 3.517A pdb=" N LYS G 455 " --> pdb=" O SER G 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 452 through 455' Processing helix chain 'G' and resid 456 through 472 Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 499 Processing helix chain 'H' and resid 19 through 24 removed outlier: 3.690A pdb=" N LEU H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 19 through 24' Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.924A pdb=" N PHE H 35 " --> pdb=" O TYR H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 85 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 253 through 255 No H-bonds generated for 'chain 'H' and resid 253 through 255' Processing helix chain 'H' and resid 256 through 266 removed outlier: 3.654A pdb=" N LEU H 260 " --> pdb=" O ASP H 256 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP H 261 " --> pdb=" O LYS H 257 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU H 262 " --> pdb=" O TYR H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 5.122A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 338 Processing helix chain 'H' and resid 342 through 355 removed outlier: 3.895A pdb=" N TYR H 348 " --> pdb=" O GLY H 344 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 378 removed outlier: 3.598A pdb=" N VAL H 373 " --> pdb=" O THR H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 455 removed outlier: 3.516A pdb=" N LYS H 455 " --> pdb=" O SER H 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 452 through 455' Processing helix chain 'H' and resid 456 through 472 Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.776A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.636A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLY A 89 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA A 249 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N GLY A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU A 273 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VAL A 304 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 299 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N MET A 385 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 19 Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.744A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 298 through 300 removed outlier: 6.899A pdb=" N ILE B 271 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLY B 89 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA B 249 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU B 65 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N PHE B 90 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N SER B 67 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N MET B 385 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 18 through 19 Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.703A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 298 through 300 removed outlier: 6.885A pdb=" N ILE C 271 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLY C 89 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ALA C 249 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N MET C 385 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB2, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.812A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 298 through 300 removed outlier: 6.863A pdb=" N ILE D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY D 89 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ALA D 249 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N MET D 385 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 18 through 19 Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.798A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 298 through 300 removed outlier: 6.833A pdb=" N ILE E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU E 65 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N PHE E 90 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER E 67 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N MET E 385 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 18 through 19 Processing sheet with id=AB8, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.713A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 298 through 300 removed outlier: 6.869A pdb=" N ILE F 271 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY F 89 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA F 249 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N MET F 385 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 18 through 19 Processing sheet with id=AC2, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.783A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 298 through 300 removed outlier: 6.878A pdb=" N ILE G 271 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY G 89 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ALA G 249 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU G 65 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N PHE G 90 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER G 67 " --> pdb=" O PHE G 90 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.772A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 298 through 300 removed outlier: 6.860A pdb=" N ILE H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) 748 hydrogen bonds defined for protein. 2133 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: 10.60 Time building geometry restraints manager: 5.