Starting phenix.real_space_refine on Wed Aug 27 00:27:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rgi_24450/08_2025/7rgi_24450_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rgi_24450/08_2025/7rgi_24450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rgi_24450/08_2025/7rgi_24450_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rgi_24450/08_2025/7rgi_24450_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rgi_24450/08_2025/7rgi_24450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rgi_24450/08_2025/7rgi_24450.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.198 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 144 5.16 5 C 13776 2.51 5 N 3768 2.21 5 O 4248 1.98 5 H 21752 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 173 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: {'NAD': 1} Classifications: {'RNA': 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: {'NAD': 1} Classifications: {'RNA': 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: {'NAD': 1} Classifications: {'RNA': 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: {'NAD': 1} Classifications: {'RNA': 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: {'NAD': 1} Classifications: {'RNA': 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: {'NAD': 1} Classifications: {'RNA': 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: {'NAD': 1} Classifications: {'RNA': 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: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 7.15, per 1000 atoms: 0.16 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: 3.65 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 23 sheets defined 42.6% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 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: 9.91 Time building geometry restraints manager: 5.02 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: 69423 2.86 - 5.73: 8188 5.73 - 8.59: 1988 8.59 - 11.45: 42 11.45 - 14.32: 23 Bond angle restraints: 79664 Sorted by residual: angle pdb=" CA ASP B 239 " pdb=" CB ASP B 239 " pdb=" CG ASP B 239 " ideal model delta sigma weight residual 112.60 119.63 -7.03 1.00e+00 1.00e+00 4.95e+01 angle pdb=" OE1 GLN G 465 " pdb=" CD GLN G 465 " pdb=" NE2 GLN G 465 " ideal model delta sigma weight residual 122.60 116.23 6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" CA ASN H 230 " pdb=" CB ASN H 230 " pdb=" CG ASN H 230 " ideal model delta sigma weight residual 112.60 118.59 -5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" CA ASN E 230 " pdb=" CB ASN E 230 " pdb=" CG ASN E 230 " ideal model delta sigma weight residual 112.60 118.52 -5.92 1.00e+00 1.00e+00 3.51e+01 angle pdb=" CA ASN F 230 " pdb=" CB ASN F 230 " pdb=" CG ASN F 230 " ideal model delta sigma weight residual 112.60 118.42 -5.82 1.00e+00 1.00e+00 3.38e+01 ... (remaining 79659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.70: 19300 26.70 - 53.41: 1094 53.41 - 80.11: 458 80.11 - 106.82: 15 106.82 - 133.52: 5 Dihedral angle restraints: 20872 sinusoidal: 11800 harmonic: 9072 Sorted by residual: dihedral pdb=" C5' IMP E 601 " pdb=" O5' IMP E 601 " pdb=" P IMP E 601 " pdb=" O2P IMP E 601 " ideal model delta sinusoidal sigma weight residual 191.93 58.41 133.52 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C5' IMP G 601 " pdb=" O5' IMP G 601 " pdb=" P IMP G 601 " pdb=" O2P IMP G 601 " ideal model delta sinusoidal sigma weight residual 191.93 58.56 133.37 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C5' IMP H 601 " pdb=" O5' IMP H 601 " pdb=" P IMP H 601 " pdb=" O2P IMP H 601 " ideal model delta sinusoidal sigma weight residual 191.93 58.59 133.35 1 2.00e+01 2.50e-03 4.05e+01 ... (remaining 20869 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 36.960 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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= 0.681 Angle : 1.771 13.832 30248 Z= 1.141 Chirality : 0.087 0.418 3512 Planarity : 0.013 0.284 3816 Dihedral : 15.121 133.519 8496 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 aren 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 covalent geometry : bond 0.01146 (22328) covalent geometry : angle 1.77144 (30248) hydrogen bonds : bond 0.15922 ( 748) hydrogen bonds : angle 6.61355 ( 2133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 659 time to evaluate : 0.830 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: 0.6369 (m-30) REVERT: A 82 MET cc_start: 0.8216 (mmm) cc_final: 0.7870 (mmm) REVERT: A 298 GLN cc_start: 0.7550 (mm110) cc_final: 0.7283 (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: 0.8095 (mtp) REVERT: B 492 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8368 (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: 0.7922 (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: 0.8642 (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: 0.7297 (mm-40) REVERT: D 319 ASP cc_start: 0.7804 (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: 0.6367 (mt-10) REVERT: E 34 ASP cc_start: 0.8825 (t0) cc_final: 0.8623 (t0) REVERT: E 298 GLN cc_start: 0.7777 (mm110) cc_final: 0.7561 (mm110) REVERT: E 319 ASP