Starting phenix.real_space_refine on Sat Oct 31 13:13:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rgi_24450/10_2026/7rgi_24450_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rgi_24450/10_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rgi_24450/10_2026/7rgi_24450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rgi_24450/10_2026/7rgi_24450.map" model { file = "/net/cci-nas-00/data/ceres_data/7rgi_24450/10_2026/7rgi_24450_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rgi_24450/10_2026/7rgi_24450_trim.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/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: 6.72, per 1000 atoms: 0.15 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: 3.68 Conformation dependent library (CDL) restraints added in 1.2 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: 1.01 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: 10.88 Time building geometry restraints manager: 5.22 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: 69449 2.86 - 5.73: 8164 5.73 - 8.59: 1986 8.59 - 11.45: 43 11.45 - 14.32: 22 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: 18442 17.97 - 35.94: 1575 35.94 - 53.91: 526 53.91 - 71.88: 427 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: 2515 0.084 - 0.167: 794 0.167 - 0.251: 167 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 38.370 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.350 ------------------------------------------------------------------------------- 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 : 0.011 0.101 22328 Z= 0.680 Angle : 1.771 13.832 30248 Z= 1.141 Chirality : 0.087 0.418 3512 Planarity : 0.013 0.284 3816 Dihedral : 14.685 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 0.01142 / 0.68 (22328) covalent geometry : angle 1.77111 / 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 : 1.118 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: 0.3886 time to fit residues: 397.0774 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 : 1.092 ------------------------------------------------------------------------------- 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: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] 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 = 0.3652 r_free = 0.3652 target = 0.159805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.130231 restraints weight = 74648.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.135270 restraints weight = 36649.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.138568 restraints weight = 23870.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.140666 restraints weight = 18242.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.142053 restraints weight = 15338.390| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22328 Z= 0.164 Angle : 0.640 7.384 30248 Z= 0.343 Chirality : 0.043 0.177 3512 Planarity : 0.004 0.054 3816 Dihedral : 9.385 80.559 3720 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.18 % Allowed : 10.92 % Favored : 87.89 % 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: -0.93 (0.16), residues: 2808 helix: -0.24 (0.16), residues: 1120 sheet: -2.25 (0.40), 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 0.015 0.001 TYR F 348 PHE 0.013 0.002 PHE C 490 HIS 0.008 0.002 HIS H 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (22328) covalent geometry : angle 0.64013 / 0.34 (30248) hydrogen bonds : bond 0.03795 / 2.50 ( 748) hydrogen bonds : angle 4.92149 / 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 573 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 546 time to evaluate : 1.067 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: A 28 ASP cc_start: 0.6828 (m-30) cc_final: 0.6597 (m-30) REVERT: A 265 GLN cc_start: 0.8042 (mt0) cc_final: 0.7812 (mt0) REVERT: B 28 ASP cc_start: 0.6651 (m-30) cc_final: 0.6149 (m-30) REVERT: B 47 ASP cc_start: 0.8388 (p0) cc_final: 0.8107 (p0) REVERT: B 265 GLN cc_start: 0.8043 (mt0) cc_final: 0.7807 (mt0) REVERT: B 298 GLN cc_start: 0.7131 (mm110) cc_final: 0.6920 (mm-40) REVERT: C 15 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6415 (mt-10) REVERT: C 82 MET cc_start: 0.7950 (mmm) cc_final: 0.7664 (mmm) REVERT: C 265 GLN cc_start: 0.8041 (mt0) cc_final: 0.7829 (mt0) REVERT: C 482 MET cc_start: 0.8391 (mtp) cc_final: 0.8165 (mtp) REVERT: C 492 LYS cc_start: 0.8963 (mtpp) cc_final: 0.8642 (ttmt) REVERT: D 16 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: D 319 ASP cc_start: 0.7939 (m-30) cc_final: 0.7578 (m-30) REVERT: D 491 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7057 (mm-30) REVERT: E 15 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6549 (mt-10) REVERT: E 28 ASP cc_start: 0.7261 (m-30) cc_final: 0.6868 (m-30) REVERT: E 265 GLN cc_start: 0.8054 (mt0) cc_final: 0.7820 (mt0) REVERT: E 337 MET cc_start: 0.6497 (ttt) cc_final: 0.6241 (ttt) REVERT: E 482 MET cc_start: 0.8462 (mtp) cc_final: 0.8230 (mtp) REVERT: F 265 GLN cc_start: 0.7988 (mt0) cc_final: 0.7748 (mt0) REVERT: F 482 MET cc_start: 0.8474 (mtp) cc_final: 0.8241 (mtp) REVERT: G 15 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6509 (mt-10) REVERT: G 319 ASP cc_start: 0.7927 (m-30) cc_final: 0.7393 (m-30) REVERT: G 482 MET cc_start: 0.8450 (mtp) cc_final: 0.8235 (mtp) REVERT: H 15 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6566 (mt-10) REVERT: H 319 