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 21704 1.12 - 1.30: 3729 1.30 - 1.47: 7946 1.47 - 1.64: 10461 1.64 - 1.82: 240 Bond restraints: 44080 Sorted by residual: bond pdb=" N ALA H 497 " pdb=" H ALA H 497 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" NH2 ARG G 259 " pdb="HH21 ARG G 259 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD2 PHE F 490 " pdb=" HD2 PHE F 490 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N SER G 496 " pdb=" H SER G 496 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N CYS B 339 " pdb=" H CYS B 339 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 44075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 69453 2.86 - 5.73: 8157 5.73 - 8.59: 1988 8.59 - 11.45: 43 11.45 - 14.32: 23 Bond angle restraints: 79664 Sorted by residual: angle pdb=" CA ASP B 239 " pdb=" CB ASP B 239 " pdb=" CG ASP B 239 " ideal model delta sigma weight residual 112.60 119.63 -7.03 1.00e+00 1.00e+00 4.95e+01 angle pdb=" OE1 GLN G 465 " pdb=" CD GLN G 465 " pdb=" NE2 GLN G 465 " ideal model delta sigma weight residual 122.60 116.23 6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" CA ASN H 230 " pdb=" CB ASN H 230 " pdb=" CG ASN H 230 " ideal model delta sigma weight residual 112.60 118.59 -5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" CA ASN E 230 " pdb=" CB ASN E 230 " pdb=" CG ASN E 230 " ideal model delta sigma weight residual 112.60 118.52 -5.92 1.00e+00 1.00e+00 3.51e+01 angle pdb=" CA ASN F 230 " pdb=" CB ASN F 230 " pdb=" CG ASN F 230 " ideal model delta sigma weight residual 112.60 118.42 -5.82 1.00e+00 1.00e+00 3.38e+01 ... (remaining 79659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 18441 17.97 - 35.94: 1574 35.94 - 53.91: 527 53.91 - 71.88: 428 71.88 - 89.85: 30 Dihedral angle restraints: 21000 sinusoidal: 11928 harmonic: 9072 Sorted by residual: dihedral pdb=" CA LEU G 273 " pdb=" C LEU G 273 " pdb=" N ASP G 274 " pdb=" CA ASP G 274 " ideal model delta harmonic sigma weight residual 180.00 -151.89 -28.11 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ALA D 392 " pdb=" C ALA D 392 " pdb=" N THR D 393 " pdb=" CA THR D 393 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA LEU F 273 " pdb=" C LEU F 273 " pdb=" N ASP F 274 " pdb=" CA ASP F 274 " ideal model delta harmonic sigma weight residual -180.00 -151.96 -28.04 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2499 0.084 - 0.167: 807 0.167 - 0.251: 170 0.251 - 0.334: 32 0.334 - 0.418: 4 Chirality restraints: 3512 Sorted by residual: chirality pdb=" CA GLU A 395 " pdb=" N GLU A 395 " pdb=" C GLU A 395 " pdb=" CB GLU A 395 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CA LYS A 106 " pdb=" N LYS A 106 " pdb=" C LYS A 106 " pdb=" CB LYS A 106 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA ALA B 338 " pdb=" N ALA B 338 " pdb=" C ALA B 338 " pdb=" CB ALA B 338 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 3509 not shown) Planarity restraints: 6552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 322 " -0.162 9.50e-02 1.11e+02 1.17e-01 2.44e+02 pdb=" NE ARG A 322 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 322 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG A 322 " -0.068 2.00e-02 2.50e+03 pdb=" NH2 ARG A 322 " -0.007 2.00e-02 2.50e+03 pdb="HH11 ARG A 322 " 0.016 2.00e-02 2.50e+03 pdb="HH12 ARG A 322 " 0.158 2.00e-02 2.50e+03 pdb="HH21 ARG A 322 " 0.170 2.00e-02 2.50e+03 pdb="HH22 ARG A 322 " -0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B NAD G 600 " -0.173 2.00e-02 2.50e+03 7.48e-02 1.54e+02 pdb=" C2A NAD G 600 " 0.038 2.00e-02 2.50e+03 pdb=" C4A NAD G 600 " 0.049 2.00e-02 2.50e+03 pdb=" C5A NAD G 600 " 0.028 2.00e-02 2.50e+03 pdb=" C6A NAD G 600 " -0.023 2.00e-02 2.50e+03 pdb=" C8A NAD G 600 " 0.061 2.00e-02 2.50e+03 pdb=" N1A NAD G 600 " 0.005 2.00e-02 2.50e+03 pdb=" N3A NAD G 600 " 0.052 2.00e-02 2.50e+03 pdb=" N6A NAD G 600 " -0.125 2.00e-02 2.50e+03 pdb=" N7A NAD G 600 " 0.061 2.00e-02 2.50e+03 pdb=" N9A NAD G 600 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 348 " -0.144 2.00e-02 2.50e+03 6.14e-02 1.13e+02 pdb=" CG TYR F 348 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR F 348 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR F 348 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR F 348 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR F 348 " 0.044 2.00e-02 2.50e+03 pdb=" CZ TYR F 348 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR F 348 " -0.115 2.00e-02 2.50e+03 pdb=" HD1 TYR F 348 " 0.044 2.00e-02 2.50e+03 pdb=" HD2 TYR F 348 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR F 348 " -0.017 2.00e-02 2.50e+03 pdb=" HE2 TYR F 348 " 0.022 2.00e-02 2.50e+03 ... (remaining 6549 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 2172 2.13 - 2.75: 72778 2.75 - 3.37: 125796 3.37 - 3.98: 167884 3.98 - 4.60: 250998 Nonbonded interactions: 619628 Sorted by model distance: nonbonded pdb=" HB2 GLU B 75 " pdb=" HG3 PRO B 397 " model vdw 1.514 2.440 nonbonded pdb=" HB2 GLU C 75 " pdb=" HG3 PRO C 397 " model vdw 1.515 2.440 nonbonded pdb=" HB2 GLU E 75 " pdb=" HG3 PRO E 397 " model vdw 1.515 2.440 nonbonded pdb=" HB2 GLU H 75 " pdb=" HG3 PRO H 397 " model vdw 1.515 2.440 nonbonded pdb=" HB2 GLU G 75 " pdb=" HG3 PRO G 397 " model vdw 1.515 2.440 ... (remaining 619623 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: 0.02 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 group one per residue 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: 2.090 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: 0.280 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 38.630 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 : 0.012 0.101 22328 