cc_start: 0.7744 (m-30) cc_final: 0.7522 (m-30) REVERT: E 482 MET cc_start: 0.8553 (mtp) cc_final: 0.8331 (mtp) REVERT: E 492 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8625 (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: 0.7410 (mm-40) REVERT: F 319 ASP cc_start: 0.7815 (m-30) cc_final: 0.7455 (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: 0.6389 (mt-10) 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: 0.7445 (m-30) REVERT: G 482 MET cc_start: 0.8589 (mtp) cc_final: 0.8377 (mtp) REVERT: H 15 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6614 (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: 0.8367 (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: 0.3586 time to fit residues: 361.8889 Evaluate side-chains 554 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 534 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 465 GLN Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 465 GLN Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 465 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN B 230 ASN 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 230 ASN E 465 GLN F 230 ASN F 465 GLN F 498 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 = 0.3664 r_free = 0.3664 target = 0.160937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.131806 restraints weight = 74543.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.136770 restraints weight = 36974.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.140036 restraints weight = 24141.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.142146 restraints weight = 18435.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.143493 restraints weight = 15472.715| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22328 Z= 0.162 Angle : 0.633 7.285 30248 Z= 0.337 Chirality : 0.043 0.175 3512 Planarity : 0.004 0.042 3816 Dihedral : 9.822 102.821 3592 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.23 % Allowed : 10.79 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.16), residues: 2808 helix: -0.23 (0.16), residues: 1120 sheet: -2.24 (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 A 341 TYR 0.016 0.002 TYR A 348 PHE 0.013 0.002 PHE C 490 HIS 0.008 0.002 HIS H 466 Details of bonding type rmsd covalent geometry : bond 0.00361 (22328) covalent geometry : angle 0.63251 (30248) hydrogen bonds : bond 0.03680 ( 748) hydrogen bonds : angle 4.88786 ( 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 568 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 540 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6803 (m-30) cc_final: 0.6551 (m-30) REVERT: A 265 GLN cc_start: 0.8040 (mt0) cc_final: 0.7811 (mt0) REVERT: B 28 ASP cc_start: 0.6647 (m-30) cc_final: 0.6152 (m-30) REVERT: B 47 ASP cc_start: 0.8413 (p0) cc_final: 0.8151 (p0) REVERT: B 265 GLN cc_start: 0.8048 (mt0) cc_final: 0.7809 (mt0) REVERT: B 298 GLN cc_start: 0.7119 (mm110) cc_final: 0.6898 (mm-40) REVERT: C 15 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6416 (mt-10) REVERT: C 82 MET cc_start: 0.7953 (mmm) cc_final: 0.7649 (mmm) REVERT: C 265 GLN cc_start: 0.8047 (mt0) cc_final: 0.7837 (mt0) REVERT: C 482 MET cc_start: 0.8340 (mtp) cc_final: 0.8136 (mtp) REVERT: D 16 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: D 319 ASP cc_start: 0.7992 (m-30) cc_final: 0.7625 (m-30) REVERT: D 491 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7058 (mm-30) REVERT: E 15 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6561 (mt-10) REVERT: E 28 ASP cc_start: 0.7292 (m-30) cc_final: 0.6884 (m-30) REVERT: E 47 ASP cc_start: 0.8527 (p0) cc_final: 0.8223 (p0) REVERT: E 265 GLN cc_start: 0.8059 (mt0) cc_final: 0.7826 (mt0) REVERT: E 482 MET cc_start: 0.8452 (mtp) cc_final: 0.8236 (mtp) REVERT: F 265 GLN cc_start: 0.7995 (mt0) cc_final: 0.7759 (mt0) REVERT: F 482 MET cc_start: 0.8479 (mtp) cc_final: 0.8248 (mtp) REVERT: G 15 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6511 (mt-10) REVERT: G 319 ASP cc_start: 0.7917 (m-30) cc_final: 0.7359 (m-30) REVERT: H 15 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6561 (mt-10) REVERT: H 265 GLN cc_start: 0.7985 (mt0) cc_final: 0.7760 (mt0) REVERT: H 319 ASP cc_start: 0.8090 (m-30) cc_final: 0.7504 (m-30) outliers start: 28 outliers final: 20 residues processed: 554 average time/residue: 0.3405 time to fit residues: 283.9686 Evaluate side-chains 526 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 504 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 242 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 465 GLN G 466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.154661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.124570 restraints weight = 75377.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.129535 restraints weight = 37481.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.132747 restraints weight = 24482.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.134771 restraints weight = 18818.