Starting phenix.real_space_refine on Wed May 6 17:12:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xl8_38441/05_2026/8xl8_38441.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xl8_38441/05_2026/8xl8_38441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xl8_38441/05_2026/8xl8_38441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xl8_38441/05_2026/8xl8_38441.map" model { file = "/net/cci-nas-00/data/ceres_data/8xl8_38441/05_2026/8xl8_38441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xl8_38441/05_2026/8xl8_38441.cif" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.123 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 246 5.16 5 C 27609 2.51 5 N 7593 2.21 5 O 8250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43716 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1615 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain breaks: 1 Chain: "B" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4153 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "C" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1615 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain breaks: 1 Chain: "D" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4153 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "E" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1615 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain breaks: 1 Chain: "F" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4153 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "G" Number of atoms: 4517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4517 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 26, 'TRANS': 557} Chain breaks: 2 Chain: "H" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4153 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "I" Number of atoms: 4517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4517 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 26, 'TRANS': 557} Chain breaks: 2 Chain: "J" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4153 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "K" Number of atoms: 4517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4517 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 26, 'TRANS': 557} Chain breaks: 2 Chain: "L" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4153 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'1VU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'1VU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'1VU': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'1VU': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'1VU': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'1VU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.28, per 1000 atoms: 0.21 Number of scatterers: 43716 At special positions: 0 Unit cell: (152.977, 158.363, 189.605, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 246 16.00 P 18 15.00 O 8250 8.00 N 7593 7.00 C 27609 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 2.2 seconds 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10272 Finding SS restraints... Secondary structure from input PDB file: 213 helices and 63 sheets defined 40.8% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 504 through 529 removed outlier: 3.770A pdb=" N GLN A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'B' and resid 39 through 66 removed outlier: 4.065A pdb=" N LEU B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 77 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 114 through 117 Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 146 through 164 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 192 through 203 Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 243 through 251 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'B' and resid 331 through 339 removed outlier: 4.045A pdb=" N ARG B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 removed outlier: 3.588A pdb=" N ARG B 343 " --> pdb=" O ASP B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 340 through 343' Processing helix chain 'B' and resid 377 through 394 Processing helix chain 'B' and resid 410 through 417 Processing helix chain 'B' and resid 417 through 431 removed outlier: 3.817A pdb=" N ASP B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'B' and resid 454 through 458 removed outlier: 3.627A pdb=" N TYR B 457 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 458 " --> pdb=" O ARG B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 454 through 458' Processing helix chain 'B' and resid 474 through 494 Processing helix chain 'B' and resid 498 through 516 Proline residue: B 508 - end of helix Processing helix chain 'B' and resid 518 through 525 removed outlier: 4.002A pdb=" N ARG B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 549 Processing helix chain 'C' and resid 504 through 529 removed outlier: 3.771A pdb=" N GLN C 529 " --> pdb=" O THR C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 Processing helix chain 'D' and resid 39 through 66 removed outlier: 4.066A pdb=" N LEU D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY D 66 " --> pdb=" O HIS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 77 Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 114 through 117 Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 146 through 164 Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 192 through 203 Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 262 through 269 Processing helix chain 'D' and resid 279 through 293 Processing helix chain 'D' and resid 314 through 322 Processing helix chain 'D' and resid 331 through 339 removed outlier: 4.045A pdb=" N ARG D 337 " --> pdb=" O GLU D 333 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 339 " --> pdb=" O ILE D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 343 removed outlier: 3.588A pdb=" N ARG D 343 " --> pdb=" O ASP D 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 340 through 343' Processing helix chain 'D' and resid 377 through 394 Processing helix chain 'D' and resid 410 through 417 Processing helix chain 'D' and resid 417 through 431 removed outlier: 3.817A pdb=" N ASP D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 452 Processing helix chain 'D' and resid 454 through 458 removed outlier: 3.628A pdb=" N TYR D 457 " --> pdb=" O GLY D 454 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 458 " --> pdb=" O ARG D 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 454 through 458' Processing helix chain 'D' and resid 474 through 494 Processing helix chain 'D' and resid 498 through 516 Proline residue: D 508 - end of helix Processing helix chain 'D' and resid 518 through 525 removed outlier: 4.005A pdb=" N ARG D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 549 Processing helix chain 'E' and resid 504 through 529 removed outlier: 3.771A pdb=" N GLN E 529 " --> pdb=" O THR E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 638 Processing helix chain 'F' and resid 39 through 66 removed outlier: 4.066A pdb=" N LEU F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY F 66 " --> pdb=" O HIS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 77 Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 114 through 117 Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 146 through 164 Processing helix chain 'F' and resid 180 through 185 Processing helix chain 'F' and resid 192 through 203 Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 243 through 251 Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 262 through 269 Processing helix chain 'F' and resid 279 through 293 Processing helix chain 'F' and resid 314 through 322 Processing helix chain 'F' and resid 331 through 339 removed outlier: 4.046A pdb=" N ARG F 337 " --> pdb=" O GLU F 333 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL F 339 " --> pdb=" O ILE F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 343 removed outlier: 3.589A pdb=" N ARG F 343 " --> pdb=" O ASP F 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 340 through 343' Processing helix chain 'F' and resid 377 through 394 Processing helix chain 'F' and resid 410 through 417 Processing helix chain 'F' and resid 417 through 431 removed outlier: 3.817A pdb=" N ASP F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 452 Processing helix chain 'F' and resid 454 through 458 removed outlier: 3.627A pdb=" N TYR F 457 " --> pdb=" O GLY F 454 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER F 458 " --> pdb=" O ARG F 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 454 through 458' Processing helix chain 'F' and resid 474 through 494 Processing helix chain 'F' and resid 498 through 516 Proline residue: F 508 - end of helix Processing helix chain 'F' and resid 518 through 525 removed outlier: 4.004A pdb=" N ARG F 525 " --> pdb=" O TYR F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 549 Processing helix chain 'G' and resid 57 through 