Starting phenix.real_space_refine on Thu Dec 26 08:43:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rgi_24450/12_2024/7rgi_24450_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rgi_24450/12_2024/7rgi_24450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rgi_24450/12_2024/7rgi_24450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rgi_24450/12_2024/7rgi_24450.map" model { file = "/net/cci-nas-00/data/ceres_data/7rgi_24450/12_2024/7rgi_24450_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rgi_24450/12_2024/7rgi_24450_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 21.35, per 1000 atoms: 0.49 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: 12.40 Conformation dependent library (CDL) restraints added in 3.3 seconds 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 23 sheets defined 42.6% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 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: 18.80 Time building geometry restraints manager: 14.07 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: 0.00 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: 1.780 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: 0.790 Extract box with map and model: 1.720 Check model and map are aligned: 0.310 Set scattering table: 0.410 Process input model: 90.100 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.990 ------------------------------------------------------------------------------- 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= 0.749 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.015 0.003 HIS F 92 PHE 0.045 0.008 PHE C 90 TYR 0.131 0.014 TYR F 348 ARG 0.007 0.001 ARG A 341 *********************** 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 : 3.256 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: 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: 0.7867 (mmm) REVERT: A 298 GLN cc_start: 0.7550 (mm110) cc_final: 0.7282 (mm-40) REVERT: A 319 ASP cc_start: 0.7787 (m-30) cc_final: 0.7541 (m-30) REVERT: A 492 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8653 (ttmt) REVERT: B 28 ASP cc_start: 0.6395 (m-30) cc_final: 0.5690 (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: 0.8098 (mtp) REVERT: B 492 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8359 (mtpt) REVERT: C 15 GLU cc_start: 0.6561 (mt-10) cc_final: 0.6242 (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: 0.8341 (mtp) REVERT: C 492 LYS cc_start: 0.8956 (mtpp) cc_final: 0.8636 (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: 0.8633 (t0) REVERT: D 298 GLN cc_start: 0.7601 (mm110) cc_final: 0.7295 (mm-40) REVERT: D 319 ASP cc_start: 0.7804 (m-30) cc_final: 0.7528 (m-30) REVERT: D 492 LYS cc_start: 0.8891 (mtpp) cc_final: 0.8495 (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: 0.8618 (t0) REVERT: E 298 GLN cc_start: 0.7777 (mm110) cc_final: 0.7559 (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: 0.8328 (mtp) REVERT: E 492 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8630 (mtpt) REVERT: F 275 SER cc_start: 0.8876 (p) cc_final: 0.8579 (m) REVERT: F 298 GLN cc_start: 0.7715 (mm110) cc_final: 0.7409 (mm-40) REVERT: F 319 ASP cc_start: 0.7815 (m-30) cc_final: 0.7456 (m-30) REVERT: F 492 LYS cc_start: 0.8876 (mtpp) cc_final: 0.8385 (mtpt) REVERT: G 15 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6391 (mt-10) REVERT: G 238 LYS cc_start: 0.7450 (mtmp) cc_final: 0.7242 (mtmt) REVERT: G 298 GLN cc_start: 0.7619 (mm110) cc_final: 0.7295 (mm-40) REVERT: G 319 ASP cc_start: 0.7744 (m-30) cc_final: 0.7446 (m-30) REVERT: G 482 MET cc_start: 0.8589 (mtp) cc_final: 0.8378 (mtp) REVERT: H 15 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6617 (mt-10) REVERT: H 298 GLN cc_start: 0.7596 (mm110) cc_final: 0.7349 (mm-40) REVERT: H 319 ASP cc_start: 0.7792 (m-30) cc_final: 0.7455 (m-30) REVERT: H 482 MET cc_start: 0.8587 (mtp) cc_final: 0.8370 (mtp) REVERT: H 492 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8497 (ttmt) outliers start: 42 outliers final: 18 residues processed: 678 average time/residue: 0.9116 time to fit residues: 916.1851 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 : 3.561 ------------------------------------------------------------------------------- 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 236 optimal weight: 0.6980 chunk 212 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 254 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 465 GLN B 230 ASN B 465 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 21 GLN G 230 ASN G 465 