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.136043 restraints weight = 15905.541| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22328 Z= 0.178 Angle : 0.585 8.271 30248 Z= 0.308 Chirality : 0.043 0.177 3512 Planarity : 0.004 0.067 3816 Dihedral : 8.567 73.069 3563 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.97 % Allowed : 13.55 % Favored : 84.47 % 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 aren not related in a simple way. whole: -0.82 (0.16), residues: 2808 helix: 0.01 (0.16), residues: 1120 sheet: -2.21 (0.41), residues: 88 loop : -0.81 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 322 TYR 0.012 0.001 TYR F 32 PHE 0.018 0.002 PHE E 490 HIS 0.008 0.002 HIS F 466 Details of bonding type rmsd covalent geometry : bond 0.00422 (22328) covalent geometry : angle 0.58512 (30248) hydrogen bonds : bond 0.03367 ( 748) hydrogen bonds : angle 4.66884 ( 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 566 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 521 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6742 (m-30) cc_final: 0.6432 (m-30) REVERT: A 47 ASP cc_start: 0.8287 (p0) cc_final: 0.7951 (p0) REVERT: A 103 GLU cc_start: 0.7906 (tp30) cc_final: 0.7567 (mm-30) REVERT: B 28 ASP cc_start: 0.6639 (m-30) cc_final: 0.6193 (m-30) REVERT: B 82 MET cc_start: 0.8296 (mmm) cc_final: 0.7873 (mmm) REVERT: B 482 MET cc_start: 0.8238 (mtp) cc_final: 0.8013 (mtp) REVERT: C 15 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6434 (mt-10) REVERT: D 352 GLU cc_start: 0.7414 (tp30) cc_final: 0.7135 (pt0) REVERT: D 491 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7209 (mm-30) REVERT: E 15 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6519 (mt-10) REVERT: E 491 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7069 (mm-30) REVERT: F 482 MET cc_start: 0.8266 (mtp) cc_final: 0.7949 (mtp) REVERT: G 15 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6423 (mt-10) REVERT: G 482 MET cc_start: 0.8384 (mtp) cc_final: 0.8131 (mtp) REVERT: H 15 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6506 (mt-10) outliers start: 45 outliers final: 37 residues processed: 533 average time/residue: 0.3848 time to fit residues: 305.8046 Evaluate side-chains 518 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 479 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 B residue 63 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 275 SER 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 18 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 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 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 275 SER 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 271 ILE Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 315 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 275 optimal weight: 0.9990 chunk 105 optimal weight: 0.2980 chunk 232 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 GLN 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 = 0.3616 r_free = 0.3616 target = 0.156225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.125831 restraints weight = 74980.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.130830 restraints weight = 37291.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.134081 restraints weight = 24367.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.136157 restraints weight = 18687.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.137379 restraints weight = 15835.875| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22328 Z= 0.140 Angle : 0.536 7.134 30248 Z= 0.280 Chirality : 0.042 0.172 3512 Planarity : 0.004 0.052 3816 Dihedral : 7.856 67.912 3558 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.02 % Allowed : 15.09 % 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 aren not related in a simple way. whole: -0.72 (0.16), residues: 2808 helix: 0.17 (0.17), residues: 1120 sheet: -2.04 (0.42), residues: 88 loop : -0.82 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 493 TYR 0.009 0.001 TYR G 289 PHE 0.018 0.001 PHE D 99 HIS 0.008 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00334 (22328) covalent geometry : angle 0.53605 (30248) hydrogen bonds : bond 0.02834 ( 748) hydrogen bonds : angle 4.45782 ( 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 523 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 477 time to evaluate : 1.242 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: 0.6661 (m-30) cc_final: 0.6384 (m-30) REVERT: A 78 MET cc_start: 0.8308 (tpp) cc_final: 0.7856 (tpt) REVERT: A 491 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: B 82 MET cc_start: 0.8248 (mmm) cc_final: 0.7850 (mmm) REVERT: B 482 MET cc_start: 0.8134 (mtp) cc_final: 0.7872 (mtp) REVERT: B 491 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7001 (mm-30) REVERT: C 15 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6342 (mt-10) REVERT: C 482 MET cc_start: 0.8331 (mtp) cc_final: 0.8073 (mtp) REVERT: C 491 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7077 (mm-30) REVERT: D 491 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7141 (mm-30) REVERT: E 15 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6425 (mt-10) REVERT: E 482 MET cc_start: 0.8275 (mtp) cc_final: 0.8014 (mtp) REVERT: E 491 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7035 (mm-30) REVERT: F 482 MET cc_start: 0.8208 (mtp) cc_final: 0.7902 (mtp) REVERT: F 491 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6997 (mm-30) REVERT: G 15 GLU cc_start: 0.6610 (mt-10) cc_final: 0.6316 (mt-10) REVERT: G 482 MET cc_start: 0.8200 (mtp) cc_final: 0.7912 (mtp) REVERT: G 491 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7014 (mm-30) REVERT: H 15 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6461 (mt-10) REVERT: H 34 ASP cc_start: 0.8797 (t0) cc_final: 0.8409 (t0) REVERT: H 491 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7074 (mm-30) outliers start: 46 outliers final: 36 residues processed: 493 average time/residue: 0.4046 time to fit residues: 303.7365 Evaluate side-chains 504 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 460 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 70 MET 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 315 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 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 466 HIS Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 158 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 ASN ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN G 466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.152666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.121911 restraints weight = 75503.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.126758 restraints weight = 38446.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.129898 restraints weight = 25605.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.131886 restraints weight = 19961.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.133188 restraints weight = 17025.976| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 22328 Z= 0.236 Angle : 0.585 6.276 30248 Z= 0.309 Chirality : 0.044 0.181 3512 Planarity : 0.004 0.060 3816 Dihedral : 8.035 70.034 3554 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.42 % Allowed : 15.00 % Favored : 81.58 % 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 aren not related in a simple way. whole: -0.97 (0.16), residues: 2808 helix: -0.05 (0.16), residues: 1128 sheet: -2.01 (0.45), residues: 88 loop : -0.97 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 493 TYR 0.011 0.002 TYR G 32 PHE 0.017 0.002 PHE E 490 HIS 0.008 0.002 HIS H 466 Details of bonding type rmsd covalent geometry : bond 0.00557 (22328) covalent geometry : angle 0.58522 (30248) hydrogen bonds : bond 0.03398 ( 748) hydrogen bonds : angle 4.62027 ( 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 550 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 472 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6837 (m-30) cc_final: 0.6531 (m-30) REVERT: A 78 MET cc_start: 0.8246 (tpp) cc_final: 0.7780 (tpt) REVERT: A 103 GLU cc_start: 0.7913 (tp30) cc_final: 0.7490 (mm-30) REVERT: A 491 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6980 (mm-30) REVERT: B 491 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: C 15 GLU cc_start: 0.6642 (mt-10) cc_final: 0.6411 (mt-10) REVERT: C 453 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7222 (mm) REVERT: C 491 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7159 (mm-30) REVERT: D 491 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7234 (mm-30) REVERT: E 15 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6459 (mt-10) REVERT: E 82 MET cc_start: 0.8177 (mmm) cc_final: 0.7899 (mmm) REVERT: E 491 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7088 (mm-30) REVERT: F 491 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7099 (mm-30) REVERT: G 15 GLU cc_start: 0.6646 (mt-10) cc_final: 0.6339 (mt-10) REVERT: G 491 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7163 (mm-30) REVERT: G 494 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.8087 (p) REVERT: G 495 MET cc_start: 0.6555 (tpt) cc_final: 0.6336 (tpt) REVERT: H 15 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6401 (mt-10) REVERT: H 491 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7096 (mm-30) outliers start: 78 outliers final: 56 residues processed: 502 average time/residue: 0.3943 time to fit residues: 302.4463 Evaluate side-chains 531 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 465 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 63 THR 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 28 ASP 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 70 MET 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 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 271 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 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 43 ASP Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 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 466 HIS Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 192 optimal weight: 1.9990 chunk 275 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 167 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 chunk 266 optimal weight: 0.6980 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN D 334 GLN G 241 GLN G 466 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.153868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.123607 restraints weight = 74966.