72 removed outlier: 3.753A pdb=" N ALA G 61 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 92 removed outlier: 4.043A pdb=" N ASP G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 106 Processing helix chain 'G' and resid 109 through 120 removed outlier: 3.948A pdb=" N ILE G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 146 Processing helix chain 'G' and resid 153 through 159 removed outlier: 4.082A pdb=" N ASP G 159 " --> pdb=" O SER G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 172 Processing helix chain 'G' and resid 295 through 313 Processing helix chain 'G' and resid 343 through 352 removed outlier: 4.249A pdb=" N THR G 347 " --> pdb=" O GLU G 343 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET G 349 " --> pdb=" O PRO G 345 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE G 350 " --> pdb=" O VAL G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 364 Processing helix chain 'G' and resid 371 through 375 removed outlier: 3.904A pdb=" N ILE G 375 " --> pdb=" O GLN G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 394 Processing helix chain 'G' and resid 443 through 456 Processing helix chain 'G' and resid 466 through 475 Processing helix chain 'G' and resid 476 through 482 Processing helix chain 'G' and resid 487 through 492 Processing helix chain 'G' and resid 493 through 496 Processing helix chain 'G' and resid 504 through 529 removed outlier: 3.772A pdb=" N GLN G 529 " --> pdb=" O THR G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 638 Processing helix chain 'H' and resid 39 through 66 removed outlier: 4.065A pdb=" N LEU H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY H 66 " --> pdb=" O HIS H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 77 Processing helix chain 'H' and resid 82 through 91 Processing helix chain 'H' and resid 114 through 117 Processing helix chain 'H' and resid 140 through 142 No H-bonds generated for 'chain 'H' and resid 140 through 142' Processing helix chain 'H' and resid 146 through 164 Processing helix chain 'H' and resid 180 through 185 Processing helix chain 'H' and resid 192 through 203 Processing helix chain 'H' and resid 221 through 226 Processing helix chain 'H' and resid 243 through 251 Processing helix chain 'H' and resid 257 through 262 Processing helix chain 'H' and resid 262 through 269 Processing helix chain 'H' and resid 279 through 293 Processing helix chain 'H' and resid 314 through 322 Processing helix chain 'H' and resid 331 through 339 removed outlier: 4.045A pdb=" N ARG H 337 " --> pdb=" O GLU H 333 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL H 339 " --> pdb=" O ILE H 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 343 removed outlier: 3.588A pdb=" N ARG H 343 " --> pdb=" O ASP H 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 340 through 343' Processing helix chain 'H' and resid 377 through 394 Processing helix chain 'H' and resid 410 through 417 Processing helix chain 'H' and resid 417 through 431 removed outlier: 3.817A pdb=" N ASP H 421 " --> pdb=" O GLY H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 452 Processing helix chain 'H' and resid 454 through 458 removed outlier: 3.628A pdb=" N TYR H 457 " --> pdb=" O GLY H 454 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER H 458 " --> pdb=" O ARG H 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 454 through 458' Processing helix chain 'H' and resid 474 through 494 Processing helix chain 'H' and resid 498 through 516 Proline residue: H 508 - end of helix Processing helix chain 'H' and resid 518 through 525 removed outlier: 4.004A pdb=" N ARG H 525 " --> pdb=" O TYR H 521 " (cutoff:3.500A) Processing helix chain 'H' and resid 536 through 549 Processing helix chain 'I' and resid 57 through 72 removed outlier: 3.753A pdb=" N ALA I 61 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 92 removed outlier: 4.043A pdb=" N ASP I 90 " --> pdb=" O SER I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 106 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.947A pdb=" N ILE I 113 " --> pdb=" O SER I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 146 Processing helix chain 'I' and resid 153 through 159 removed outlier: 4.082A pdb=" N ASP I 159 " --> pdb=" O SER I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 172 Processing helix chain 'I' and resid 295 through 313 Processing helix chain 'I' and resid 343 through 352 removed outlier: 4.250A pdb=" N THR I 347 " --> pdb=" O GLU I 343 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE I 350 " --> pdb=" O VAL I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 364 Processing helix chain 'I' and resid 371 through 375 removed outlier: 3.904A pdb=" N ILE I 375 " --> pdb=" O GLN I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 391 through 394 Processing helix chain 'I' and resid 443 through 456 Processing helix chain 'I' and resid 466 through 475 Processing helix chain 'I' and resid 476 through 482 Processing helix chain 'I' and resid 487 through 492 Processing helix chain 'I' and resid 493 through 496 Processing helix chain 'I' and resid 504 through 529 removed outlier: 3.771A pdb=" N GLN I 529 " --> pdb=" O THR I 525 " (cutoff:3.500A) Processing helix chain 'I' and resid 634 through 638 Processing helix chain 'J' and resid 39 through 66 removed outlier: 4.066A pdb=" N LEU J 65 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY J 66 " --> pdb=" O HIS J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 77 Processing helix chain 'J' and resid 82 through 91 Processing helix chain 'J' and resid 114 through 117 Processing helix chain 'J' and resid 140 through 142 No H-bonds generated for 'chain 'J' and resid 140 through 142' Processing helix chain 'J' and resid 146 through 164 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 203 Processing helix chain 'J' and resid 221 through 226 Processing helix chain 'J' and resid 243 through 251 Processing helix chain 'J' and resid 257 through 262 Processing helix chain 'J' and resid 262 through 269 Processing helix chain 'J' and resid 279 through 293 Processing helix chain 'J' and resid 314 through 322 Processing helix chain 'J' and resid 331 through 339 removed outlier: 4.046A pdb=" N ARG J 337 " --> pdb=" O GLU J 333 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL J 339 " --> pdb=" O ILE J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 343 removed outlier: 3.588A pdb=" N ARG J 343 " --> pdb=" O ASP J 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 340 through 343' Processing helix chain 'J' and resid 377 through 394 Processing helix chain 'J' and resid 410 through 417 Processing helix chain 'J' and resid 417 through 431 removed outlier: 3.817A pdb=" N ASP J 421 " --> pdb=" O GLY J 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 447 through 452 Processing helix chain 'J' and resid 454 through 458 removed outlier: 3.627A pdb=" N TYR J 457 " --> pdb=" O GLY J 454 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER J 458 " --> pdb=" O ARG J 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 454 through 458' Processing helix chain 'J' and resid 474 through 494 Processing helix chain 'J' and resid 498 through 516 Proline residue: J 508 - end of helix Processing helix chain 'J' and resid 518 through 525 removed outlier: 4.004A pdb=" N ARG J 525 " --> pdb=" O TYR J 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 549 Processing helix chain 'K' and resid 57 through 72 removed outlier: 3.753A pdb=" N ALA K 61 " --> pdb=" O ARG K 57 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 92 removed outlier: 4.044A pdb=" N ASP K 90 " --> pdb=" O SER K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 106 Processing helix chain 'K' and resid 109 through 120 removed outlier: 3.947A pdb=" N ILE K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 146 Processing helix chain 'K' and resid 153 through 159 removed outlier: 4.081A pdb=" N ASP K 159 " --> pdb=" O SER K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 172 Processing helix chain 'K' and resid 295 through 313 Processing helix chain 'K' and resid 343 through 352 removed outlier: 4.250A pdb=" N THR K 347 " --> pdb=" O GLU K 343 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET K 349 " --> pdb=" O PRO K 345 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE K 350 " --> pdb=" O VAL K 346 " (cutoff:3.500A) Processing helix chain 'K' and resid 354 through 364 Processing helix chain 'K' and resid 371 through 375 removed outlier: 3.904A pdb=" N ILE K 375 " --> pdb=" O GLN K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 391 through 394 Processing helix chain 'K' and resid 443 through 456 Processing helix chain 'K' and resid 466 through 475 Processing helix chain 'K' and resid 476 through 482 Processing helix chain 'K' and resid 487 through 492 Processing helix chain 'K' and resid 493 through 496 Processing helix chain 'K' and resid 504 through 529 removed outlier: 