Z= 0.683 Angle : 1.773 13.832 30248 Z= 1.137 Chirality : 0.087 0.418 3512 Planarity : 0.013 0.284 3816 Dihedral : 14.704 89.846 8624 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.09 % Favored : 93.77 % Rotamer: Outliers : 1.84 % Allowed : 6.36 % Favored : 91.80 % Cbeta Deviations : 0.16 % 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: -2.07 (0.15), residues: 2808 helix: -1.53 (0.14), residues: 1144 sheet: -1.42 (0.26), residues: 296 loop : -1.07 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 341 TYR 0.131 0.014 TYR F 348 PHE 0.045 0.008 PHE C 90 HIS 0.015 0.003 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.01154 / 0.68 (22328) covalent geometry : angle 1.77317 / 1.14 (30248) hydrogen bonds : bond 0.15922 / 10.79 ( 748) hydrogen bonds : angle 6.61355 / 4.63 ( 2133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 659 time to evaluate : 0.803 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 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 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: A 28 ASP cc_start: 0.6799 (m-30) cc_final: 0.6368 (m-30) REVERT: A 82 MET cc_start: 0.8215 (mmm) cc_final: 0.7869 (mmm) REVERT: A 298 GLN cc_start: 0.7550 (mm110) cc_final: 0.7284 (mm-40) REVERT: A 319 ASP cc_start: 0.7787 (m-30) cc_final: 0.7534 (m-30) REVERT: A 492 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8664 (ttmt) REVERT: B 28 ASP cc_start: 0.6395 (m-30) cc_final: 0.5708 (m-30) REVERT: B 298 GLN cc_start: 0.7525 (mm110) cc_final: 0.7309 (mm-40) REVERT: B 482 MET cc_start: 0.8502 (mtp) cc_final: 0.8094 (mtp) REVERT: B 492 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8366 (mtpt) REVERT: C 15 GLU cc_start: 0.6561 (mt-10) cc_final: 0.6241 (mt-10) REVERT: C 16 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7884 (m-30) REVERT: C 58 LYS cc_start: 0.8127 (tttm) cc_final: 0.7920 (mtpp) REVERT: C 482 MET cc_start: 0.8563 (mtp) cc_final: 0.8340 (mtp) REVERT: C 492 LYS cc_start: 0.8956 (mtpp) cc_final: 0.8643 (ttmt) REVERT: D 16 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: D 34 ASP cc_start: 0.8926 (t0) cc_final: 0.8640 (t0) REVERT: D 298 GLN cc_start: 0.7601 (mm110) cc_final: 0.7296 (mm-40) REVERT: D 319 ASP cc_start: 0.7803 (m-30) cc_final: 0.7526 (m-30) REVERT: D 492 LYS cc_start: 0.8891 (mtpp) cc_final: 0.8497 (ttmt) REVERT: E 15 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6368 (mt-10) REVERT: E 34 ASP cc_start: 0.8825 (t0) cc_final: 0.8622 (t0) REVERT: E 298 GLN cc_start: 0.7777 (mm110) cc_final: 0.7561 (mm110) REVERT: E 319 ASP cc_start: 0.7745 (m-30) cc_final: 0.7523 (m-30) REVERT: E 482 MET cc_start: 0.8553 (mtp) cc_final: 0.8331 (mtp) REVERT: E 492 LYS cc_start: 0.8990 (mtpp) cc_final: 0.8626 (mtpt) REVERT: F 275 SER cc_start: 0.8876 (p) cc_final: 0.8582 (m) REVERT: F 298 GLN cc_start: 0.7715 (mm110) cc_final: 0.7409 (mm-40) REVERT: F 319 ASP cc_start: 0.7815 (m-30) cc_final: 0.7456 (m-30) REVERT: F 492 LYS cc_start: 0.8876 (mtpp) cc_final: 0.8392 (mtpt) REVERT: G 15 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6387 (mt-10) REVERT: G 238 LYS cc_start: 0.7450 (mtmp) cc_final: 0.7250 (mtmt) REVERT: G 298 GLN cc_start: 0.7619 (mm110) cc_final: 0.7297 (mm-40) REVERT: G 319 ASP cc_start: 0.7744 (m-30) cc_final: 0.7446 (m-30) REVERT: G 482 MET cc_start: 0.8589 (mtp) cc_final: 0.8378 (mtp) REVERT: H 15 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6613 (mt-10) REVERT: H 298 GLN cc_start: 0.7596 (mm110) cc_final: 0.7348 (mm-40) REVERT: H 319 ASP cc_start: 0.7792 (m-30) cc_final: 0.7458 (m-30) REVERT: H 482 MET cc_start: 0.8587 (mtp) cc_final: 0.8366 (mtp) REVERT: H 492 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8504 (ttmt) outliers start: 42 outliers final: 18 residues processed: 678 average time/residue: 0.3791 time to fit residues: 383.8759 Evaluate side-chains 554 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 534 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 465 GLN Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 465 GLN Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 465 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 ASN A 465 GLN B 465 GLN B 498 GLN C 230 ASN C 465 GLN ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN D 230 ASN D 465 GLN ** D 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN F 230 ASN F 465 GLN F 498 GLN G 21 GLN G 230 ASN G 465 GLN H 230 ASN H 465 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.159752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.130184 restraints weight = 74608.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.135212 restraints weight = 36627.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.138511 restraints weight = 23867.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.140630 restraints weight = 18244.