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.128486 restraints weight = 37367.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.131674 restraints weight = 24565.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.133685 restraints weight = 18920.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.134977 restraints weight = 16040.462| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22328 Z= 0.130 Angle : 0.517 5.684 30248 Z= 0.271 Chirality : 0.042 0.155 3512 Planarity : 0.004 0.045 3816 Dihedral : 7.669 68.023 3554 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.46 % Allowed : 16.89 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.16), residues: 2808 helix: 0.15 (0.17), residues: 1120 sheet: -1.84 (0.46), residues: 88 loop : -0.93 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 493 TYR 0.008 0.001 TYR C 348 PHE 0.008 0.001 PHE E 490 HIS 0.011 0.001 HIS G 466 Details of bonding type rmsd covalent geometry : bond 0.00305 (22328) covalent geometry : angle 0.51719 (30248) hydrogen bonds : bond 0.02754 ( 748) hydrogen bonds : angle 4.36807 ( 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 529 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 473 time to evaluate : 1.192 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: 0.8229 (tpp) cc_final: 0.7854 (tpt) REVERT: B 482 MET cc_start: 0.8263 (mtp) cc_final: 0.8060 (mtp) REVERT: B 491 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7028 (mm-30) REVERT: C 15 GLU cc_start: 0.6550 (mt-10) cc_final: 0.6309 (mt-10) REVERT: C 453 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7119 (mm) REVERT: C 482 MET cc_start: 0.8323 (mtp) cc_final: 0.8101 (mtp) REVERT: C 491 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7092 (mm-30) REVERT: D 491 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7205 (mm-30) REVERT: E 15 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6383 (mt-10) REVERT: E 82 MET cc_start: 0.8044 (mmm) cc_final: 0.7732 (mmm) REVERT: E 482 MET cc_start: 0.8277 (mtp) cc_final: 0.8042 (mtp) REVERT: E 491 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7050 (mm-30) REVERT: F 482 MET cc_start: 0.8288 (mtp) cc_final: 0.8066 (mtp) REVERT: F 491 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: G 15 GLU cc_start: 0.6561 (mt-10) cc_final: 0.6253 (mt-10) REVERT: G 482 MET cc_start: 0.8268 (mtp) cc_final: 0.8047 (mtp) REVERT: G 491 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7044 (mm-30) REVERT: H 15 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6395 (mt-10) REVERT: H 491 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7056 (mm-30) outliers start: 56 outliers final: 39 residues processed: 497 average time/residue: 0.4097 time to fit residues: 310.9370 Evaluate side-chains 509 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 462 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 309 GLN Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 70 MET 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 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 51 LEU 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 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 491 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 154 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 chunk 263 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 232 optimal weight: 0.1980 chunk 208 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 21 GLN H 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.155408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.124758 restraints weight = 74694.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.129733 restraints weight = 37367.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.132971 restraints weight = 24508.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.135009 restraints weight = 18900.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.136408 restraints weight = 15998.911| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22328 Z= 0.135 Angle : 0.513 5.963 30248 Z= 0.268 Chirality : 0.042 0.153 3512 Planarity : 0.003 0.042 3816 Dihedral : 7.394 66.467 3554 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.41 % Allowed : 17.72 % Favored : 79.87 % 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 aren not related in a simple way. whole: -0.75 (0.16), residues: 2808 helix: 0.27 (0.17), residues: 1120 sheet: -1.90 (0.63), residues: 48 loop : -1.00 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 493 TYR 0.008 0.001 TYR A 348 PHE 0.022 0.001 PHE G 99 HIS 0.008 0.001 HIS C 466 Details of bonding type rmsd covalent geometry : bond 0.00320 (22328) covalent geometry : angle 0.51268 (30248) hydrogen bonds : bond 0.02657 ( 748) hydrogen bonds : angle 4.30957 ( 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 509 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 454 time to evaluate : 1.155 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: 0.8188 (tpp) cc_final: 0.7824 (tpt) REVERT: A 99 PHE cc_start: 0.8417 (t80) cc_final: 