3.771A pdb=" N GLN K 529 " --> pdb=" O THR K 525 " (cutoff:3.500A) Processing helix chain 'K' and resid 634 through 638 Processing helix chain 'L' and resid 39 through 66 removed outlier: 4.066A pdb=" N LEU L 65 " --> pdb=" O GLU L 61 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY L 66 " --> pdb=" O HIS L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 77 Processing helix chain 'L' and resid 82 through 91 Processing helix chain 'L' and resid 114 through 117 Processing helix chain 'L' and resid 140 through 142 No H-bonds generated for 'chain 'L' and resid 140 through 142' Processing helix chain 'L' and resid 146 through 164 Processing helix chain 'L' and resid 180 through 185 Processing helix chain 'L' and resid 192 through 203 Processing helix chain 'L' and resid 221 through 226 Processing helix chain 'L' and resid 243 through 251 Processing helix chain 'L' and resid 257 through 262 Processing helix chain 'L' and resid 262 through 269 Processing helix chain 'L' and resid 279 through 293 Processing helix chain 'L' and resid 314 through 322 Processing helix chain 'L' and resid 331 through 339 removed outlier: 4.045A pdb=" N ARG L 337 " --> pdb=" O GLU L 333 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL L 339 " --> pdb=" O ILE L 335 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 343 removed outlier: 3.589A pdb=" N ARG L 343 " --> pdb=" O ASP L 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 340 through 343' Processing helix chain 'L' and resid 377 through 394 Processing helix chain 'L' and resid 410 through 417 Processing helix chain 'L' and resid 417 through 431 removed outlier: 3.816A pdb=" N ASP L 421 " --> pdb=" O GLY L 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 447 through 452 Processing helix chain 'L' and resid 454 through 458 removed outlier: 3.626A pdb=" N TYR L 457 " --> pdb=" O GLY L 454 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER L 458 " --> pdb=" O ARG L 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 454 through 458' Processing helix chain 'L' and resid 474 through 494 Processing helix chain 'L' and resid 498 through 516 Proline residue: L 508 - end of helix Processing helix chain 'L' and resid 518 through 525 removed outlier: 4.005A pdb=" N ARG L 525 " --> pdb=" O TYR L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 536 through 549 Processing sheet with id=AA1, first strand: chain 'A' and resid 549 through 557 removed outlier: 4.619A pdb=" N TYR A 549 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A 625 " --> pdb=" O SER A 622 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 683 through 686 removed outlier: 4.309A pdb=" N MET A 675 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL A 676 " --> pdb=" O GLU A 658 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 694 through 697 removed outlier: 6.901A pdb=" N GLU A 713 " --> pdb=" O LYS A 695 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.663A pdb=" N THR B 121 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ILE B 168 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N MET B 132 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU B 170 " --> pdb=" O MET B 132 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE B 134 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 210 " --> pdb=" O GLU B 229 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 233 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN B 230 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA B 277 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 232 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AA6, first strand: chain 'B' and resid 215 through 217 removed outlier: 6.662A pdb=" N CYS B 216 " --> pdb=" O PHE B 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 345 through 347 removed outlier: 4.721A pdb=" N THR B 357 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU B 399 " --> pdb=" O PRO B 366 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLY B 368 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU B 401 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B 370 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE B 461 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 443 through 445 removed outlier: 3.509A pdb=" N SER B 471 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 549 through 557 removed outlier: 4.619A pdb=" N TYR C 549 " --> pdb=" O TYR C 568 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 625 " --> pdb=" O SER C 622 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 683 through 686 removed outlier: 4.310A pdb=" N MET C 675 " --> pdb=" O ILE C 686 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL C 676 " --> pdb=" O GLU C 658 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 694 through 697 removed outlier: 6.901A pdb=" N GLU C 713 " --> pdb=" O LYS C 695 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.664A pdb=" N THR D 121 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ILE D 168 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N MET D 132 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU D 170 " --> pdb=" O MET D 132 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE D 134 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA D 210 " --> pdb=" O GLU D 229 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D 233 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN D 230 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA D 277 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE D 232 " --> pdb=" O ALA D 277 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AB5, first strand: chain 'D' and resid 215 through 217 removed outlier: 6.661A pdb=" N CYS D 216 " --> pdb=" O PHE D 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 347 removed outlier: 4.721A pdb=" N THR D 357 " --> pdb=" O PHE D 347 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU D 399 " --> pdb=" O PRO D 366 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY D 368 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU D 401 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL D 370 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE D 461 " --> pdb=" O LYS D 436 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 443 through 445 removed outlier: 3.509A pdb=" N SER D 471 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 549 through 557 removed outlier: 4.618A pdb=" N TYR E 549 " --> pdb=" O TYR E 568 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR E 596 " --> pdb=" O LEU E 611 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY E 625 " --> pdb=" O SER E 622 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 683 through 686 removed outlier: 4.308A pdb=" N MET E 675 " --> pdb=" O ILE E 686 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL E 676 " --> pdb=" O GLU E 658 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 694 through 697 removed outlier: 6.901A pdb=" N GLU E 713 " --> pdb=" O LYS E 695 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 98 through 100 removed outlier: 4.664A pdb=" N THR F 121 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ILE F 168 " --> pdb=" O GLU F 130 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N MET F 132 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU F 170 " --> pdb=" O MET F 132 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE F 134 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA F 210 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL F 233 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN F 230 " --> pdb=" O HIS F 275 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA F 277 " --> pdb=" O ASN F 230 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE F 232 " --> pdb=" O ALA F 277 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 144 through 145 Processing sheet with id=AC4, first strand: chain 'F' and resid 215 through 217 removed outlier: 6.661A pdb=" N CYS F 216 " --> pdb=" O PHE F 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 345 through 347 removed outlier: 4.720A pdb=" N THR F 357 " --> pdb=" O PHE F 347 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU F 399 " --> pdb=" O PRO F 366 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY F 368 " --> pdb=" O LEU F 399 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU F 401 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL F 370 " --> pdb=" O LEU F 401 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE F 461 " --> pdb=" O LYS F 436 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 443 through 445 removed outlier: 3.509A pdb=" N SER F 471 " --> pdb=" O SER F 444 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 148 through 149 removed outlier: 4.024A pdb=" N VAL G 78 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR G 75 " --> pdb=" O GLU G 94 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N TYR G 96 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA G 77 " --> pdb=" O TYR G 96 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY K 625 " --> pdb=" O SER K 622 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR K 549 " --> pdb=" O TYR K 568 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR K 596 " --> pdb=" O LEU K 611 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 268 through 275 removed outlier: 5.477A pdb=" N TYR G 270 " --> pdb=" O PHE G 261 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE G 261 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE G 272 " --> pdb=" O GLN G 259 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLN G 259 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE G 324 " --> pdb=" O PHE G 333 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N PHE G 333 " --> pdb=" O ILE G 324 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 279 through 280 Processing sheet with id=AD1, first strand: chain 'G' and resid 286 through 288 removed outlier: 6.725A pdb=" N HIS G 380 " --> pdb=" O TRP G 440 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP G 440 " --> pdb=" O HIS G 380 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE G 382 " --> pdb=" O VAL G 438 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL G 438 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA G 384 " --> pdb=" O LYS G 436 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS G 436 " --> pdb=" O ALA G 384 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE G 386 " --> pdb=" O ILE G 434 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 389 through 390 removed outlier: 3.670A pdb=" N MET G 396 " --> pdb=" O ASP G 390 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 404 through 406 Processing sheet with id=AD4, first strand: chain 'I' and resid 148 through 149 removed outlier: 4.024A pdb=" N VAL I 78 " --> pdb=" O ILE I 54 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR I 75 " --> pdb=" O GLU I 94 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N TYR I 96 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA I 77 " --> pdb=" O TYR I 96 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY G 625 " --> pdb=" O SER G 622 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR G 549 " --> pdb=" O TYR G 568 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR G 596 " --> pdb=" O LEU G 611 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 683 through 686 removed outlier: 4.308A pdb=" N MET G 675 " --> pdb=" O ILE G 686 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL G 676 " --> pdb=" O GLU G 658 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 694 through 697 removed outlier: 6.901A pdb=" N GLU G 713 " --> pdb=" O LYS G 695 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 98 through 100 removed outlier: 4.664A pdb=" N THR H 121 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ILE H 168 " --> pdb=" O GLU H 130 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N MET H 132 " --> pdb=" O ILE H 168 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU H 170 " --> pdb=" O MET H 132 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE H 134 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA H 210 " --> pdb=" O GLU H 229 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL H 233 " --> pdb=" O VAL H 212 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN H 230 " --> pdb=" O HIS H 275 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ALA H 277 " --> pdb=" O ASN H 230 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE H 232 " --> pdb=" O ALA H 277 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 144 through 145 Processing sheet with id=AD9, first strand: chain 'H' and resid 215 through 217 removed outlier: 6.662A pdb=" N CYS H 216 " --> pdb=" O PHE H 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'H' and resid 345 through 347 removed outlier: 4.721A pdb=" N THR H 357 " --> pdb=" O PHE H 347 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU H 399 " --> pdb=" O PRO H 366 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY H 368 " --> pdb=" O LEU H 399 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU H 401 " --> pdb=" O GLY H 368 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL H 370 " --> pdb=" O LEU H 401 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE H 461 " --> pdb=" O LYS H 436 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 443 through 445 removed outlier: 3.509A pdb=" N SER H 471 " --> pdb=" O SER H 444 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 268 through 275 removed outlier: 5.477A pdb=" N TYR I 270 " --> pdb=" O PHE I 261 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE I 261 " --> pdb=" O TYR I 270 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE I 272 " --> pdb=" O GLN I 259 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN I 259 " --> pdb=" O PHE I 272 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE I 324 " --> pdb=" O PHE I 333 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N PHE I 333 " --> pdb=" O ILE I 324 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 279 through 280 Processing sheet with id=AE5, first strand: chain 'I' and resid 286 through 288 removed outlier: 6.725A pdb=" N HIS I 380 " --> pdb=" O TRP I 440 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TRP I 440 " --> pdb=" O HIS I 380 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE I 382 " --> pdb=" O VAL I 438 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL I 438 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA I 384 " --> pdb=" O LYS I 436 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS I 436 " --> pdb=" O ALA I 384 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE I 386 " --> pdb=" O ILE I 434 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 389 through 390 removed outlier: 3.670A pdb=" N MET I 396 " --> pdb=" O ASP I 390 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 404 through 406 Processing sheet with id=AE8, first strand: chain 'K' and resid 148 through 149 removed outlier: 4.023A pdb=" N VAL K 78 " --> pdb=" O ILE K 54 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR K 75 " --> pdb=" O GLU K 94 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N TYR K 96 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA K 77 " --> pdb=" O TYR K 96 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY I 625 " --> pdb=" O SER I 622 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR I 549 " --> pdb=" O TYR I 568 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR I 596 " --> pdb=" O LEU I 611 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 683 through 686 removed outlier: 4.309A pdb=" N MET I 675 " --> pdb=" O ILE I 686 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL I 676 " --> pdb=" O GLU I 658 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 694 through 697 removed outlier: 6.901A pdb=" N GLU I 713 " --> pdb=" O LYS I 695 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 98 through 100 removed outlier: 4.663A pdb=" N THR J 121 " --> pdb=" O LEU J 100 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ILE J 168 " --> pdb=" O GLU J 130 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N MET J 132 " --> pdb=" O ILE J 168 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU J 170 " --> pdb=" O MET J 132 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE J 134 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA J 210 " --> pdb=" O GLU J 229 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL J 233 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN J 230 " --> pdb=" O HIS J 275 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA J 277 " --> pdb=" O ASN J 230 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE J 232 " --> pdb=" O ALA J 277 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 144 through 145 Processing sheet with id=AF4, first strand: chain 'J' and resid 215 through 217 removed outlier: 6.662A pdb=" N CYS J 216 " --> pdb=" O PHE J 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'J' and resid 345 through 347 removed outlier: 4.721A pdb=" N THR J 357 " --> pdb=" O PHE J 347 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU J 399 " --> pdb=" O PRO J 366 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLY J 368 " --> pdb=" O LEU J 399 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU J 401 " --> pdb=" O GLY J 368 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL J 370 " --> pdb=" O LEU J 401 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE J 461 " --> pdb=" O LYS J 436 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 443 through 445 removed outlier: 3.509A pdb=" N SER J 471 " --> pdb=" O SER J 444 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 268 through 275 removed outlier: 5.476A pdb=" N TYR K 270 " --> pdb=" O PHE K 261 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE K 261 " --> pdb=" O TYR K 270 