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.141911 restraints weight = 15316.621| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22328 Z= 0.156 Angle : 0.637 7.404 30248 Z= 0.340 Chirality : 0.043 0.179 3512 Planarity : 0.004 0.057 3816 Dihedral : 8.973 80.581 3720 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.23 % Allowed : 10.75 % Favored : 88.03 % 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: -0.93 (0.16), residues: 2808 helix: -0.24 (0.16), residues: 1120 sheet: -2.25 (0.41), residues: 88 loop : -0.74 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 322 TYR 0.016 0.002 TYR F 348 PHE 0.013 0.002 PHE B 24 HIS 0.008 0.002 HIS H 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (22328) covalent geometry : angle 0.63659 / 0.34 (30248) hydrogen bonds : bond 0.03832 / 2.53 ( 748) hydrogen bonds : angle 4.92284 / 3.44 ( 2133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 549 time to evaluate : 1.154 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 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: A 28 ASP cc_start: 0.6832 (m-30) cc_final: 0.6600 (m-30) REVERT: A 265 GLN cc_start: 0.8043 (mt0) cc_final: 0.7811 (mt0) REVERT: B 28 ASP cc_start: 0.6648 (m-30) cc_final: 0.6122 (m-30) REVERT: B 265 GLN cc_start: 0.8040 (mt0) cc_final: 0.7801 (mt0) REVERT: B 298 GLN cc_start: 0.7133 (mm110) cc_final: 0.6928 (mm-40) REVERT: C 15 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6448 (mt-10) REVERT: C 82 MET cc_start: 0.7946 (mmm) cc_final: 0.7655 (mmm) REVERT: C 265 GLN cc_start: 0.8040 (mt0) cc_final: 0.7827 (mt0) REVERT: C 482 MET cc_start: 0.8391 (mtp) cc_final: 0.8179 (mtp) REVERT: C 492 LYS cc_start: 0.8958 (mtpp) cc_final: 0.8638 (ttmt) REVERT: D 16 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7577 (m-30) REVERT: D 319 ASP cc_start: 0.7944 (m-30) cc_final: 0.7594 (m-30) REVERT: D 491 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7056 (mm-30) REVERT: E 15 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6552 (mt-10) REVERT: E 28 ASP cc_start: 0.7253 (m-30) cc_final: 0.6862 (m-30) REVERT: E 337 MET cc_start: 0.6494 (ttt) cc_final: 0.6231 (ttt) REVERT: E 482 MET cc_start: 0.8463 (mtp) cc_final: 0.8249 (mtp) REVERT: F 265 GLN cc_start: 0.7986 (mt0) cc_final: 0.7747 (mt0) REVERT: G 15 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6511 (mt-10) REVERT: G 319 ASP cc_start: 0.7931 (m-30) cc_final: 0.7416 (m-30) REVERT: G 482 MET cc_start: 0.8450 (mtp) cc_final: 0.8236 (mtp) REVERT: H 15 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6550 (mt-10) REVERT: H 319 ASP cc_start: 0.8098 (m-30) cc_final: 0.7528 (m-30) REVERT: H 337 MET cc_start: 0.6463 (ttt) cc_final: 0.6210 (ttt) outliers start: 28 outliers final: 20 residues processed: 561 average time/residue: 0.3779 time to fit residues: 321.1419 Evaluate side-chains 527 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 505 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 212 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 GLN E 265 GLN F 298 GLN G 466 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.155639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.125637 restraints weight = 75258.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.130595 restraints weight = 37318.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.133821 restraints weight = 24356.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.135860 restraints weight = 18703.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.137245 restraints weight = 15783.216| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22328 Z= 0.162 Angle : 0.573 7.882 30248 Z= 0.303 Chirality : 0.042 0.173 3512 Planarity : 0.004 0.058 3816 Dihedral : 8.007 73.709 3691 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.89 % Allowed : 13.51 % Favored : 84.61 % 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: -0.78 (0.16), residues: 2808 helix: 0.04 (0.16), residues: 1120 sheet: -2.13 (0.40), residues: 88 loop : -0.79 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 322 TYR 0.010 0.001 TYR F 32 PHE 0.015 0.001 PHE E 490 HIS 0.007 0.002 HIS F 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (22328) covalent geometry : angle 0.57258 / 0.30 (30248) hydrogen bonds : bond 0.03291 / 2.18 ( 748) hydrogen bonds : angle 4.64407 / 3.25 ( 2133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 529 time to evaluate : 1.082 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: A 28 ASP cc_start: 0.6768 (m-30) cc_final: 0.6471 (m-30) REVERT: A 298 GLN cc_start: 0.7111 (mm110) cc_final: 0.6871 (mm-40) REVERT: B 28 ASP cc_start: 0.6694 (m-30) cc_final: 0.6241 (m-30) REVERT: B 47 ASP cc_start: 0.8417 (p0) cc_final: 0.8213 (p0) REVERT: B 82 MET cc_start: 0.8252 (mmm) cc_final: 0.7908 (mmm) REVERT: C 15 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6468 (mt-10) REVERT: C 58 LYS cc_start: 0.8204 (tttm) cc_final: 0.7991 (mtpp) REVERT: C 82 MET cc_start: 0.8005 (mmm) cc_final: 0.7592 (mmm) REVERT: D 16 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: D 352 GLU cc_start: 0.7436 (tp30) cc_final: 0.7043 (pt0) REVERT: D 491 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7123 (mm-30) REVERT: E 15 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6516 (mt-10) REVERT: E 491 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6993 (mm-30) REVERT: G 15 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6422 (mt-10) REVERT: H 15 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6436 (mt-10) outliers start: 43 outliers final: 35 residues processed: 540 average time/residue: 0.3704 time to fit residues: 303.7878 Evaluate side-chains 528 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 490 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 315 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 0.9980 chunk 219 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 466 HIS G 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.157270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.127417 restraints weight = 74904.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.132336 restraints weight = 37481.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.135544 restraints weight = 24601.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.137548 restraints weight = 18954.