ASP cc_start: 0.8096 (m-30) cc_final: 0.7513 (m-30) outliers start: 27 outliers final: 20 residues processed: 557 average time/residue: 0.3775 time to fit residues: 320.3405 Evaluate side-chains 525 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 503 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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: [36, 107, 93, 74, 181, 214, 77, 212, 218, 242, 102] chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 214 optimal weight: 0.0980 chunk 77 optimal weight: 0.9980 chunk 212 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 242 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 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 = 0.3622 r_free = 0.3622 target = 0.156928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.126604 restraints weight = 75128.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.131613 restraints weight = 37369.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.134840 restraints weight = 24474.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.136964 restraints weight = 18802.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.138202 restraints weight = 15873.241| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22328 Z= 0.130 Angle : 0.552 8.153 30248 Z= 0.292 Chirality : 0.042 0.172 3512 Planarity : 0.004 0.052 3816 Dihedral : 8.443 73.946 3691 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.62 % Allowed : 13.07 % Favored : 85.31 % 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: -0.71 (0.16), residues: 2808 helix: 0.09 (0.16), residues: 1120 sheet: -2.12 (0.40), residues: 88 loop : -0.73 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 322 TYR 0.010 0.001 TYR B 348 PHE 0.013 0.001 PHE E 490 HIS 0.007 0.002 HIS H 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (22328) covalent geometry : angle 0.55195 / 0.29 (30248) hydrogen bonds : bond 0.03096 / 2.06 ( 748) hydrogen bonds : angle 4.57621 / 3.21 ( 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 571 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 534 time to evaluate : 1.114 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: A 28 ASP cc_start: 0.6729 (m-30) cc_final: 0.6417 (m-30) REVERT: A 298 GLN cc_start: 0.7123 (mm110) cc_final: 0.6865 (mm110) REVERT: A 322 ARG cc_start: 0.7819 (ttp80) cc_final: 0.7551 (ttp80) REVERT: B 28 ASP cc_start: 0.6718 (m-30) cc_final: 0.6306 (m-30) REVERT: B 82 MET cc_start: 0.8220 (mmm) cc_final: 0.7871 (mmm) REVERT: C 15 GLU cc_start: 0.6706 (mt-10) cc_final: 0.6446 (mt-10) REVERT: D 16 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: D 491 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: E 15 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6461 (mt-10) REVERT: E 28 ASP cc_start: 0.7227 (m-30) cc_final: 0.6825 (m-30) REVERT: E 34 ASP cc_start: 0.8839 (t0) cc_final: 0.8482 (t0) REVERT: E 491 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7065 (mm-30) REVERT: E 493 ARG cc_start: 0.8171 (mtm180) cc_final: 0.7943 (mtm180) REVERT: F 298 GLN cc_start: 0.7236 (mm110) cc_final: 0.7015 (mm-40) REVERT: F 482 MET cc_start: 0.8300 (mtp) cc_final: 0.8042 (mtp) REVERT: G 15 GLU cc_start: 0.6664 (mt-10) cc_final: 0.6377 (mt-10) REVERT: H 15 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6511 (mt-10) outliers start: 37 outliers final: 30 residues processed: 541 average time/residue: 0.3811 time to fit residues: 313.7778 Evaluate side-chains 533 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 500 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 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 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 245 LEU 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 272 VAL 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 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: [165, 219, 73, 201, 42, 275, 105, 232, 51, 162, 98] chunk 165 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 275 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 466 HIS G 498 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.155350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.124855 restraints weight = 75184.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.129760 restraints weight = 38039.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.132920 restraints weight = 25174.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.134981 restraints weight = 19440.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.136230 restraints weight = 16540.058| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3170 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= 0.178 Angle : 0.561 6.432 30248 Z= 0.294 Chirality : 0.043 0.173 3512 Planarity : 0.004 0.059 3816 Dihedral : 8.285 84.438 3687 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.24 % Allowed : 14.87 % 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: -0.74 (0.16), residues: 2808 helix: 0.11 (0.17), residues: 1128 sheet: -2.02 (0.42), residues: 88 loop : -0.80 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 322 TYR 0.010 0.001 TYR F 32 PHE 0.015 0.002 PHE E 490 HIS 0.008 0.002 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (22328) covalent geometry : angle 0.56058 / 0.29 (30248) hydrogen bonds : bond 0.03182 / 2.11 ( 748) hydrogen bonds : angle 4.56113 / 3.19 ( 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 