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE K 272 " --> pdb=" O GLN K 259 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLN K 259 " --> pdb=" O PHE K 272 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE K 324 " --> pdb=" O PHE K 333 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N PHE K 333 " --> pdb=" O ILE K 324 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 279 through 280 Processing sheet with id=AF9, first strand: chain 'K' and resid 286 through 288 removed outlier: 6.727A pdb=" N HIS K 380 " --> pdb=" O TRP K 440 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP K 440 " --> pdb=" O HIS K 380 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE K 382 " --> pdb=" O VAL K 438 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL K 438 " --> pdb=" O PHE K 382 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA K 384 " --> pdb=" O LYS K 436 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS K 436 " --> pdb=" O ALA K 384 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE K 386 " --> pdb=" O ILE K 434 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 389 through 390 removed outlier: 3.670A pdb=" N MET K 396 " --> pdb=" O ASP K 390 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 404 through 406 Processing sheet with id=AG3, first strand: chain 'K' and resid 683 through 686 removed outlier: 4.309A pdb=" N MET K 675 " --> pdb=" O ILE K 686 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL K 676 " --> pdb=" O GLU K 658 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 694 through 697 removed outlier: 6.901A pdb=" N GLU K 713 " --> pdb=" O LYS K 695 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 98 through 100 removed outlier: 4.664A pdb=" N THR L 121 " --> pdb=" O LEU L 100 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ILE L 168 " --> pdb=" O GLU L 130 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N MET L 132 " --> pdb=" O ILE L 168 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU L 170 " --> pdb=" O MET L 132 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE L 134 " --> pdb=" O LEU L 170 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA L 210 " --> pdb=" O GLU L 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL L 233 " --> pdb=" O VAL L 212 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN L 230 " --> pdb=" O HIS L 275 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA L 277 " --> pdb=" O ASN L 230 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE L 232 " --> pdb=" O ALA L 277 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 144 through 145 Processing sheet with id=AG7, first strand: chain 'L' and resid 215 through 217 removed outlier: 6.661A pdb=" N CYS L 216 " --> pdb=" O PHE L 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'L' and resid 345 through 347 removed outlier: 4.721A pdb=" N THR L 357 " --> pdb=" O PHE L 347 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU L 399 " --> pdb=" O PRO L 366 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY L 368 " --> pdb=" O LEU L 399 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU L 401 " --> pdb=" O GLY L 368 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL L 370 " --> pdb=" O LEU L 401 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE L 461 " --> pdb=" O LYS L 436 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 443 through 445 removed outlier: 3.509A pdb=" N SER L 471 " --> pdb=" O SER L 444 " (cutoff:3.500A) 2064 hydrogen bonds defined for protein. 5823 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: 12.80 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 7516 1.31 - 1.44: 11211 1.44 - 1.56: 25406 1.56 - 1.69: 36 1.69 - 1.81: 405 Bond restraints: 44574 Sorted by residual: bond pdb=" O10 1VU L 601 " pdb=" P1 1VU L 601 " ideal model delta sigma weight residual 2.250 1.603 0.647 2.00e-02 2.50e+03 1.05e+03 bond pdb=" O10 1VU F 601 " pdb=" P1 1VU F 601 " ideal model delta sigma weight residual 2.250 1.604 0.646 2.00e-02 2.50e+03 1.04e+03 bond pdb=" O10 1VU J 601 " pdb=" P1 1VU J 601 " ideal model delta sigma weight residual 2.250 1.604 0.646 2.00e-02 2.50e+03 1.04e+03 bond pdb=" O10 1VU D 601 " pdb=" P1 1VU D 601 " ideal model delta sigma weight residual 2.250 1.604 0.646 2.00e-02 2.50e+03 1.04e+03 bond pdb=" O10 1VU B 601 " pdb=" P1 1VU B 601 " ideal model delta sigma weight residual 2.250 1.604 0.646 2.00e-02 2.50e+03 1.04e+03 ... (remaining 44569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.69: 60198 11.69 - 23.39: 45 23.39 - 35.08: 6 35.08 - 46.77: 0 46.77 - 58.46: 6 Bond angle restraints: 60255 Sorted by residual: angle pdb=" O14 1VU H 601 " pdb=" P2 1VU H 601 " pdb=" O15 1VU H 601 " ideal model delta sigma weight residual 53.72 112.18 -58.46 3.00e+00 1.11e-01 3.80e+02 angle pdb=" O14 1VU D 601 " pdb=" P2 1VU D 601 " pdb=" O15 1VU D 601 " ideal model delta sigma weight residual 53.72 112.18 -58.46 3.00e+00 1.11e-01 3.80e+02 angle pdb=" O14 1VU L 601 " pdb=" P2 1VU L 601 " pdb=" O15 1VU L 601 " ideal model delta sigma weight residual 53.72 112.15 -58.43 3.00e+00 1.11e-01 3.79e+02 angle pdb=" O14 1VU B 601 " pdb=" P2 1VU B 601 " pdb=" O15 1VU B 601 " ideal model delta sigma weight residual 53.72 112.15 -58.43 3.00e+00 1.11e-01 3.79e+02 angle pdb=" O14 1VU F 601 " pdb=" P2 1VU F 601 " pdb=" O15 1VU F 601 " ideal model delta sigma weight residual 53.72 112.13 -58.41 3.00e+00 1.11e-01 3.79e+02 ... (remaining 60250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.29: 26400 32.29 - 64.58: 678 64.58 - 96.87: 64 96.87 - 129.16: 6 129.16 - 161.44: 20 Dihedral angle restraints: 27168 sinusoidal: 11082 harmonic: 16086 Sorted by residual: dihedral pdb=" CA PHE B 185 " pdb=" C PHE B 185 " pdb=" N PRO B 186 " pdb=" CA PRO B 186 " ideal model delta harmonic sigma weight residual -180.00 -153.49 -26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA PHE L 185 " pdb=" C PHE L 185 " pdb=" N PRO L 186 " pdb=" CA PRO L 186 " ideal model delta harmonic sigma weight residual 180.00 -153.53 -26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA PHE J 185 " pdb=" C PHE J 185 " pdb=" N PRO J 186 " pdb=" CA PRO J 186 " ideal model delta harmonic sigma weight residual -180.00 -153.54 -26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 27165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 5920 0.101 - 0.203: 678 0.203 - 0.304: 53 0.304 - 0.406: 6 0.406 - 0.507: 6 Chirality restraints: 6663 Sorted by residual: chirality pdb=" CA LEU H 178 " pdb=" N LEU H 178 " pdb=" C LEU H 178 " pdb=" CB LEU H 178 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" CA LEU D 178 " pdb=" N LEU D 178 " pdb=" C LEU D 178 " pdb=" CB LEU D 178 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" CA LEU L 178 " pdb=" N LEU L 178 " pdb=" C LEU L 178 " pdb=" CB LEU L 178 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.41e+00 ... (remaining 6660 not shown) Planarity restraints: 7815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 1VU B 601 " 0.323 2.00e-02 2.50e+03 2.79e-01 9.73e+02 pdb=" C8 1VU B 601 " -0.077 2.00e-02 2.50e+03 pdb=" C9 1VU B 601 " 0.032 2.00e-02 2.50e+03 pdb=" N1 1VU B 601 " -0.485 2.00e-02 2.50e+03 pdb=" O2 1VU B 601 " 0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 1VU F 601 " -0.314 2.00e-02 2.50e+03 2.71e-01 9.20e+02 pdb=" C8 1VU F 601 " 0.075 2.00e-02 2.50e+03 pdb=" C9 1VU F 601 " -0.020 2.00e-02 2.50e+03 pdb=" N1 1VU F 601 " 0.468 2.00e-02 2.50e+03 pdb=" O2 1VU F 601 " -0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 1VU J 601 " -0.293 2.00e-02 2.50e+03 2.52e-01 7.95e+02 pdb=" C8 1VU J 601 " 0.069 2.00e-02 2.50e+03 pdb=" C9 1VU J 601 " 0.002 2.00e-02 2.50e+03 pdb=" N1 1VU J 601 " 0.430 2.00e-02 2.50e+03 pdb=" O2 1VU J 601 " -0.207 2.00e-02 2.50e+03 ... (remaining 7812 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 7891 2.77 - 3.30: 38464 3.30 - 3.83: 71927 3.83 - 4.37: 85902 4.37 - 4.90: 151100 Nonbonded interactions: 355284 Sorted by model distance: nonbonded pdb=" NE2 GLN B 393 " pdb=" O SER F 202 " model vdw 2.232 3.120 nonbonded pdb=" O SER B 202 " pdb=" NE2 GLN D 393 " model vdw 2.233 3.120 nonbonded pdb=" OH TYR G 590 " pdb=" CD LYS G 608 " model vdw 2.244 3.440 nonbonded pdb=" OH TYR K 590 " pdb=" CD LYS K 608 " model vdw 2.245 3.440 nonbonded pdb=" OH TYR I 590 " pdb=" CD LYS I 608 " model vdw 2.245 3.440 ... (remaining 355279 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.060 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 43.280 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.140 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:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 : 0.014 0.647 44580 Z= 0.700 Angle : 1.299 58.465 60255 Z= 0.653 Chirality : 0.068 0.507 6663 Planarity : 0.011 0.279 7815 Dihedral : 15.292 161.444 16896 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.94 % Favored : 94.63 % Rotamer: Outliers : 0.70 % Allowed : 5.19 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.10), residues: 