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.138911 restraints weight = 16060.258| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22328 Z= 0.153 Angle : 0.545 7.223 30248 Z= 0.285 Chirality : 0.042 0.171 3512 Planarity : 0.004 0.056 3816 Dihedral : 7.622 69.035 3689 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.97 % Allowed : 15.13 % Favored : 82.89 % 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: -0.72 (0.16), residues: 2808 helix: 0.15 (0.17), residues: 1128 sheet: -2.06 (0.42), residues: 88 loop : -0.81 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 493 TYR 0.010 0.001 TYR A 32 PHE 0.018 0.001 PHE D 99 HIS 0.008 0.002 HIS C 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (22328) covalent geometry : angle 0.54497 / 0.28 (30248) hydrogen bonds : bond 0.02957 / 1.96 ( 748) hydrogen bonds : angle 4.49301 / 3.15 ( 2133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 484 time to evaluate : 1.095 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: A 28 ASP cc_start: 0.6717 (m-30) cc_final: 0.6435 (m-30) REVERT: A 34 ASP cc_start: 0.9030 (m-30) cc_final: 0.8709 (m-30) REVERT: A 78 MET cc_start: 0.8292 (tpp) cc_final: 0.7873 (tpt) REVERT: A 491 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7065 (mm-30) REVERT: B 28 ASP cc_start: 0.6557 (m-30) cc_final: 0.6225 (m-30) REVERT: C 15 GLU cc_start: 0.6622 (mt-10) cc_final: 0.6363 (mt-10) REVERT: C 99 PHE cc_start: 0.8368 (t80) cc_final: 0.8149 (t80) REVERT: C 482 MET cc_start: 0.8294 (mtp) cc_final: 0.8028 (mtp) REVERT: C 491 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6956 (mm-30) REVERT: D 491 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7093 (mm-30) REVERT: E 15 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6454 (mt-10) REVERT: E 491 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: F 493 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7876 (mtm180) REVERT: G 15 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6336 (mt-10) REVERT: G 482 MET cc_start: 0.8280 (mtp) cc_final: 0.8008 (mtp) REVERT: G 491 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: H 15 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6404 (mt-10) REVERT: H 491 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7055 (mm-30) outliers start: 45 outliers final: 37 residues processed: 499 average time/residue: 0.3785 time to fit residues: 288.1136 Evaluate side-chains 504 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 461 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 158 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 33 ASN G 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.153650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.122886 restraints weight = 75051.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.127787 restraints weight = 37618.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.131012 restraints weight = 24833.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.133029 restraints weight = 19185.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.134328 restraints weight = 16282.182| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22328 Z= 0.180 Angle : 0.548 6.723 30248 Z= 0.288 Chirality : 0.043 0.177 3512 Planarity : 0.004 0.054 3816 Dihedral : 7.581 68.571 3682 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.54 % Allowed : 15.92 % Favored : 81.54 % 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: -0.80 (0.16), residues: 2808 helix: 0.14 (0.17), residues: 1120 sheet: -1.97 (0.45), residues: 88 loop : -0.91 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 493 TYR 0.010 0.001 TYR A 32 PHE 0.013 0.001 PHE E 490 HIS 0.021 0.001 HIS G 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (22328) covalent geometry : angle 0.54836 / 0.29 (30248) hydrogen bonds : bond 0.03035 / 2.00 ( 748) hydrogen bonds : angle 4.49309 / 3.15 ( 2133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 470 time to evaluate : 1.208 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: A 28 ASP cc_start: 0.6825 (m-30) cc_final: 0.6556 (m-30) REVERT: A 78 MET cc_start: 0.8267 (tpp) cc_final: 0.7862 (tpt) REVERT: A 491 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7032 (mm-30) REVERT: B 491 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7038 (mm-30) REVERT: C 15 GLU cc_start: 0.6619 (mt-10) cc_final: 0.6391 (mt-10) REVERT: C 99 PHE cc_start: 0.8388 (t80) cc_final: 0.8135 (t80) REVERT: C 453 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7189 (mm) REVERT: C 491 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6987 (mm-30) REVERT: D 491 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: E 82 MET cc_start: 0.8090 (mmm) cc_final: 0.7690 (mmm) REVERT: E 491 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7064 (mm-30) REVERT: F 491 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7031 (mm-30) REVERT: G 15 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6314 (mt-10) REVERT: G 482 MET cc_start: 0.8262 (mtp) cc_final: 0.7950 (mtp) REVERT: G 491 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7028 (mm-30) REVERT: G 494 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8129 (p) REVERT: H 15 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6398 (mt-10) REVERT: H 491 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7037 (mm-30) outliers start: 58 outliers final: 43 residues processed: 493 average time/residue: 0.3516 time to fit residues: 266.7825 Evaluate side-chains 518 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 465 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 192 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 241 GLN G 466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.149992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.119435 restraints weight = 75814.