0.8142 (t80) REVERT: A 491 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6929 (mm-30) REVERT: B 482 MET cc_start: 0.8265 (mtp) cc_final: 0.8059 (mtp) REVERT: B 491 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7038 (mm-30) REVERT: C 15 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6382 (mt-10) REVERT: C 453 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7400 (mm) REVERT: C 482 MET cc_start: 0.8256 (mtp) cc_final: 0.8023 (mtp) REVERT: C 491 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7129 (mm-30) REVERT: D 491 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7171 (mm-30) REVERT: E 15 GLU cc_start: 0.6583 (mt-10) cc_final: 0.6383 (mt-10) REVERT: E 82 MET cc_start: 0.8098 (mmm) cc_final: 0.7732 (mmm) REVERT: E 482 MET cc_start: 0.8236 (mtp) cc_final: 0.7993 (mtp) REVERT: E 491 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6967 (mm-30) REVERT: F 482 MET cc_start: 0.8253 (mtp) cc_final: 0.8031 (mtp) REVERT: F 491 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6969 (mm-30) REVERT: G 15 GLU cc_start: 0.6560 (mt-10) cc_final: 0.6245 (mt-10) REVERT: G 298 GLN cc_start: 0.7147 (mm110) cc_final: 0.6810 (mm-40) REVERT: G 482 MET cc_start: 0.8275 (mtp) cc_final: 0.8044 (mtp) REVERT: G 491 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7000 (mm-30) REVERT: H 15 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6386 (mt-10) REVERT: H 491 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7031 (mm-30) outliers start: 55 outliers final: 44 residues processed: 481 average time/residue: 0.3932 time to fit residues: 289.7604 Evaluate side-chains 505 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 452 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 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 370 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 70 MET 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 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 272 VAL Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 491 GLU 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 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 370 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 114 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 209 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 334 GLN F 334 GLN G 21 GLN H 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.155930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.126137 restraints weight = 76192.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.130995 restraints weight = 38179.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.134157 restraints weight = 25139.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.136185 restraints weight = 19399.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.137445 restraints weight = 16406.461| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22328 Z= 0.139 Angle : 0.512 5.378 30248 Z= 0.268 Chirality : 0.042 0.167 3512 Planarity : 0.003 0.039 3816 Dihedral : 7.271 66.075 3554 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.76 % Allowed : 17.81 % 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 aren not related in a simple way. whole: -0.89 (0.16), residues: 2808 helix: 0.30 (0.17), residues: 1120 sheet: -1.60 (0.34), residues: 144 loop : -1.16 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 259 TYR 0.008 0.001 TYR A 348 PHE 0.016 0.001 PHE G 99 HIS 0.009 0.001 HIS C 466 Details of bonding type rmsd covalent geometry : bond 0.00330 (22328) covalent geometry : angle 0.51222 (30248) hydrogen bonds : bond 0.02638 ( 748) hydrogen bonds : angle 4.29215 ( 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 518 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 455 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8189 (tpp) cc_final: 0.7817 (tpt) REVERT: A 99 PHE cc_start: 0.8376 (t80) cc_final: 0.8097 (t80) REVERT: A 491 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6900 (mm-30) REVERT: B 298 GLN cc_start: 0.7204 (mm110) cc_final: 0.6914 (mm110) REVERT: B 482 MET cc_start: 0.8256 (mtp) cc_final: 0.8036 (mtp) REVERT: B 491 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7069 (mm-30) REVERT: C 15 GLU cc_start: 0.6568 (mt-10) cc_final: 0.6322 (mt-10) REVERT: C 482 MET cc_start: 0.8251 (mtp) cc_final: 0.8000 (mtp) REVERT: C 491 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7110 (mm-30) REVERT: D 491 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7163 (mm-30) REVERT: E 15 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6371 (mt-10) REVERT: E 82 MET cc_start: 0.8103 (mmm) cc_final: 0.7725 (mmm) REVERT: E 482 MET cc_start: 0.8248 (mtp) cc_final: 0.7986 (mtp) REVERT: E 491 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: F 491 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.6955 (mm-30) REVERT: G 15 GLU cc_start: 0.6540 (mt-10) cc_final: 0.6226 (mt-10) REVERT: G 298 GLN cc_start: 0.7159 (mm110) cc_final: 0.6919 (mm-40) REVERT: G 491 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7038 (mm-30) REVERT: H 15 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6372 (mt-10) REVERT: H 298 