GLN H 230 ASN H 465 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22328 Z= 0.225 Angle : 0.640 7.298 30248 Z= 0.344 Chirality : 0.043 0.180 3512 Planarity : 0.004 0.062 3816 Dihedral : 9.986 106.815 3592 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.18 % Allowed : 10.70 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2808 helix: -0.25 (0.16), residues: 1120 sheet: -2.26 (0.40), residues: 88 loop : -0.73 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS H 466 PHE 0.013 0.002 PHE A 490 TYR 0.016 0.001 TYR F 348 ARG 0.002 0.000 ARG A 322 *********************** 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 572 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 545 time to evaluate : 3.540 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: A 28 ASP cc_start: 0.6746 (m-30) cc_final: 0.6466 (m-30) REVERT: A 265 GLN cc_start: 0.7976 (mt0) cc_final: 0.7743 (mt0) REVERT: B 28 ASP cc_start: 0.6501 (m-30) cc_final: 0.5983 (m-30) REVERT: B 47 ASP cc_start: 0.8329 (p0) cc_final: 0.8032 (p0) REVERT: B 265 GLN cc_start: 0.7981 (mt0) cc_final: 0.7735 (mt0) REVERT: B 496 SER cc_start: 0.9072 (m) cc_final: 0.8861 (m) REVERT: C 15 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6401 (mt-10) REVERT: C 82 MET cc_start: 0.7981 (mmm) cc_final: 0.7715 (mmm) REVERT: C 492 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8722 (ttmt) REVERT: D 16 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: D 319 ASP cc_start: 0.7828 (m-30) cc_final: 0.7605 (m-30) REVERT: D 491 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7099 (mm-30) REVERT: E 15 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6511 (mt-10) REVERT: E 28 ASP cc_start: 0.7295 (m-30) cc_final: 0.6681 (m-30) REVERT: E 337 MET cc_start: 0.6542 (ttt) cc_final: 0.6304 (ttt) REVERT: E 482 MET cc_start: 0.8595 (mtp) cc_final: 0.8392 (mtp) REVERT: F 265 GLN cc_start: 0.7963 (mt0) cc_final: 0.7717 (mt0) REVERT: G 15 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6474 (mt-10) REVERT: G 319 ASP cc_start: 0.7800 (m-30) cc_final: 0.7412 (m-30) REVERT: H 15 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6544 (mt-10) REVERT: H 319 ASP cc_start: 0.7989 (m-30) cc_final: 0.7562 (m-30) REVERT: H 492 LYS cc_start: 0.8977 (mtpp) cc_final: 0.8576 (mtpt) outliers start: 27 outliers final: 20 residues processed: 556 average time/residue: 0.8389 time to fit residues: 704.7756 Evaluate side-chains 528 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 506 time to evaluate : 3.149 ------------------------------------------------------------------------------- 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 141 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 GLN B 498 GLN F 298 GLN G 265 GLN ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2953 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= 0.365 Angle : 0.626 7.975 30248 Z= 0.332 Chirality : 0.045 0.181 3512 Planarity : 0.004 0.068 3816 Dihedral : 8.867 77.085 3563 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.32 % Allowed : 13.73 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.16), residues: 2808 helix: -0.14 (0.16), residues: 1120 sheet: -2.37 (0.41), residues: 88 loop : -0.90 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 466 PHE 0.021 0.002 PHE E 490 TYR 0.014 0.001 TYR A 32 ARG 0.003 0.000 ARG E 322 *********************** 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 568 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 515 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6791 (m-30) cc_final: 0.6463 (m-30) REVERT: A 34 ASP cc_start: 0.8857 (m-30) cc_final: 0.8656 (m-30) REVERT: B 28 ASP cc_start: 0.6523 (m-30) cc_final: 0.5989 (m-30) REVERT: B 82 MET cc_start: 0.8237 (mmm) cc_final: 0.7969 (mmm) REVERT: B 241 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7725 (mp10) REVERT: B 298 GLN cc_start: 0.7144 (mm110) cc_final: 0.6673 (mm-40) REVERT: B 482 MET cc_start: 0.8485 (mtp) cc_final: 0.8272 (mtp) REVERT: B 498 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7491 (mt0) REVERT: C 15 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6512 (mt-10) REVERT: C 82 MET cc_start: 0.7960 (mmm) cc_final: 0.7585 (mmm) REVERT: D 16 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: D 491 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7309 (mm-30) REVERT: E 15 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6520 (mt-10) REVERT: E 491 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7142 (mm-30) REVERT: G 15 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6387 (mt-10) REVERT: G 82 MET cc_start: 0.8074 (mmm) cc_final: 0.7754 (mmm) REVERT: G 482 MET cc_start: 0.8565 (mtp) cc_final: 0.8338 (mtp) outliers start: 53 outliers final: 44 residues processed: 536 average time/residue: 0.8981 time to fit residues: 733.0331 Evaluate side-chains 525 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 476 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 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 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 370 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 171 optimal weight: 0.5980 chunk 255 optimal weight: 2.9990 chunk 270 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 242 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22328 Z= 0.216 Angle : 0.544 7.303 30248 Z= 0.285 Chirality : 0.042 0.168 3512 Planarity : 0.004 0.054 3816 Dihedral : 8.144 70.013 3561 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.15 % Allowed : 15.31 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.16), residues: 2808 helix: 0.05 (0.17), residues: 1128 sheet: -2.10 (0.42), residues: 88 loop : -0.86 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 466 PHE 0.014 0.001 PHE D 99 TYR 0.009 0.001 TYR B 348 ARG 0.003 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 481 time to evaluate : 3.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6605 (m-30) cc_final: 0.6298 (m-30) REVERT: A 78 MET cc_start: 0.8194 (tpp) cc_final: 0.7761 (tpt) REVERT: A 491 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7103 (mm-30) REVERT: B 28 ASP cc_start: 0.6513 (m-30) cc_final: 0.6077 (m-30) REVERT: B 82 MET cc_start: 0.8167 (mmm) cc_final: 0.7857 (mmm) REVERT: B 482 MET cc_start: 0.8333 (mtp) cc_final: 0.8092 (mtp) REVERT: C 15 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6323 (mt-10) REVERT: C 82 MET cc_start: 0.7800 (mmm) cc_final: 0.7482 (mmm) REVERT: C 99 PHE cc_start: 0.8240 (t80) cc_final: 0.8031 (t80) REVERT: C 491 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7124 (mm-30) REVERT: D 491 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7209 (mm-30) REVERT: E 15 GLU cc_start: 0.6604 (mt-10) cc_final: 0.6392 (mt-10) REVERT: E 82 MET cc_start: 0.8089 (mmm) cc_final: 0.7688 (mmm) REVERT: E 482 MET cc_start: 0.8491 (mtp) cc_final: 0.8266 (mtp) REVERT: E 491 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7111 (mm-30) REVERT: F 491 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7057 (mm-30) REVERT: F 495 MET cc_start: 0.6636 (tpt) cc_final: 0.6431 (tpt) REVERT: G 15 GLU cc_start: 0.6570 (mt-10) cc_final: 0.6282 (mt-10) REVERT: G 82 MET cc_start: 0.8046 (mmm) cc_final: 0.7653 (mmm) REVERT: G 482 MET cc_start: 0.8365 (mtp) cc_final: 0.8100 (mtp) REVERT: G 491 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7146 (mm-30) REVERT: H 15 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6386 (mt-10) REVERT: H 491 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7114 (mm-30) outliers start: 49 outliers final: 40 residues processed: 498 average time/residue: 0.8208 time to fit residues: 626.6453 Evaluate side-chains 504 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 457 time to evaluate : 3.336 ------------------------------------------------------------------------------- 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 393 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain 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 245 LEU 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 393 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 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 18 LEU 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 225 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 230 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 ASN G 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22328 Z= 0.249 Angle : 0.538 6.939 30248 Z= 0.283 Chirality : 0.042 0.169 3512 Planarity : 0.004 0.050 3816 Dihedral : 7.873 83.590 3554 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.41 % Allowed : 16.05 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.16), residues: 2808 helix: 0.08 (0.17), residues: 1128 sheet: -1.99 (0.44), residues: 88 loop : -0.89 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS G 466 PHE 0.012 0.001 PHE A 490 TYR 0.009 0.001 TYR A 32 ARG 0.004 0.000 ARG D 322 *********************** 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 524 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 469 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6662 (m-30) cc_final: 0.6363 (m-30) REVERT: A 78 MET cc_start: 0.8204 (tpp) cc_final: 0.7800 (tpt) REVERT: A 491 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7064 (mm-30) REVERT: B 82 MET cc_start: 0.8080 (mmm) cc_final: 0.7747 (mmm) REVERT: B 482 MET cc_start: 0.8347 (mtp) cc_final: 0.8100 (mtp) REVERT: B 491 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7118 (mm-30) REVERT: C 15 GLU cc_start: 0.6568 (mt-10) cc_final: 0.6339 (mt-10) REVERT: C 453 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7455 (mm) REVERT: C 491 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7139 (mm-30) REVERT: D 491 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7226 (mm-30) REVERT: E 15 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6361 (mt-10) REVERT: E 82 MET cc_start: 0.8128 (mmm) cc_final: 0.7756 (mmm) REVERT: E 482 MET cc_start: 0.8447 (mtp) cc_final: 0.8188 (mtp) REVERT: E 491 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7091 (mm-30) REVERT: F 491 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7035 (mm-30) REVERT: G 15 GLU cc_start: 0.6562 (mt-10) cc_final: 0.6225 (mt-10) REVERT: G 82 MET cc_start: 0.8068 (mmm) cc_final: 0.7694 (mmm) REVERT: G 482 MET cc_start: 0.8377 (mtp) cc_final: 0.8089 (mtp) REVERT: G 491 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7131 (mm-30) REVERT: H 15 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6321 (mt-10) REVERT: H 491 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7093 (mm-30) outliers start: 55 outliers final: 41 residues processed: 493 average time/residue: 0.8117 time to fit residues: 612.9412 Evaluate side-chains 510 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 460 time to evaluate : 3.518 ------------------------------------------------------------------------------- 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 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 239 ASP 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 275 SER Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain 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 466 HIS Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 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 91 optimal weight: 0.0040 chunk 243 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 158 optimal weight: 0.0670 chunk 66 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 overall best weight: 0.5334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN E 21 GLN G 466 HIS H 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22328 Z= 0.163 Angle : 0.501 5.987 30248 Z= 0.262 Chirality : 0.041 0.148 3512 Planarity : 0.003 0.040 3816 Dihedral : 7.481 82.339 3554 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.32 % Allowed : 16.67 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2808 helix: 0.24 (0.17), residues: 1128 sheet: -1.87 (0.45), residues: 88 loop : -0.80 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS G 466 PHE 0.009 0.001 PHE C 99 TYR 0.008 0.001 TYR C 348 ARG 0.003 0.000 ARG D 322 *********************** 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 508 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 455 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8321 (tpp) cc_final: 0.7912 (tpt) REVERT: A 491 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7072 (mm-30) REVERT: B 82 MET cc_start: 0.8078 (mmm) cc_final: 0.7754 (mmm) REVERT: B 298 GLN cc_start: 0.7102 (mm110) cc_final: 0.6833 (mm-40) REVERT: B 482 MET cc_start: 0.8297 (mtp) cc_final: 0.8049 (mtp) REVERT: B 491 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7093 (mm-30) REVERT: C 15 GLU cc_start: 0.6515 (mt-10) cc_final: 0.6240 (mt-10) REVERT: C 453 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7550 (mm) REVERT: C 491 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6984 (mm-30) REVERT: D 491 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7128 (mm-30) REVERT: E 15 GLU cc_start: 0.6525 (mt-10) cc_final: 0.6303 (mt-10) REVERT: E 482 MET cc_start: 0.8421 (mtp) cc_final: 0.8168 (mtp) REVERT: E 491 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7095 (mm-30) REVERT: F 491 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: G 15 GLU cc_start: 0.6573 (mt-10) cc_final: 0.6274 (mt-10) REVERT: G 298 GLN cc_start: 0.7150 (mm110) cc_final: 0.6806 (mm-40) REVERT: G 482 MET cc_start: 0.8337 (mtp) cc_final: 0.8055 (mtp) REVERT: G 491 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7038 (mm-30) REVERT: H 15 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6355 (mt-10) REVERT: H 34 ASP cc_start: 0.8705 (t0) cc_final: 0.8447 (t0) REVERT: H 298 GLN cc_start: 0.7245 (mm110) cc_final: 0.6986 (mm-40) REVERT: H 491 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7121 (mm-30) outliers start: 53 outliers final: 36 residues processed: 486 average time/residue: 0.7990 time to fit residues: 597.6844 Evaluate side-chains 490 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 445 time to evaluate : 3.186 ------------------------------------------------------------------------------- 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 393 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 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 272 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 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 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 315 ASP Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 153 optimal weight: 0.5980 chunk 228 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 269 optimal weight: 0.0970 chunk 168 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN B 498 GLN D 334 GLN E 334 GLN H 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3724 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= 0.225 Angle : 0.513 5.572 30248 Z= 0.269 Chirality : 0.042 0.159 3512 Planarity : 0.004 0.041 3816 Dihedral : 7.372 83.664 3554 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.54 % Allowed : 17.19 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2808 helix: 0.30 (0.17), residues: 1128 sheet: -1.81 (0.47), residues: 88 loop : -0.84 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS G 466 PHE 0.010 0.001 PHE E 490 TYR 0.008 0.001 TYR A 32 ARG 0.002 0.000 ARG D 322 *********************** 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 505 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 447 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8829 (m-30) cc_final: 0.8621 (m-30) REVERT: A 78 MET cc_start: 0.8169 (tpp) cc_final: 0.7767 (tpt) REVERT: A 99 PHE cc_start: 0.8457 (t80) cc_final: 0.8193 (t80) REVERT: A 491 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7047 (mm-30) REVERT: B 82 MET cc_start: 0.8030 (mmm) cc_final: 0.7607 (mmm) REVERT: B 298 GLN cc_start: 0.7127 (mm110) cc_final: 0.6841 (mm-40) REVERT: B 491 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7008 (mm-30) REVERT: C 15 GLU cc_start: 0.6542 (mt-10) cc_final: 0.6295 (mt-10) REVERT: C 453 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7432 (mm) REVERT: C 491 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6993 (mm-30) REVERT: D 491 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7211 (mm-30) REVERT: E 15 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6424 (mt-10) REVERT: E 482 MET cc_start: 0.8344 (mtp) cc_final: 0.8063 (mtp) REVERT: E 491 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7034 (mm-30) REVERT: F 491 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: G 15 GLU cc_start: 0.6553 (mt-10) cc_final: 0.6209 (mt-10) REVERT: G 82 MET cc_start: 0.7903 (mmm) cc_final: 0.7650 (mmm) REVERT: G 298 GLN cc_start: 0.7161 (mm110) cc_final: 0.6797 (mm-40) REVERT: G 491 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7119 (mm-30) REVERT: H 15 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6356 (mt-10) REVERT: H 298 GLN cc_start: 0.7202 (mm110) cc_final: 0.6963 (mm-40) REVERT: H 491 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7071 (mm-30) outliers start: 58 outliers final: 45 residues processed: 476 average time/residue: 0.8126 time to fit residues: 596.2586 Evaluate side-chains 495 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 441 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 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 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 104 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 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 166 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 334 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22328 Z= 0.200 Angle : 0.506 5.414 30248 Z= 0.265 Chirality : 0.042 0.179 3512 Planarity : 0.003 0.037 3816 Dihedral : 7.212 84.878 3554 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.50 % Allowed : 17.89 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2808 helix: 0.34 (0.17), residues: 1128 sheet: -1.84 (0.47), residues: 88 loop : -0.82 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 466 PHE 0.008 0.001 PHE E 490 TYR 0.008 0.001 TYR C 348 ARG 0.003 0.000 ARG D 322 *********************** 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 506 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 449 time to evaluate : 3.