530 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 479 time to evaluate : 1.168 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 28 ASP cc_start: 0.6692 (m-30) cc_final: 0.6401 (m-30) REVERT: A 78 MET cc_start: 0.8288 (tpp) cc_final: 0.7837 (tpt) REVERT: B 28 ASP cc_start: 0.6648 (m-30) cc_final: 0.6227 (m-30) REVERT: B 82 MET cc_start: 0.8279 (mmm) cc_final: 0.7871 (mmm) REVERT: C 15 GLU cc_start: 0.6658 (mt-10) cc_final: 0.6403 (mt-10) REVERT: C 82 MET cc_start: 0.7880 (mmm) cc_final: 0.7506 (mmm) REVERT: C 99 PHE cc_start: 0.8357 (t80) cc_final: 0.8142 (t80) REVERT: C 482 MET cc_start: 0.8360 (mtp) cc_final: 0.8096 (mtp) REVERT: C 491 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7020 (mm-30) REVERT: D 491 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7162 (mm-30) REVERT: E 15 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6482 (mt-10) REVERT: E 82 MET cc_start: 0.8161 (mmm) cc_final: 0.7658 (mmm) REVERT: E 482 MET cc_start: 0.8280 (mtp) cc_final: 0.8030 (mtp) REVERT: E 491 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7023 (mm-30) REVERT: F 482 MET cc_start: 0.8222 (mtp) cc_final: 0.7912 (mtp) REVERT: F 493 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7883 (mtm180) REVERT: G 15 GLU cc_start: 0.6655 (mt-10) cc_final: 0.6377 (mt-10) REVERT: G 482 MET cc_start: 0.8298 (mtp) cc_final: 0.8030 (mtp) REVERT: G 491 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: H 15 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6470 (mt-10) outliers start: 51 outliers final: 45 residues processed: 494 average time/residue: 0.3798 time to fit residues: 285.9816 Evaluate side-chains 510 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 461 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 272 VAL Chi-restraints excluded: chain A residue 319 ASP 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 271 ILE Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 275 SER 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 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 393 THR 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 G residue 43 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 319 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 63 THR Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 315 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: [158, 263, 23, 76, 85, 165, 217, 193, 90, 51, 67] 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: 1.9990 chunk 165 optimal weight: 0.9990 chunk 217 optimal weight: 0.5980 chunk 193 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 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 = 0.3596 r_free = 0.3596 target = 0.154448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.124172 restraints weight = 75060.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.129071 restraints weight = 37548.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.132285 restraints weight = 24568.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.134282 restraints weight = 18901.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.135644 restraints weight = 16006.236| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3395 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= 0.168 Angle : 0.538 5.927 30248 Z= 0.283 Chirality : 0.042 0.173 3512 Planarity : 0.004 0.055 3816 Dihedral : 8.169 81.414 3682 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.46 % Allowed : 15.79 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.16), residues: 2808 helix: 0.14 (0.17), residues: 1128 sheet: -1.98 (0.43), residues: 88 loop : -0.83 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 493 TYR 0.012 0.001 TYR H 289 PHE 0.012 0.001 PHE F 490 HIS 0.023 0.001 HIS G 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (22328) covalent geometry : angle 0.53782 / 0.28 (30248) hydrogen bonds : bond 0.02996 / 1.98 ( 748) hydrogen bonds : angle 4.48481 / 3.14 ( 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 518 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 462 time to evaluate : 1.145 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: 0.6714 (m-30) cc_final: 0.6413 (m-30) REVERT: A 78 MET cc_start: 0.8307 (tpp) cc_final: 0.7885 (tpt) REVERT: A 491 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7077 (mm-30) REVERT: B 28 ASP cc_start: 0.6679 (m-30) cc_final: 0.6330 (m-30) REVERT: B 82 MET cc_start: 0.8132 (mmm) cc_final: 0.7726 (mmm) REVERT: B 491 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7022 (mm-30) REVERT: C 15 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6389 (mt-10) REVERT: C 99 PHE cc_start: 0.8373 (t80) cc_final: 0.8129 (t80) REVERT: C 482 MET cc_start: 0.8277 (mtp) cc_final: 0.8014 (mtp) REVERT: C 491 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6990 (mm-30) REVERT: D 491 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: E 82 MET cc_start: 0.8120 (mmm) cc_final: 0.7671 (mmm) REVERT: E 482 MET cc_start: 0.8229 (mtp) cc_final: 0.7958 (mtp) REVERT: E 491 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7067 (mm-30) REVERT: F 482 MET cc_start: 0.8191 (mtp) cc_final: 0.7871 (mtp) REVERT: F 491 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7011 (mm-30) REVERT: G 15 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6353 (mt-10) REVERT: G 482 MET cc_start: 0.8285 (mtp) cc_final: 0.8009 (mtp) REVERT: G 491 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7029 (mm-30) REVERT: H 15 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6390 (mt-10) REVERT: H 491 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7085 (mm-30) outliers start: 56 outliers final: 45 residues processed: 482 average time/residue: 0.3660 time to fit residues: 272.1438 Evaluate side-chains 508 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 455 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 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 245 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 275 SER 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 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 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 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 51 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 319 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 319 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: [192, 275, 221, 202, 16, 167, 73, 211, 41, 18, 266] chunk 192 optimal weight: 0.9980 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: 0.6980 chunk 266 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 334 GLN G 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.152555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.121762 restraints weight = 75210.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.126620 restraints weight = 37793.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.129840 restraints weight = 24968.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.131847 restraints weight = 19325.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.133160 restraints weight = 16402.954| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22328 Z= 0.203 Angle : 0.556 5.434 30248 Z= 0.294 Chirality : 0.043 0.189 3512 Planarity : 0.004 0.054 3816 Dihedral : 8.186 81.785 3682 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.29 % Allowed : 15.26 % Favored : 81.45 % 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: -0.84 (0.16), residues: 2808 helix: 0.08 (0.17), residues: 1128 sheet: -1.90 (0.46), residues: 88 loop : -0.92 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 322 TYR 0.011 0.001 TYR A 32 PHE 0.015 0.002 PHE A 490 HIS 0.008 0.001 HIS H 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (22328) covalent geometry : angle 0.55599 / 0.29 (30248) hydrogen bonds : bond 0.03162 / 2.10 ( 748) hydrogen bonds : angle 4.53110 / 3.17 ( 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 545 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 470 time to evaluate : 1.133 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: 0.8244 (tpp) cc_final: 0.7845 (tpt) REVERT: B 28 ASP cc_start: 0.6792 (m-30) cc_final: 0.6392 (m-30) REVERT: B 82 MET cc_start: 0.8126 (mmm) cc_final: 0.7704 (mmm) REVERT: B 491 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7033 (mm-30) REVERT: C 15 GLU cc_start: 0.6609 (mt-10) cc_final: 0.6396 (mt-10) REVERT: C 453 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7366 (mm) REVERT: C 491 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7042 (mm-30) REVERT: D 491 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7225 (mm-30) REVERT: E 82 MET cc_start: 0.8095 (mmm) cc_final: 0.7699 (mmm) REVERT: E 491 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7066 (mm-30) REVERT: F 491 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7029 (mm-30) REVERT: G 15 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6374 (mt-10) REVERT: G 491 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: H 15 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6382 (mt-10) REVERT: H 491 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7060 (mm-30) outliers start: 75 outliers final: 59 residues processed: 502 average time/residue: 0.3569 time to fit residues: 278.2749 Evaluate side-chains 533 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 466 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 272 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 ASP 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 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 395 GLU 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 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 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 275 SER 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 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 51 LEU 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 319 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 63 THR 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 319 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: [154, 212, 196, 263, 222, 96, 113, 232, 208, 216, 24] 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: 0.4980 chunk 96 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 334 GLN E 33 ASN G 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.154242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.123304 restraints weight = 74947.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.128263 restraints weight = 37580.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.131496 restraints weight = 24736.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.133546 restraints weight = 19101.