5586 helix: -1.69 (0.10), residues: 2007 sheet: -0.01 (0.15), residues: 1092 loop : -2.11 (0.11), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 525 TYR 0.018 0.002 TYR D 457 PHE 0.024 0.003 PHE L 344 TRP 0.017 0.003 TRP J 276 HIS 0.008 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.01431 (44574) covalent geometry : angle 1.29895 (60255) hydrogen bonds : bond 0.17562 ( 2064) hydrogen bonds : angle 7.27739 ( 5823) Misc. bond : bond 0.11644 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 888 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.8817 (mtt) cc_final: 0.8386 (mtm) REVERT: B 178 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8345 (tp) REVERT: C 682 MET cc_start: 0.4883 (tpp) cc_final: 0.4372 (ptt) REVERT: D 49 MET cc_start: 0.8640 (tpp) cc_final: 0.8327 (tpp) REVERT: D 141 LYS cc_start: 0.8230 (tptt) cc_final: 0.7966 (mmmm) REVERT: D 411 ARG cc_start: 0.7493 (ttt90) cc_final: 0.7177 (ttt180) REVERT: E 576 MET cc_start: 0.7974 (mtt) cc_final: 0.7709 (mtp) REVERT: F 49 MET cc_start: 0.7899 (tpp) cc_final: 0.7477 (tpp) REVERT: G 86 SER cc_start: 0.3949 (t) cc_final: 0.3737 (p) REVERT: G 323 PHE cc_start: 0.3602 (m-80) cc_final: 0.3321 (m-80) REVERT: G 334 MET cc_start: 0.2497 (mtp) cc_final: 0.2151 (mtp) REVERT: G 382 PHE cc_start: 0.5888 (m-80) cc_final: 0.5361 (m-80) REVERT: G 387 TYR cc_start: 0.6033 (m-80) cc_final: 0.5137 (m-80) REVERT: G 406 SER cc_start: 0.6089 (t) cc_final: 0.5828 (m) REVERT: G 444 ARG cc_start: 0.4209 (ttt-90) cc_final: 0.3851 (tpp80) REVERT: G 659 LYS cc_start: 0.4885 (mttt) cc_final: 0.4568 (tptt) REVERT: G 681 LYS cc_start: 0.5486 (mttp) cc_final: 0.5259 (pttm) REVERT: H 49 MET cc_start: 0.8230 (tpp) cc_final: 0.7930 (tpp) REVERT: H 140 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8494 (t) REVERT: H 178 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8514 (mt) REVERT: H 457 TYR cc_start: 0.8697 (m-80) cc_final: 0.8425 (m-80) REVERT: H 511 LYS cc_start: 0.7941 (tttm) cc_final: 0.7534 (tmmt) REVERT: I 70 LYS cc_start: 0.4957 (ttpt) cc_final: 0.4305 (mttp) REVERT: I 160 MET cc_start: 0.1313 (mmm) cc_final: 0.1063 (tpt) REVERT: I 170 MET cc_start: 0.1253 (mtt) cc_final: 0.0976 (tmt) REVERT: I 378 GLN cc_start: 0.3993 (mt0) cc_final: 0.3733 (mm-40) REVERT: I 383 GLU cc_start: 0.6034 (tt0) cc_final: 0.5591 (mt-10) REVERT: I 387 TYR cc_start: 0.6514 (m-80) cc_final: 0.6206 (m-80) REVERT: I 674 LEU cc_start: 0.6650 (mt) cc_final: 0.6277 (mt) REVERT: I 677 MET cc_start: 0.7252 (ttp) cc_final: 0.6780 (ppp) REVERT: K 69 LYS cc_start: 0.4317 (mttm) cc_final: 0.3939 (ttmt) REVERT: K 136 MET cc_start: 0.2304 (ptt) cc_final: 0.1375 (tmt) REVERT: K 449 THR cc_start: 0.5482 (m) cc_final: 0.5049 (t) REVERT: K 469 PHE cc_start: 0.5613 (t80) cc_final: 0.5317 (t80) REVERT: L 222 TYR cc_start: 0.8100 (m-10) cc_final: 0.7441 (m-10) outliers start: 32 outliers final: 1 residues processed: 908 average time/residue: 0.8417 time to fit residues: 913.6533 Evaluate side-chains 497 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 493 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain K residue 70 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 394 optimal weight: 2.9990 chunk 430 optimal weight: 0.9980 chunk 41 optimal weight: 0.0070 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.7980 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A 684 HIS B 48 GLN B 107 GLN B 198 GLN B 324 ASN B 389 GLN C 529 GLN C 531 HIS D 48 GLN D 198 GLN D 386 HIS D 389 GLN E 531 HIS E 684 HIS F 107 GLN F 198 GLN F 236 GLN F 285 HIS G 115 GLN G 255 HIS ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 531 HIS G 533 GLN H 75 HIS H 107 GLN H 198 GLN H 230 ASN H 295 ASN I 265 HIS I 445 GLN I 491 GLN I 492 HIS I 529 GLN I 684 HIS J 45 ASN J 198 GLN J 230 ASN J 236 GLN J 477 GLN K 464 HIS K 531 HIS L 45 ASN L 75 HIS L 107 GLN L 198 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.219620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128153 restraints weight = 49096.794| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.74 r_work: 0.3332 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 44580 Z= 0.143 Angle : 0.649 10.479 60255 Z= 0.333 Chirality : 0.045 0.180 6663 Planarity : 0.005 0.055 7815 Dihedral : 11.886 173.891 6609 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.42 % Allowed : 12.23 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.11), residues: 5586 helix: 0.32 (0.11), residues: 2031 sheet: 0.19 (0.14), residues: 1077 loop : -1.60 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 707 TYR 0.019 0.002 TYR I 619 PHE 0.026 0.002 PHE G 138 TRP 0.013 0.002 TRP L 276 HIS 0.007 0.001 HIS K 493 Details of bonding type rmsd covalent geometry : bond 0.00296 (44574) covalent geometry : angle 0.64930 (60255) hydrogen bonds : bond 0.04380 ( 2064) hydrogen bonds : angle 5.09860 ( 5823) Misc. bond : bond 0.00127 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 537 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 ASP cc_start: 0.8100 (t0) cc_final: 0.7821 (t70) REVERT: B 189 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: B 377 PHE cc_start: 0.7770 (m-10) cc_final: 0.7570 (m-80) REVERT: D 41 LEU cc_start: 0.8201 (tp) cc_final: 0.7961 (tm) REVERT: D 49 MET cc_start: 0.8649 (tpp) cc_final: 0.8348 (tpp) REVERT: D 141 LYS cc_start: 0.8140 (tptt) cc_final: 0.7658 (mmmm) REVERT: D 235 LYS cc_start: 0.7795 (mttt) cc_final: 0.7404 (pptt) REVERT: D 296 TYR cc_start: 0.8054 (t80) cc_final: 0.7579 (t80) REVERT: D 563 MET cc_start: 0.7515 (mmt) cc_final: 0.7038 (mmt) REVERT: E 576 MET cc_start: 0.7214 (mtt) cc_final: 0.6990 (mtt) REVERT: F 47 LYS cc_start: 0.7537 (mppt) cc_final: 0.7308 (mppt) REVERT: F 49 MET cc_start: 0.7611 (tpp) cc_final: 0.6959 (tpp) REVERT: F 76 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7205 (mm) REVERT: F 189 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.6957 (m-30) REVERT: F 471 SER cc_start: 0.7630 (m) cc_final: 0.7286 (t) REVERT: F 476 GLU cc_start: 0.5979 (mt-10) cc_final: 0.5523 (pp20) REVERT: F 513 PHE cc_start: 0.7150 (m-80) cc_final: 0.6859 (m-80) REVERT: G 86 SER cc_start: 0.2341 (t) cc_final: 0.1966 (p) REVERT: G 94 GLU cc_start: 0.4821 (OUTLIER) cc_final: 0.4589 (pt0) REVERT: G 114 ILE cc_start: 0.5389 (mm) cc_final: 0.5136 (tp) REVERT: G 255 HIS cc_start: 0.1696 (OUTLIER) cc_final: 0.1166 (m-70) REVERT: G 287 GLU cc_start: 0.3457 (OUTLIER) cc_final: 0.2192 (tp30) REVERT: G 334 MET cc_start: 0.2158 (mtp) cc_final: 0.1918 (mtp) REVERT: G 336 MET cc_start: 0.4264 (OUTLIER) cc_final: 0.3923 (tmm) REVERT: G 349 MET cc_start: 0.2609 (mmm) cc_final: 0.2133 (mmm) REVERT: G 387 TYR cc_start: 0.4419 (m-80) cc_final: 0.3630 (m-80) REVERT: G 406 SER cc_start: 0.6956 (t) cc_final: 0.6533 (m) REVERT: G 450 LYS cc_start: 0.5101 (OUTLIER) cc_final: 0.4808 (tptp) REVERT: G 579 GLU cc_start: 0.8347 (tt0) cc_final: 0.7705 (tp30) REVERT: G 681 LYS cc_start: 0.5432 (mttp) cc_final: 0.4838 (pttm) REVERT: G 683 GLU cc_start: 0.4754 (OUTLIER) cc_final: 0.4148 (pm20) REVERT: H 44 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: H 49 MET cc_start: 0.8456 (tpp) cc_final: 0.8054 (tpp) REVERT: H 130 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8685 (mp0) REVERT: H 178 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8115 (mt) REVERT: H 297 GLN cc_start: 0.8391 (tp40) cc_final: 0.8016 (tt0) REVERT: H 299 LYS cc_start: 0.8254 (mmpt) cc_final: 0.7989 (mppt) REVERT: H 471 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8532 (p) REVERT: H 511 LYS cc_start: 0.7527 (tttm) cc_final: 0.6960 (tmmt) REVERT: H 515 GLU cc_start: 0.8030 (tt0) cc_final: 0.7783 (tm-30) REVERT: I 125 ILE cc_start: 0.5368 (mt) cc_final: 0.4935 (pt) REVERT: I 160 MET cc_start: 0.1300 (mmm) cc_final: 0.0650 (tpt) REVERT: I 378 GLN cc_start: 0.3605 (mt0) cc_final: 0.3094 (mm-40) REVERT: I 382 PHE cc_start: 0.4823 (m-80) cc_final: 0.4614 (m-80) REVERT: I 396 MET cc_start: 0.3987 (mpm) cc_final: 0.3391 (ttp) REVERT: I 680 MET cc_start: 0.6132 (mmm) cc_final: 0.5672 (mmp) REVERT: J 48 GLN cc_start: 0.8665 (mt0) cc_final: 0.8384 (mt0) REVERT: J 61 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: J 130 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8440 (mt-10) REVERT: J 514 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6861 (pp20) REVERT: K 63 ARG cc_start: 0.2718 (OUTLIER) cc_final: 0.2359 (ttt-90) REVERT: K 69 LYS cc_start: 0.2924 (mttm) cc_final: 0.2593 (tmtt) REVERT: K 91 MET cc_start: 0.5189 (mtt) cc_final: 0.4983 (mtp) REVERT: K 136 MET cc_start: 0.2080 (ptt) cc_final: 0.0947 (tmt) REVERT: K 285 ILE cc_start: 0.4060 (OUTLIER) cc_final: 0.3858 (mm) REVERT: K 383 GLU cc_start: 0.3676 (tt0) cc_final: 0.3144 (tt0) REVERT: K 406 SER cc_start: 0.3721 (t) cc_final: 0.3457 (p) REVERT: K 635 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7843 (pmtt) REVERT: K 653 MET cc_start: 0.1293 (ttt) cc_final: 0.0173 (ttp) REVERT: L 41 LEU cc_start: 0.7646 (tp) cc_final: 