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8788 (m-30) cc_final: 0.8569 (m-30) REVERT: A 99 PHE cc_start: 0.8410 (t80) cc_final: 0.8091 (t80) REVERT: A 298 GLN cc_start: 0.7169 (mm110) cc_final: 0.6952 (mm-40) REVERT: A 491 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6956 (mm-30) REVERT: B 82 MET cc_start: 0.8007 (mmm) cc_final: 0.7600 (mmm) REVERT: B 298 GLN cc_start: 0.7158 (mm110) cc_final: 0.6876 (mm-40) REVERT: B 491 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7052 (mm-30) REVERT: C 15 GLU cc_start: 0.6563 (mt-10) cc_final: 0.6317 (mt-10) REVERT: C 453 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7427 (mm) REVERT: C 491 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6972 (mm-30) REVERT: D 491 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7091 (mm-30) REVERT: E 15 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6344 (mt-10) REVERT: E 82 MET cc_start: 0.7957 (mmm) cc_final: 0.7653 (mmm) REVERT: E 482 MET cc_start: 0.8325 (mtp) cc_final: 0.8032 (mtp) REVERT: E 491 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7020 (mm-30) REVERT: F 491 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7024 (mm-30) REVERT: G 15 GLU cc_start: 0.6496 (mt-10) cc_final: 0.6182 (mt-10) REVERT: G 298 GLN cc_start: 0.7067 (mm110) cc_final: 0.6730 (mm-40) REVERT: G 491 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7083 (mm-30) REVERT: H 15 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6321 (mt-10) REVERT: H 298 GLN cc_start: 0.7163 (mm110) cc_final: 0.6922 (mm-40) REVERT: H 491 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7110 (mm-30) outliers start: 57 outliers final: 44 residues processed: 477 average time/residue: 0.8127 time to fit residues: 598.0565 Evaluate side-chains 493 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 440 time to evaluate : 3.349 ------------------------------------------------------------------------------- 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 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 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 70 MET Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 0.8980 chunk 258 optimal weight: 0.1980 chunk 235 optimal weight: 0.9980 chunk 251 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 237 optimal weight: 0.9980 chunk 250 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 466 HIS H 241 GLN ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22328 Z= 0.211 Angle : 0.511 6.567 30248 Z= 0.267 Chirality : 0.042 0.169 3512 Planarity : 0.003 0.036 3816 Dihedral : 7.106 85.569 3554 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.59 % Allowed : 18.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2808 helix: 0.35 (0.17), residues: 1128 sheet: -1.85 (0.48), residues: 88 loop : -0.83 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 466 PHE 0.009 0.001 PHE E 490 TYR 0.008 0.001 TYR A 348 ARG 0.003 0.000 ARG D 322 *********************** 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 503 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 444 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8785 (m-30) cc_final: 0.8577 (m-30) REVERT: A 99 PHE cc_start: 0.8337 (t80) cc_final: 0.8073 (t80) REVERT: B 298 GLN cc_start: 0.7135 (mm110) cc_final: 0.6935 (mm-40) REVERT: B 491 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: C 15 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6264 (mt-10) REVERT: C 453 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7392 (mm) REVERT: C 491 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7011 (mm-30) REVERT: D 491 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7150 (mm-30) REVERT: E 15 GLU cc_start: 0.6504 (mt-10) cc_final: 0.6282 (mt-10) REVERT: E 82 MET cc_start: 0.8015 (mmm) cc_final: 0.7719 (mmm) REVERT: E 491 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: F 491 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7066 (mm-30) REVERT: G 15 GLU cc_start: 0.6477 (mt-10) cc_final: 0.6162 (mt-10) REVERT: G 82 MET cc_start: 0.7981 (mmm) cc_final: 0.7673 (mmm) REVERT: G 298 GLN cc_start: 0.7164 (mm110) cc_final: 0.6917 (mm-40) REVERT: G 491 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7083 (mm-30) REVERT: H 15 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6312 (mt-10) REVERT: H 298 GLN cc_start: 0.7144 (mm110) cc_final: 