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.124221 restraints weight = 38138.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.127351 restraints weight = 25238.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.129312 restraints weight = 19524.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.130591 restraints weight = 16703.368| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 22328 Z= 0.263 Angle : 0.609 5.971 30248 Z= 0.320 Chirality : 0.045 0.186 3512 Planarity : 0.004 0.059 3816 Dihedral : 7.916 70.369 3682 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.99 % Allowed : 15.70 % Favored : 80.31 % 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: -1.23 (0.16), residues: 2808 helix: -0.10 (0.16), residues: 1128 sheet: -1.73 (0.30), residues: 184 loop : -1.24 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 493 TYR 0.012 0.002 TYR A 32 PHE 0.018 0.002 PHE B 490 HIS 0.009 0.002 HIS H 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.26 (22328) covalent geometry : angle 0.60874 / 0.32 (30248) hydrogen bonds : bond 0.03524 / 2.34 ( 748) hydrogen bonds : angle 4.70107 / 3.29 ( 2133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 474 time to evaluate : 1.062 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: A 28 ASP cc_start: 0.6927 (m-30) cc_final: 0.6582 (m-30) REVERT: A 103 GLU cc_start: 0.7966 (tp30) cc_final: 0.7645 (mm-30) REVERT: A 491 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7035 (mm-30) REVERT: B 82 MET cc_start: 0.8093 (mmm) cc_final: 0.7654 (mmm) REVERT: B 491 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7076 (mm-30) REVERT: C 15 GLU cc_start: 0.6654 (mt-10) cc_final: 0.6411 (mt-10) REVERT: C 491 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7095 (mm-30) REVERT: D 491 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7195 (mm-30) REVERT: E 82 MET cc_start: 0.8087 (mmm) cc_final: 0.7764 (mmm) REVERT: E 491 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7107 (mm-30) REVERT: F 491 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7185 (mm-30) REVERT: G 15 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6439 (mt-10) REVERT: G 491 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7102 (mm-30) REVERT: H 491 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7109 (mm-30) outliers start: 91 outliers final: 68 residues processed: 514 average time/residue: 0.3450 time to fit residues: 275.4618 Evaluate side-chains 544 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 468 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 154 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 232 optimal weight: 0.6980 chunk 208 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 334 GLN G 466 HIS H 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.153745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.123046 restraints weight = 75070.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.127963 restraints weight = 37655.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.131175 restraints weight = 24851.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.133203 restraints weight = 19189.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.134511 restraints weight = 16259.288| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22328 Z= 0.138 Angle : 0.528 5.757 30248 Z= 0.277 Chirality : 0.042 0.160 3512 Planarity : 0.004 0.045 3816 Dihedral : 7.554 68.498 3682 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.37 % Allowed : 18.07 % Favored : 79.56 % 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: -0.90 (0.16), residues: 2808 helix: 0.10 (0.17), residues: 1120 sheet: -1.98 (0.45), residues: 88 loop : -1.00 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 493 TYR 0.009 0.001 TYR A 348 PHE 0.011 0.001 PHE C 99 HIS 0.009 0.001 HIS G 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (22328) covalent geometry : angle 0.52819 / 0.28 (30248) hydrogen bonds : bond 0.02794 / 1.85 ( 748) hydrogen bonds : angle 4.43563 / 3.10 ( 2133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 463 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 PHE cc_start: 0.8410 (t80) cc_final: 0.8200 (t80) REVERT: A 491 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.6898 (mm-30) REVERT: B 298 GLN cc_start: 0.7212 (mm110) cc_final: 0.6897 (mm110) REVERT: B 491 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7094 (mm-30) REVERT: C 15 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6365 (mt-10) REVERT: C 491 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: D 491 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7159 (mm-30) REVERT: E 82 MET cc_start: 0.8052 (mmm) cc_final: 0.7562 (mmm) REVERT: E 491 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7114 (mm-30) REVERT: F 491 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7043 (mm-30) REVERT: G 15 GLU cc_start: 0.6551 (mt-10) cc_final: 0.6232 (mt-10) REVERT: G 482 MET cc_start: 0.8335 (mtp) cc_final: 0.8093 (mtp) REVERT: G 491 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7096 (mm-30) REVERT: H 15 GLU cc_start: 0.6769 (mt-10) cc_final: 0.6380 (mt-10) REVERT: H 82 MET cc_start: 0.7700 (mmm) cc_final: 0.7207 (mmm) REVERT: H 491 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7028 (mm-30) outliers start: 54 outliers final: 43 residues processed: 491 average time/residue: 0.3657 time to fit residues: 277.2461 Evaluate side-chains 504 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 453 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 114 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 209 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 21 GLN ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN G 334 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.155951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.125951 restraints weight = 76342.