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.134813 restraints weight = 16211.099| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3664 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= 0.144 Angle : 0.519 6.016 30248 Z= 0.272 Chirality : 0.042 0.164 3512 Planarity : 0.004 0.046 3816 Dihedral : 7.999 84.211 3682 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.50 % Allowed : 16.93 % Favored : 80.57 % 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: -0.74 (0.16), residues: 2808 helix: 0.17 (0.17), residues: 1128 sheet: -1.84 (0.47), residues: 88 loop : -0.87 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 322 TYR 0.008 0.001 TYR A 32 PHE 0.010 0.001 PHE E 490 HIS 0.010 0.001 HIS G 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (22328) covalent geometry : angle 0.51860 / 0.27 (30248) hydrogen bonds : bond 0.02796 / 1.85 ( 748) hydrogen bonds : angle 4.40224 / 3.08 ( 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 516 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 459 time to evaluate : 1.042 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 78 MET cc_start: 0.8224 (tpp) cc_final: 0.7848 (tpt) REVERT: B 491 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7074 (mm-30) REVERT: C 15 GLU cc_start: 0.6539 (mt-10) cc_final: 0.6303 (mt-10) REVERT: C 453 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7406 (mm) REVERT: C 482 MET cc_start: 0.8321 (mtp) cc_final: 0.8114 (mtp) REVERT: C 491 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6988 (mm-30) REVERT: D 491 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7202 (mm-30) REVERT: E 82 MET cc_start: 0.8056 (mmm) cc_final: 0.7567 (mmm) REVERT: E 482 MET cc_start: 0.8296 (mtp) cc_final: 0.8090 (mtp) REVERT: E 491 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7077 (mm-30) REVERT: F 482 MET cc_start: 0.8269 (mtp) cc_final: 0.8067 (mtp) REVERT: F 491 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7009 (mm-30) REVERT: G 15 GLU cc_start: 0.6575 (mt-10) cc_final: 0.6255 (mt-10) REVERT: G 482 MET cc_start: 0.8347 (mtp) cc_final: 0.8142 (mtp) REVERT: G 491 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7062 (mm-30) REVERT: H 15 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6471 (mt-10) REVERT: H 491 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7050 (mm-30) outliers start: 57 outliers final: 45 residues processed: 483 average time/residue: 0.3487 time to fit residues: 263.3750 Evaluate side-chains 503 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 450 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 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 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 275 SER 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 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 275 SER 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 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 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 51 LEU 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 319 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 275 SER 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: [114, 5, 124, 119, 140, 242, 192, 139, 65, 209, 12] chunk 114 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 466 HIS ** 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 = 0.3562 r_free = 0.3562 target = 0.151552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.121003 restraints weight = 75875.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.125590 restraints weight = 39980.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.128605 restraints weight = 27105.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.130519 restraints weight = 21222.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.131792 restraints weight = 18274.263| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22328 Z= 0.209 Angle : 0.561 5.905 30248 Z= 0.296 Chirality : 0.044 0.172 3512 Planarity : 0.004 0.048 3816 Dihedral : 8.139 83.129 3682 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.98 % Allowed : 17.59 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.16), residues: 2808 helix: 0.08 (0.17), residues: 1128 sheet: -2.07 (0.47), residues: 88 loop : -0.99 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 341 TYR 0.010 0.001 TYR F 32 PHE 0.024 0.002 PHE E 99 HIS 0.012 0.001 HIS G 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (22328) covalent geometry : angle 0.56101 / 0.30 (30248) hydrogen bonds : bond 0.03144 / 2.07 ( 748) hydrogen bonds : angle 4.54195 / 3.18 ( 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 531 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 463 time to evaluate : 1.101 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 78 MET cc_start: 0.8218 (tpp) cc_final: 0.7833 (tpt) REVERT: A 99 PHE cc_start: 0.8452 (t80) cc_final: 0.8179 (t80) REVERT: B 298 GLN cc_start: 0.7253 (mm110) cc_final: 0.6943 (mm110) REVERT: B 491 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7091 (mm-30) REVERT: C 15 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6427 (mt-10) REVERT: C 491 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7081 (mm-30) REVERT: D 491 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7215 (mm-30) REVERT: E 82 MET cc_start: 0.8134 (mmm) cc_final: 0.7730 (mmm) REVERT: E 491 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7074 (mm-30) REVERT: F 491 