GLN cc_start: 0.7051 (mm110) cc_final: 0.6735 (mm-40) REVERT: H 491 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7035 (mm-30) outliers start: 63 outliers final: 48 residues processed: 487 average time/residue: 0.3914 time to fit residues: 292.9878 Evaluate side-chains 505 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 449 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 70 MET 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 306 THR Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 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 315 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 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 315 ASP Chi-restraints excluded: chain F residue 362 ILE 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 275 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 275 optimal weight: 0.7980 chunk 242 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 466 HIS ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.156468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.125343 restraints weight = 75921.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.130212 restraints weight = 39111.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.133405 restraints weight = 26251.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.135442 restraints weight = 20519.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.136751 restraints weight = 17551.588| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22328 Z= 0.179 Angle : 0.544 6.628 30248 Z= 0.286 Chirality : 0.043 0.176 3512 Planarity : 0.004 0.039 3816 Dihedral : 7.390 69.515 3554 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.76 % Allowed : 18.07 % Favored : 79.17 % 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 aren not related in a simple way. whole: -1.00 (0.16), residues: 2808 helix: 0.17 (0.17), residues: 1128 sheet: -1.69 (0.33), residues: 144 loop : -1.19 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 TYR 0.012 0.001 TYR A 32 PHE 0.013 0.002 PHE G 99 HIS 0.010 0.001 HIS C 466 Details of bonding type rmsd covalent geometry : bond 0.00423 (22328) covalent geometry : angle 0.54426 (30248) hydrogen bonds : bond 0.02894 ( 748) hydrogen bonds : angle 4.37115 ( 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: 63 poor density : 453 time to evaluate : 1.200 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: 0.8157 (tpp) cc_final: 0.7825 (tpt) REVERT: A 99 PHE cc_start: 0.8376 (t80) cc_final: 0.8088 (t80) REVERT: A 493 ARG cc_start: 0.8508 (mtm180) cc_final: 0.8301 (mtm-85) REVERT: B 298 GLN cc_start: 0.7223 (mm110) cc_final: 0.6924 (mm110) REVERT: B 491 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7040 (mm-30) REVERT: C 15 GLU cc_start: 0.6583 (mt-10) cc_final: 0.6358 (mt-10) REVERT: C 337 MET cc_start: 0.6763 (ttt) cc_final: 0.6513 (ttt) REVERT: C 491 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7081 (mm-30) REVERT: D 491 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7145 (mm-30) REVERT: E 15 GLU cc_start: 0.6629 (mt-10) cc_final: 0.6400 (mt-10) REVERT: E 82 MET cc_start: 0.8081 (mmm) cc_final: 0.7693 (mmm) REVERT: E 491 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7009 (mm-30) REVERT: F 99 PHE cc_start: 0.8425 (t80) cc_final: 0.8194 (t80) REVERT: F 491 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7026 (mm-30) REVERT: G 15 GLU cc_start: 0.6551 (mt-10) cc_final: 0.6268 (mt-10) REVERT: G 298 GLN cc_start: 0.7159 (mm110) cc_final: 0.6915 (mm-40) REVERT: G 309 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8724 (pt0) REVERT: G 491 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7043 (mm-30) REVERT: H 15 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6394 (mt-10) REVERT: H 298 GLN cc_start: 0.7057 (mm110) cc_final: 0.6750 (mm-40) REVERT: H 491 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7096 (mm-30) outliers start: 63 outliers final: 51 residues processed: 484 average time/residue: 0.3853 time to fit residues: 287.6403 Evaluate side-chains 506 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 447 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 309 GLN Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 70 MET 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 306 THR Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 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 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL 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 31 THR 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 306 THR Chi-restraints excluded: chain F residue 315 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 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 370 VAL Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 241 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 274 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 148 optimal weight: 0.1980 chunk 218 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.158231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.127092 restraints weight = 75652.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.132066 restraints weight = 38841.