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.130832 restraints weight = 38416.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.133990 restraints weight = 25289.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.135957 restraints weight = 19561.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.137279 restraints weight = 16633.426| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 0.045 22328 Z= 0.148 Angle : 0.527 6.522 30248 Z= 0.276 Chirality : 0.042 0.164 3512 Planarity : 0.004 0.041 3816 Dihedral : 7.371 68.538 3682 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.54 % Allowed : 18.42 % Favored : 79.04 % 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: -1.00 (0.16), residues: 2808 helix: 0.14 (0.17), residues: 1128 sheet: -1.78 (0.29), residues: 184 loop : -1.13 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 493 TYR 0.008 0.001 TYR A 348 PHE 0.010 0.001 PHE E 490 HIS 0.009 0.001 HIS C 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (22328) covalent geometry : angle 0.52732 / 0.28 (30248) hydrogen bonds : bond 0.02768 / 1.83 ( 748) hydrogen bonds : angle 4.40404 / 3.08 ( 2133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 454 time to evaluate : 1.095 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 78 MET cc_start: 0.8176 (tpp) cc_final: 0.7853 (tpt) REVERT: A 99 PHE cc_start: 0.8413 (t80) cc_final: 0.8137 (t80) REVERT: A 491 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6854 (mm-30) REVERT: B 298 GLN cc_start: 0.7216 (mm110) cc_final: 0.6917 (mm110) REVERT: B 491 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7083 (mm-30) REVERT: C 15 GLU cc_start: 0.6573 (mt-10) cc_final: 0.6285 (mt-10) REVERT: C 491 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7038 (mm-30) REVERT: D 491 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7148 (mm-30) REVERT: E 82 MET cc_start: 0.8068 (mmm) cc_final: 0.7608 (mmm) REVERT: E 491 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7067 (mm-30) REVERT: F 491 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7063 (mm-30) REVERT: G 15 GLU cc_start: 0.6539 (mt-10) cc_final: 0.6226 (mt-10) REVERT: G 482 MET cc_start: 0.8326 (mtp) cc_final: 0.8052 (mtp) REVERT: G 491 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: H 15 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6326 (mt-10) REVERT: H 491 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7074 (mm-30) outliers start: 58 outliers final: 45 residues processed: 482 average time/residue: 0.3414 time to fit residues: 256.5415 Evaluate side-chains 504 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 451 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 275 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 207 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 267 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 465 GLN ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.155169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.124840 restraints weight = 75929.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.129659 restraints weight = 38385.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.132795 restraints weight = 25427.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.134743 restraints weight = 19759.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.136026 restraints weight = 16868.006| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22328 Z= 0.142 Angle : 0.522 5.815 30248 Z= 0.273 Chirality : 0.042 0.162 3512 Planarity : 0.004 0.037 3816 Dihedral : 7.251 68.271 3682 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.59 % Allowed : 18.38 % Favored : 79.04 % 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: -0.96 (0.16), residues: 2808 helix: 0.17 (0.17), residues: 1128 sheet: -1.79 (0.29), residues: 184 loop : -1.09 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 259 TYR 0.008 0.001 TYR A 348 PHE 0.013 0.001 PHE E 99 HIS 0.008 0.001 HIS C 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (22328) covalent geometry : angle 0.52165 / 0.27 (30248) hydrogen bonds : bond 0.02663 / 1.77 ( 748) hydrogen bonds : angle 4.36033 / 3.05 ( 2133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 458 time to evaluate : 1.080 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 78 MET cc_start: 0.8323 (tpp) cc_final: 0.7937 (tpt) REVERT: A 99 PHE cc_start: 0.8380 (t80) cc_final: 0.8101 (t80) REVERT: A 491 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6774 (mm-30) REVERT: B 298 GLN cc_start: 0.7201 (mm110) cc_final: 0.6907 (mm110) REVERT: B 491 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7042 (mm-30) REVERT: C 15 GLU cc_start: 0.6541 (mt-10) cc_final: 0.6291 (mt-10) REVERT: C 337 MET cc_start: 0.6717 (ttt) cc_final: 0.6488 (ttt) REVERT: C 491 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7096 (mm-30) REVERT: D 491 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7114 (mm-30) REVERT: E 82 MET cc_start: 0.8071 (mmm) cc_final: 0.7598 (mmm) REVERT: E 491 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7059 (mm-30) REVERT: F 99 PHE cc_start: 0.8347 (t80) cc_final: 0.8145 (t80) REVERT: F 491 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6977 (mm-30) REVERT: G 15 GLU cc_start: 0.6530 (mt-10) cc_final: 0.6220 (mt-10) REVERT: G 109 LYS cc_start: 0.7119 (pttt) cc_final: 0.6425 (ptmm) REVERT: G 298 GLN cc_start: 0.7075 (mm110) cc_final: 0.6768 (mm-40) REVERT: G 491 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: H 15 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6373 (mt-10) REVERT: H 109 LYS cc_start: 0.6944 (pttt) cc_final: 0.6296 (ptmm) REVERT: H 491 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7060 (mm-30) outliers start: 59 outliers final: 49 residues processed: 485 average time/residue: 0.3701 time to fit residues: 279.3005 Evaluate side-chains 510 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 453 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 241 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 238 optimal weight: 0.6980 chunk 251 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 218 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 465 GLN ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.156858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.125485 restraints weight = 75880.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.130413 restraints weight = 39053.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.133629 restraints weight = 26108.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.135639 restraints weight = 20404.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.136991 restraints weight = 17467.274| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22328 Z= 0.132 Angle : 0.515 5.824 30248 Z= 0.269 Chirality : 0.042 0.175 3512 Planarity : 0.003 0.036 3816 Dihedral : 7.089 68.527 3682 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.68 % Allowed : 18.51 % Favored : 78.82 % 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: -0.94 (0.16), residues: 2808 helix: 0.23 (0.17), residues: 1128 sheet: -1.67 (0.34), residues: 144 loop : -1.16 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 493 TYR 0.008 0.001 TYR G 348 PHE 0.009 0.001 PHE E 99 HIS 0.009 0.001 HIS E 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (22328) covalent geometry : angle 0.51549 / 0.27 (30248) hydrogen bonds : bond 0.02582 / 1.71 ( 748) hydrogen bonds : angle 4.31789 / 3.03 ( 2133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 463 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8318 (tpp) cc_final: 0.7919 (tpt) REVERT: A 99 PHE cc_start: 0.8349 (t80) cc_final: 0.8076 (t80) REVERT: B 109 LYS cc_start: 0.7043 (pttt) cc_final: 0.6609 (ptpt) REVERT: B 491 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: C 15 GLU cc_start: 0.6525 (mt-10) cc_final: 0.6273 (mt-10) REVERT: C 337 MET cc_start: 0.6556 (ttt) cc_final: 0.6354 (ttt) REVERT: C 491 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7079 (mm-30) REVERT: D 491 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: E 491 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7059 (mm-30) REVERT: F 99 PHE cc_start: 0.8357 (t80) cc_final: 0.8153 (t80) REVERT: F 491 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6971 (mm-30) REVERT: G 15 GLU cc_start: 0.6527 (mt-10) cc_final: 0.6215 (mt-10) REVERT: G 109 LYS cc_start: 0.7122 (pttt) cc_final: 0.6380 (ptmm) REVERT: G 298 GLN cc_start: 0.7059 (mm110) cc_final: 0.6696 (mm-40) REVERT: G 491 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7044 (mm-30) REVERT: H 15 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6374 (mt-10) REVERT: H 109 LYS cc_start: 0.6947 (pttt) cc_final: 0.6288 (ptmm) REVERT: H 491 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7083 (mm-30) outliers start: 61 outliers final: 52 residues processed: 495 average time/residue: 0.3856 time to fit residues: 295.8771 Evaluate side-chains 514 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 455 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 104 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 174 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 198 optimal weight: 0.0970 chunk 150 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.158785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.127434 restraints weight = 75640.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.132428 restraints weight = 38690.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.135649 restraints weight = 25808.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.137793 restraints weight = 20066.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.139139 restraints weight = 17040.511| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22328 Z= 0.109 Angle : 0.504 5.396 30248 Z= 0.262 Chirality : 0.041 0.177 3512 Planarity : 0.003 0.038 3816 Dihedral : 6.844 73.682 3682 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.37 % Allowed : 19.43 % Favored : 78.20 % 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: -0.81 (0.16), residues: 2808 helix: 0.32 (0.17), residues: 1128 sheet: -1.51 (0.35), residues: 144 loop : -1.08 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 322 TYR 0.008 0.001 TYR G 348 PHE 0.011 0.001 PHE E 99 HIS 0.013 0.001 HIS H 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (22328) covalent geometry : angle 0.50361 / 0.26 (30248) hydrogen bonds : bond 0.02402 / 1.59 ( 748) hydrogen bonds : angle 4.21464 / 2.96 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7487.43 seconds wall clock time: 128 minutes 19.64 seconds (7699.64 seconds total)