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: G 15 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6330 (mt-10) REVERT: G 491 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7036 (mm-30) REVERT: H 15 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6365 (mt-10) REVERT: H 109 LYS cc_start: 0.6856 (pttt) cc_final: 0.6236 (ptmm) REVERT: H 491 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7096 (mm-30) outliers start: 68 outliers final: 57 residues processed: 494 average time/residue: 0.3540 time to fit residues: 273.9025 Evaluate side-chains 521 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 457 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 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 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 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 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 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 275 SER 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 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 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 370 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 51 LEU 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 319 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: [275, 242, 264, 55, 118, 176, 8, 207, 199, 267, 7] chunk 275 optimal weight: 0.9990 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: 0.9980 chunk 8 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 199 optimal weight: 0.6980 chunk 267 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN G 466 HIS ** 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 = 0.3607 r_free = 0.3607 target = 0.155556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.125610 restraints weight = 75851.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.130431 restraints weight = 38311.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.133578 restraints weight = 25286.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.135486 restraints weight = 19568.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.136816 restraints weight = 16680.566| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22328 Z= 0.138 Angle : 0.522 6.548 30248 Z= 0.274 Chirality : 0.042 0.173 3512 Planarity : 0.004 0.040 3816 Dihedral : 7.959 85.517 3682 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.59 % Allowed : 18.46 % Favored : 78.95 % 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: 0.17 (0.17), residues: 1128 sheet: -2.00 (0.46), residues: 88 loop : -0.93 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 322 TYR 0.009 0.001 TYR A 348 PHE 0.018 0.001 PHE G 99 HIS 0.019 0.001 HIS G 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (22328) covalent geometry : angle 0.52238 / 0.27 (30248) hydrogen bonds : bond 0.02722 / 1.80 ( 748) hydrogen bonds : angle 4.39007 / 3.07 ( 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 516 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 457 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8209 (tpp) cc_final: 0.7888 (tpt) REVERT: A 99 PHE cc_start: 0.8368 (t80) cc_final: 0.8101 (t80) REVERT: B 298 GLN cc_start: 0.7215 (mm110) cc_final: 0.6912 (mm110) REVERT: B 491 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7046 (mm-30) REVERT: C 15 GLU cc_start: 0.6530 (mt-10) cc_final: 0.6284 (mt-10) REVERT: C 453 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7339 (mm) REVERT: C 491 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7031 (mm-30) REVERT: D 491 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7195 (mm-30) REVERT: D 493 ARG cc_start: 0.8410 (mtm180) cc_final: 0.8201 (mtm180) REVERT: E 82 MET cc_start: 0.8062 (mmm) cc_final: 0.7603 (mmm) REVERT: E 491 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7075 (mm-30) REVERT: F 491 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7019 (mm-30) REVERT: G 15 GLU cc_start: 0.6492 (mt-10) cc_final: 0.6188 (mt-10) REVERT: G 34 ASP cc_start: 0.9007 (m-30) cc_final: 0.8750 (m-30) REVERT: G 491 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7057 (mm-30) REVERT: H 15 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6369 (mt-10) REVERT: H 491 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7047 (mm-30) outliers start: 59 outliers final: 49 residues processed: 484 average time/residue: 0.3506 time to fit residues: 266.4310 Evaluate side-chains 502 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 445 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 306 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 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 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 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 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 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 272 VAL Chi-restraints excluded: chain G residue 275 SER 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 465 GLN 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 275 SER 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: [241, 222, 13, 42, 2, 156, 274, 238, 251, 148, 218] chunk 241 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 chunk 238 optimal weight: 0.3980 chunk 251 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 GLN ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN H 465 GLN ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.154538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.124472 restraints weight = 76486.