0.7377 (tp) REVERT: L 48 GLN cc_start: 0.8589 (mt0) cc_final: 0.8264 (mt0) REVERT: L 64 LYS cc_start: 0.8190 (tttt) cc_final: 0.7929 (ttpm) REVERT: L 69 GLU cc_start: 0.7022 (tp30) cc_final: 0.6376 (tp30) REVERT: L 99 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: L 333 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8386 (mm-30) REVERT: L 515 GLU cc_start: 0.7675 (tt0) cc_final: 0.7156 (tm-30) outliers start: 111 outliers final: 28 residues processed: 606 average time/residue: 0.7718 time to fit residues: 568.1622 Evaluate side-chains 508 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 461 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain E residue 554 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 255 HIS Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain G residue 560 ASN Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 683 GLU Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 471 SER Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 349 MET Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 285 ILE Chi-restraints excluded: chain K residue 635 LYS Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 110 ASP Chi-restraints excluded: chain L residue 272 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 186 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 363 optimal weight: 3.9990 chunk 428 optimal weight: 0.6980 chunk 154 optimal weight: 10.0000 chunk 425 optimal weight: 3.9990 chunk 436 optimal weight: 0.9990 chunk 485 optimal weight: 0.3980 chunk 204 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS D 297 GLN F 297 GLN F 389 GLN G 429 HIS H 75 HIS H 230 ASN H 389 GLN ** I 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 472 ASN J 389 GLN K 464 HIS K 561 ASN K 684 HIS L 75 HIS L 198 GLN L 230 ASN L 389 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.216042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124140 restraints weight = 47393.873| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.63 r_work: 0.3222 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 44580 Z= 0.151 Angle : 0.615 9.505 60255 Z= 0.319 Chirality : 0.045 0.187 6663 Planarity : 0.005 0.051 7815 Dihedral : 10.363 153.846 6602 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.92 % Allowed : 13.17 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.11), residues: 5586 helix: 0.90 (0.11), residues: 2121 sheet: 0.25 (0.14), residues: 1122 loop : -1.36 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 525 TYR 0.021 0.002 TYR B 457 PHE 0.019 0.002 PHE I 479 TRP 0.015 0.002 TRP L 276 HIS 0.032 0.001 HIS G 255 Details of bonding type rmsd covalent geometry : bond 0.00344 (44574) covalent geometry : angle 0.61544 (60255) hydrogen bonds : bond 0.04608 ( 2064) hydrogen bonds : angle 4.80751 ( 5823) Misc. bond : bond 0.00091 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 480 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 HIS cc_start: 0.7451 (t-90) cc_final: 0.7230 (t-90) REVERT: A 597 TYR cc_start: 0.7874 (m-80) cc_final: 0.7435 (m-80) REVERT: A 675 MET cc_start: 0.4088 (mtt) cc_final: 0.3677 (mpt) REVERT: A 683 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6581 (pm20) REVERT: B 36 ASP cc_start: 0.8231 (t0) cc_final: 0.8014 (t70) REVERT: B 189 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7416 (m-30) REVERT: B 353 ASP cc_start: 0.8324 (p0) cc_final: 0.7955 (p0) REVERT: B 408 MET cc_start: 0.5344 (tpt) cc_final: 0.4327 (tpp) REVERT: D 141 LYS cc_start: 0.7956 (tptt) cc_final: 0.7525 (mmmm) REVERT: D 234 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6761 (ptp90) REVERT: D 235 LYS cc_start: 0.7945 (mttt) cc_final: 0.7589 (pptt) REVERT: D 296 TYR cc_start: 0.8243 (t80) cc_final: 0.7665 (t80) REVERT: D 297 GLN cc_start: 0.8043 (tt0) cc_final: 0.7829 (tt0) REVERT: D 299 LYS cc_start: 0.8552 (pttm) cc_final: 0.8161 (mtpp) REVERT: D 327 ARG cc_start: 0.7494 (mtt180) cc_final: 0.7029 (mtt180) REVERT: D 412 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6962 (pm20) REVERT: F 47 LYS cc_start: 0.7589 (mppt) cc_final: 0.7353 (mppt) REVERT: F 49 MET cc_start: 0.7565 (tpp) cc_final: 0.7027 (tpp) REVERT: F 57 HIS cc_start: 0.7903 (t-170) cc_final: 0.6654 (m90) REVERT: F 61 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: F 130 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8275 (mt-10) REVERT: F 189 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7017 (m-30) REVERT: F 425 MET cc_start: 0.8814 (ttt) cc_final: 0.8351 (ttt) REVERT: F 476 GLU cc_start: 0.5841 (mt-10) cc_final: 0.5424 (pp20) REVERT: F 563 MET cc_start: 0.8011 (mmt) cc_final: 0.7777 (mmt) REVERT: G 86 SER cc_start: 0.2287 (t) cc_final: 0.1992 (p) REVERT: G 94 GLU cc_start: 0.4812 (OUTLIER) cc_final: 0.4601 (pt0) REVERT: G 114 ILE cc_start: 0.5398 (mm) cc_final: 0.5162 (tp) REVERT: G 287 GLU cc_start: 0.3599 (OUTLIER) cc_final: 0.2435 (tp30) REVERT: G 336 MET cc_start: 0.4161 (OUTLIER) cc_final: 0.3888 (tmm) REVERT: G 349 MET cc_start: 0.2185 (mmm) cc_final: 0.1700 (mmm) REVERT: G 387 TYR cc_start: 0.4482 (m-80) cc_final: 0.3730 (m-80) REVERT: G 406 SER cc_start: 0.7083 (t) cc_final: 0.6565 (m) REVERT: G 457 GLN cc_start: 0.4729 (mt0) cc_final: 0.4455 (mt0) REVERT: G 556 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7789 (mttm) REVERT: G 614 LEU cc_start: 0.7782 (tm) cc_final: 0.7498 (tp) REVERT: G 616 ASN cc_start: 0.7613 (m-40) cc_final: 0.7383 (m-40) REVERT: G 683 GLU cc_start: 0.4764 (OUTLIER) cc_final: 0.4179 (pm20) REVERT: H 48 GLN cc_start: 0.8473 (mt0) cc_final: 0.8018 (mt0) REVERT: H 269 LYS cc_start: 0.7446 (mmmt) cc_final: 0.7074 (mmmt) REVERT: H 297 GLN cc_start: 0.8477 (tp40) cc_final: 0.8162 (tt0) REVERT: H 299 LYS cc_start: 0.8354 (mmpt) cc_final: 0.8083 (mppt) REVERT: H 471 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8631 (p) REVERT: H 511 LYS cc_start: 0.7545 (tttm) cc_final: 0.7067 (ttpp) REVERT: H 515 GLU cc_start: 0.8057 (tt0) cc_final: 0.7718 (tm-30) REVERT: I 125 ILE cc_start: 0.5269 (mt) cc_final: 0.4834 (pt) REVERT: I 160 MET cc_start: 0.1224 (mmm) cc_final: 0.0724 (tpt) REVERT: I 378 GLN cc_start: 0.3529 (mt0) cc_final: 0.3050 (mm-40) REVERT: I 396 MET cc_start: 0.4415 (OUTLIER) cc_final: 0.3704 (ttp) REVERT: I 675 MET cc_start: 0.4295 (OUTLIER) cc_final: 0.3973 (mpp) REVERT: I 680 MET cc_start: 0.6406 (mmm) cc_final: 0.6148 (tpp) REVERT: J 34 GLN cc_start: 0.7043 (tp40) cc_final: 0.6800 (mm-40) REVERT: J 130 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8463 (mt-10) REVERT: J 476 GLU cc_start: 0.5695 (OUTLIER) cc_final: 0.5344 (pp20) REVERT: J 514 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7027 (pp20) REVERT: K 69 LYS cc_start: 0.3523 (mttm) cc_final: 0.3104 (tmtt) REVERT: K 87 MET cc_start: 0.3228 (OUTLIER) cc_final: 0.2962 (mmm) REVERT: K 91 MET cc_start: 0.4932 (mtt) cc_final: 0.4690 (mtp) REVERT: K 94 GLU cc_start: 0.5072 (mm-30) cc_final: 0.4717 (tt0) REVERT: K 136 MET cc_start: 0.2054 (ptt) cc_final: 0.0851 (tmt) REVERT: K 285 ILE cc_start: 0.3887 (OUTLIER) cc_final: 0.3482 (mm) REVERT: K 415 ARG cc_start: 0.3200 (tpp80) cc_final: 0.2777 (mtt180) REVERT: K 635 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8041 (mtmt) REVERT: L 48 GLN cc_start: 0.8735 (mt0) cc_final: 0.8364 (mt0) REVERT: L 64 LYS cc_start: 0.8383 (tttt) cc_final: 0.8092 (ttpm) REVERT: L 69 GLU cc_start: 0.7155 (tp30) cc_final: 0.6524 (tp30) REVERT: L 99 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: L 234 ARG cc_start: 0.7075 (ptt90) cc_final: 0.6691 (ppp80) REVERT: L 235 LYS cc_start: 0.7610 (mttt) cc_final: 0.6776 (tmtt) REVERT: L 297 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: L 299 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8262 (mmtm) REVERT: L 333 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8359 (mm-30) REVERT: L 473 MET cc_start: 0.7912 (ptp) cc_final: 0.7628 (ptm) REVERT: L 515 GLU cc_start: 0.7715 (tt0) cc_final: 0.7197 (tm-30) outliers start: 134 outliers final: 45 residues processed: 565 average time/residue: 0.8089 time to fit residues: 552.2688 Evaluate side-chains 510 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 442 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 412 GLU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain E residue 554 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 556 LYS Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 683 GLU Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 471 SER Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 396 MET Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 635 LYS Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 675 MET Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 226 MET Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 476 GLU Chi-restraints excluded: chain J residue 514 GLU Chi-restraints excluded: chain K residue 87 MET Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 285 ILE Chi-restraints excluded: chain K residue 635 LYS