0.6915 (mm-40) REVERT: H 491 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7087 (mm-30) outliers start: 59 outliers final: 48 residues processed: 472 average time/residue: 0.8345 time to fit residues: 612.0094 Evaluate side-chains 492 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 436 time to evaluate : 3.368 ------------------------------------------------------------------------------- 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 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 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 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 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 165 optimal weight: 0.9990 chunk 265 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 278 optimal weight: 0.9980 chunk 256 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 466 HIS H 465 GLN ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22328 Z= 0.229 Angle : 0.527 6.723 30248 Z= 0.275 Chirality : 0.042 0.179 3512 Planarity : 0.004 0.036 3816 Dihedral : 7.089 85.778 3554 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.46 % Allowed : 18.60 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2808 helix: 0.31 (0.17), residues: 1128 sheet: -1.92 (0.47), residues: 88 loop : -0.81 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.027 0.001 HIS G 466 PHE 0.010 0.001 PHE E 490 TYR 0.008 0.001 TYR A 348 ARG 0.003 0.000 ARG D 322 ********************** 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 497 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 441 time to evaluate : 3.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8787 (m-30) cc_final: 0.8584 (m-30) REVERT: A 78 MET cc_start: 0.8259 (tpp) cc_final: 0.7850 (tpt) REVERT: A 99 PHE cc_start: 0.8346 (t80) cc_final: 0.8084 (t80) REVERT: B 491 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7054 (mm-30) REVERT: C 15 GLU cc_start: 0.6498 (mt-10) cc_final: 0.6248 (mt-10) REVERT: C 453 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7456 (mm) REVERT: C 491 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7122 (mm-30) REVERT: D 491 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7160 (mm-30) REVERT: E 15 GLU cc_start: 0.6491 (mt-10) cc_final: 0.6265 (mt-10) REVERT: E 82 MET cc_start: 0.8009 (mmm) cc_final: 0.7713 (mmm) REVERT: E 482 MET cc_start: 0.8489 (mtp) cc_final: 0.8289 (mtp) REVERT: E 491 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7030 (mm-30) REVERT: F 99 PHE cc_start: 0.8396 (t80) cc_final: 0.8188 (t80) REVERT: F 491 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6997 (mm-30) REVERT: G 15 GLU cc_start: 0.6467 (mt-10) cc_final: 0.6147 (mt-10) REVERT: G 82 MET cc_start: 0.7980 (mmm) cc_final: 0.7651 (mmm) REVERT: G 298 GLN cc_start: 0.7158 (mm110) cc_final: 0.6918 (mm-40) REVERT: G 491 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7086 (mm-30) REVERT: H 15 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6327 (mt-10) REVERT: H 298 GLN cc_start: 0.7144 (mm110) cc_final: 0.6902 (mm-40) REVERT: H 491 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7058 (mm-30) outliers start: 56 outliers final: 46 residues processed: 467 average time/residue: 0.8015 time to fit residues: 575.1683 Evaluate side-chains 490 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 436 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 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 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 222 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.156838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.125379 restraints weight = 75630.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.130395 restraints weight = 38442.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.133633 restraints weight = 25525.747| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4007 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= 0.205 Angle : 0.514 5.437 30248 Z= 0.268 Chirality : 0.042 0.175 3512 Planarity : 0.003 0.035 3816 Dihedral : 6.927 87.025 3554 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.50 % Allowed : 18.77 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2808 helix: 0.34 (0.17), residues: 1128 sheet: -1.66 (0.68), residues: 48 loop : -0.89 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS G 466 PHE 0.009 0.001 PHE G 490 TYR 0.008 0.001 TYR A 348 ARG 0.003 0.000 ARG D 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11147.73 seconds wall clock time: 201 minutes 20.44 seconds (12080.44 seconds total)