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.129364 restraints weight = 37988.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.132530 restraints weight = 24861.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.134528 restraints weight = 19155.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.135853 restraints weight = 16235.469| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22328 Z= 0.178 Angle : 0.676 59.200 30248 Z= 0.380 Chirality : 0.043 0.241 3512 Planarity : 0.004 0.040 3816 Dihedral : 7.960 85.558 3682 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.76 % Allowed : 18.46 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.16), residues: 2808 helix: 0.18 (0.17), residues: 1128 sheet: -2.01 (0.46), residues: 88 loop : -0.93 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 322 TYR 0.008 0.001 TYR A 348 PHE 0.014 0.001 PHE G 99 HIS 0.017 0.001 HIS G 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (22328) covalent geometry : angle 0.67553 / 0.38 (30248) hydrogen bonds : bond 0.02788 / 1.84 ( 748) hydrogen bonds : angle 4.41516 / 3.09 ( 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 506 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 443 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8213 (tpp) cc_final: 0.7892 (tpt) REVERT: A 99 PHE cc_start: 0.8370 (t80) cc_final: 0.8105 (t80) REVERT: B 298 GLN cc_start: 0.7216 (mm110) cc_final: 0.6917 (mm110) REVERT: B 491 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: C 15 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6289 (mt-10) REVERT: C 453 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7343 (mm) REVERT: C 491 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7040 (mm-30) REVERT: D 491 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: D 493 ARG cc_start: 0.8415 (mtm180) cc_final: 0.8204 (mtm180) REVERT: E 82 MET cc_start: 0.8076 (mmm) cc_final: 0.7612 (mmm) REVERT: E 491 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: F 491 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7062 (mm-30) REVERT: G 15 GLU cc_start: 0.6503 (mt-10) cc_final: 0.6225 (mt-10) REVERT: G 34 ASP cc_start: 0.9031 (m-30) cc_final: 0.8754 (m-30) REVERT: G 491 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: H 15 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6373 (mt-10) REVERT: H 491 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7051 (mm-30) outliers start: 63 outliers final: 55 residues processed: 469 average time/residue: 0.3492 time to fit residues: 255.6082 Evaluate side-chains 505 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 442 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 306 THR Chi-restraints excluded: chain A residue 465 GLN 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 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 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 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 275 SER 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 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 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 465 GLN Chi-restraints excluded: chain F residue 491 GLU 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 309 GLN Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 319 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 275 SER Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 465 GLN 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: [104, 149, 174, 35, 198, 150, 45, 274, 72, 76, 102] chunk 104 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 174 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 198 optimal weight: 0.3980 chunk 150 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 GLN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 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 = 0.3598 r_free = 0.3598 target = 0.154738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.124600 restraints weight = 76770.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.129494 restraints weight = 38138.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.132672 restraints weight = 24990.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.134678 restraints weight = 19271.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.135886 restraints weight = 16323.844| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.229 22328 Z= 0.212 Angle : 0.995 59.199 30248 Z= 0.612 Chirality : 0.044 0.527 3512 Planarity : 0.004 0.039 3816 Dihedral : 7.969 85.557 3682 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.68 % Allowed : 18.51 % Favored : 78.82 % Cbeta Deviations : 0.08 % 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: 0.16 (0.17), residues: 1128 sheet: -2.00 (0.46), residues: 88 loop : -0.93 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 322 TYR 0.008 0.001 TYR A 348 PHE 0.011 0.001 PHE G 99 HIS 0.013 0.001 HIS G 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (22328) covalent geometry : angle 0.99531 / 0.61 (30248) hydrogen bonds : bond 0.02703 / 1.78 ( 748) hydrogen bonds : angle 4.41686 / 3.09 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7546.51 seconds wall clock time: 129 minutes 12.60 seconds (7752.60 seconds total)