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.135313 restraints weight = 25917.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.137344 restraints weight = 20187.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.138634 restraints weight = 17254.226| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22328 Z= 0.130 Angle : 0.525 6.641 30248 Z= 0.274 Chirality : 0.042 0.212 3512 Planarity : 0.003 0.036 3816 Dihedral : 7.228 68.789 3554 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.63 % Allowed : 18.38 % Favored : 78.99 % 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 aren not related in a simple way. whole: -0.93 (0.16), residues: 2808 helix: 0.25 (0.17), residues: 1120 sheet: -1.70 (0.34), residues: 144 loop : -1.16 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 493 TYR 0.008 0.001 TYR F 348 PHE 0.013 0.001 PHE G 99 HIS 0.013 0.001 HIS G 466 Details of bonding type rmsd covalent geometry : bond 0.00310 (22328) covalent geometry : angle 0.52518 (30248) hydrogen bonds : bond 0.02615 ( 748) hydrogen bonds : angle 4.29289 ( 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 507 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 447 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8153 (tpp) cc_final: 0.7836 (tpt) REVERT: A 99 PHE cc_start: 0.8349 (t80) cc_final: 0.8065 (t80) REVERT: B 491 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7015 (mm-30) REVERT: C 15 GLU cc_start: 0.6515 (mt-10) cc_final: 0.6265 (mt-10) REVERT: C 337 MET cc_start: 0.6597 (ttt) cc_final: 0.6376 (ttt) REVERT: C 491 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: D 491 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7125 (mm-30) REVERT: E 15 GLU cc_start: 0.6541 (mt-10) cc_final: 0.6308 (mt-10) REVERT: E 82 MET cc_start: 0.8082 (mmm) cc_final: 0.7651 (mmm) REVERT: E 482 MET cc_start: 0.8323 (mtp) cc_final: 0.8105 (mtp) REVERT: E 491 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7037 (mm-30) REVERT: F 99 PHE cc_start: 0.8355 (t80) cc_final: 0.8145 (t80) REVERT: F 491 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6964 (mm-30) REVERT: G 15 GLU cc_start: 0.6503 (mt-10) cc_final: 0.6192 (mt-10) REVERT: G 298 GLN cc_start: 0.7126 (mm110) cc_final: 0.6901 (mm-40) REVERT: G 491 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: H 15 GLU cc_start: 0.6758 (mt-10) cc_final: 0.6317 (mt-10) REVERT: H 298 GLN cc_start: 0.7117 (mm110) cc_final: 0.6905 (mm-40) REVERT: H 491 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7080 (mm-30) outliers start: 60 outliers final: 49 residues processed: 474 average time/residue: 0.3879 time to fit residues: 283.0295 Evaluate side-chains 498 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 442 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 309 GLN Chi-restraints excluded: chain A residue 319 ASP 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 309 GLN Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 70 MET 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 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 51 LEU 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 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 306 THR Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 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 309 GLN Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 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: chunk 104 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 198 optimal weight: 0.3980 chunk 150 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 274 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 GLN D 465 GLN ** E 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 = 0.3622 r_free = 0.3622 target = 0.156958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.125453 restraints weight = 76389.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.130449 restraints weight = 38668.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.133705 restraints weight = 25665.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.135823 restraints weight = 19975.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.137118 restraints weight = 17013.736| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 22328 Z= 0.149 Angle : 0.527 5.835 30248 Z= 0.275 Chirality : 0.042 0.177 3512 Planarity : 0.003 0.036 3816 Dihedral : 7.159 69.488 3554 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.94 % Allowed : 18.38 % Favored : 78.68 % 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 aren not related in a simple way. whole: -0.94 (0.16), residues: 2808 helix: 0.26 (0.17), residues: 1120 sheet: -1.67 (0.34), residues: 144 loop : -1.18 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 493 TYR 0.008 0.001 TYR A 348 PHE 0.012 0.001 PHE G 99 HIS 0.014 0.001 HIS H 466 Details of bonding type rmsd covalent geometry : bond 0.00353 (22328) covalent geometry : angle 0.52742 (30248) hydrogen bonds : bond 0.02675 ( 748) hydrogen bonds : angle 4.30822 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7801.89 seconds wall clock time: 133 minutes 57.31 seconds (8037.31 seconds total)