Chi-restraints excluded: chain L residue 58 GLU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 161 MET Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 272 VAL Chi-restraints excluded: chain L residue 297 GLN Chi-restraints excluded: chain L residue 299 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 102 optimal weight: 0.9980 chunk 324 optimal weight: 0.4980 chunk 196 optimal weight: 7.9990 chunk 447 optimal weight: 2.9990 chunk 296 optimal weight: 0.0970 chunk 180 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 368 optimal weight: 8.9990 chunk 472 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN G 255 HIS ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN H 480 ASN I 265 HIS I 279 GLN I 472 ASN K 492 HIS L 75 HIS L 477 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.216061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129523 restraints weight = 48150.273| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.83 r_work: 0.3236 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 44580 Z= 0.135 Angle : 0.582 10.561 60255 Z= 0.302 Chirality : 0.045 0.220 6663 Planarity : 0.004 0.050 7815 Dihedral : 9.622 111.547 6600 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.81 % Allowed : 13.87 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.11), residues: 5586 helix: 1.18 (0.12), residues: 2139 sheet: 0.34 (0.15), residues: 1122 loop : -1.22 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 268 TYR 0.018 0.001 TYR B 457 PHE 0.023 0.001 PHE G 323 TRP 0.011 0.001 TRP L 276 HIS 0.005 0.001 HIS F 57 Details of bonding type rmsd covalent geometry : bond 0.00307 (44574) covalent geometry : angle 0.58157 (60255) hydrogen bonds : bond 0.04165 ( 2064) hydrogen bonds : angle 4.64290 ( 5823) Misc. bond : bond 0.00023 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 450 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LYS cc_start: 0.7718 (mtpp) cc_final: 0.7175 (mmpt) REVERT: A 675 MET cc_start: 0.4201 (mtt) cc_final: 0.3774 (mpt) REVERT: A 683 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6624 (pm20) REVERT: B 36 ASP cc_start: 0.8188 (t0) cc_final: 0.7960 (t70) REVERT: B 58 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: B 326 LYS cc_start: 0.7436 (mmmt) cc_final: 0.6530 (mptt) REVERT: B 353 ASP cc_start: 0.8314 (p0) cc_final: 0.7948 (p0) REVERT: B 377 PHE cc_start: 0.7967 (m-80) cc_final: 0.7722 (m-80) REVERT: B 408 MET cc_start: 0.5556 (tpt) cc_final: 0.4665 (tpp) REVERT: D 64 LYS cc_start: 0.8262 (ttpt) cc_final: 0.7602 (tmtt) REVERT: D 141 LYS cc_start: 0.8027 (tptt) cc_final: 0.7626 (mmmm) REVERT: D 234 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6836 (ptp90) REVERT: D 235 LYS cc_start: 0.8055 (mttt) cc_final: 0.7671 (pptt) REVERT: D 296 TYR cc_start: 0.8348 (t80) cc_final: 0.7791 (t80) REVERT: D 299 LYS cc_start: 0.8555 (pttm) cc_final: 0.8212 (mtpp) REVERT: D 393 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8432 (tt0) REVERT: D 412 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: F 57 HIS cc_start: 0.7942 (t-170) cc_final: 0.6729 (m90) REVERT: F 61 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: F 130 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: F 189 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.6979 (m-30) REVERT: F 353 ASP cc_start: 0.8602 (p0) cc_final: 0.8354 (p0) REVERT: F 425 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8312 (ttt) REVERT: F 476 GLU cc_start: 0.5809 (mt-10) cc_final: 0.5379 (pp20) REVERT: G 86 SER cc_start: 0.2656 (t) cc_final: 0.2287 (p) REVERT: G 114 ILE cc_start: 0.5389 (mm) cc_final: 0.5145 (tp) REVERT: G 255 HIS cc_start: 0.1438 (OUTLIER) cc_final: 0.0619 (t-90) REVERT: G 284 LYS cc_start: 0.4908 (mttt) cc_final: 0.4269 (mmtm) REVERT: G 406 SER cc_start: 0.7212 (t) cc_final: 0.6660 (m) REVERT: G 614 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7549 (tp) REVERT: G 683 GLU cc_start: 0.4796 (OUTLIER) cc_final: 0.4259 (pm20) REVERT: H 48 GLN cc_start: 0.8477 (mt0) cc_final: 0.8050 (mt0) REVERT: H 269 LYS cc_start: 0.7569 (mmmt) cc_final: 0.7166 (mmmt) REVERT: H 297 GLN cc_start: 0.8460 (tp40) cc_final: 0.8245 (tt0) REVERT: H 471 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8679 (p) REVERT: H 473 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8058 (mtt) REVERT: H 480 ASN cc_start: 0.6657 (m-40) cc_final: 0.6440 (m110) REVERT: H 511 LYS cc_start: 0.7597 (tttm) cc_final: 0.6988 (ttpt) REVERT: H 515 GLU cc_start: 0.8132 (tt0) cc_final: 0.7819 (tm-30) REVERT: I 125 ILE cc_start: 0.5131 (mt) cc_final: 0.4705 (pt) REVERT: I 160 MET cc_start: 0.1045 (mmm) cc_final: 0.0592 (tpt) REVERT: I 339 ARG cc_start: 0.1811 (ptt-90) cc_final: 0.1375 (pmt170) REVERT: I 378 GLN cc_start: 0.3635 (mt0) cc_final: 0.3077 (mm-40) REVERT: I 396 MET cc_start: 0.4293 (OUTLIER) cc_final: 0.3582 (ttp) REVERT: I 680 MET cc_start: 0.6454 (mmm) cc_final: 0.6029 (tpp) REVERT: J 34 GLN cc_start: 0.7115 (tp40) cc_final: 0.6913 (mm-40) REVERT: J 61 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: J 130 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8475 (mt-10) REVERT: J 213 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8230 (mtt) REVERT: J 324 ASN cc_start: 0.8398 (t0) cc_final: 0.8161 (t0) REVERT: J 393 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: J 514 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7071 (pp20) REVERT: K 69 LYS cc_start: 0.3594 (mttm) cc_final: 0.3171 (tmtt) REVERT: K 87 MET cc_start: 0.3088 (OUTLIER) cc_final: 0.2828 (mmm) REVERT: K 94 GLU cc_start: 0.5133 (mm-30) cc_final: 0.3920 (tm-30) REVERT: K 136 MET cc_start: 0.2111 (ptt) cc_final: 0.0794 (tmt) REVERT: K 285 ILE cc_start: 0.3892 (OUTLIER) cc_final: 0.3585 (mm) REVERT: K 415 ARG cc_start: 0.3351 (tpp80) cc_final: 0.2925 (mtt180) REVERT: K 635 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8057 (mtmt) REVERT: L 64 LYS cc_start: 0.8359 (tttt) cc_final: 0.8076 (ttpm) REVERT: L 69 GLU cc_start: 0.7024 (tp30) cc_final: 0.6511 (tp30) REVERT: L 99 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8264 (mt-10) REVERT: L 162 GLN cc_start: 0.9023 (mt0) cc_final: 0.8776 (tt0) REVERT: L 228 ASP cc_start: 0.8346 (m-30) cc_final: 0.8132 (m-30) REVERT: L 234 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6827 (ppp80) REVERT: L 235 LYS cc_start: 0.7518 (mttt) cc_final: 0.6767 (tmtt) REVERT: L 297 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: L 299 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8212 (mmtm) REVERT: L 333 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8295 (mm-30) REVERT: L 408 MET cc_start: 0.5839 (tpt) cc_final: 0.5571 (tpt) REVERT: L 515 GLU cc_start: 0.7744 (tt0) cc_final: 0.7291 (tm-30) outliers start: 129 outliers final: 50 residues processed: 529 average time/residue: 0.7869 time to fit residues: 505.4056 Evaluate side-chains 503 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 427 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 610 LYS Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 412 GLU Chi-restraints excluded: chain E residue 554 THR Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 425 MET Chi-restraints excluded: chain F residue 555 LYS Chi-restraints excluded: chain G residue 255 HIS Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 683 GLU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 471 SER Chi-restraints excluded: chain H residue 473 MET Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 396 MET Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 635 LYS Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 213 MET Chi-restraints excluded: chain J residue 246 LEU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 393 GLN Chi-restraints excluded: chain J residue 514 GLU Chi-restraints excluded: chain K residue 87 MET Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 285 ILE Chi-restraints excluded: chain K residue 635 LYS Chi-restraints excluded: chain K residue 653 MET Chi-restraints excluded: chain L residue 58 GLU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 161 MET Chi-restraints excluded: chain L residue 234 ARG Chi-restraints excluded: chain L residue 272 VAL Chi-restraints excluded: chain L residue 297 GLN Chi-restraints excluded: chain L residue 299 LYS Chi-restraints excluded: chain L residue 557 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 180 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 256 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 454 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 464 optimal weight: 9.9990 chunk 276 optimal weight: 0.0970 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN D 386 HIS F 477 GLN G 255 HIS ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN I 265 HIS J 297 GLN L 75 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.215321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122871 restraints weight = 47036.970| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.52 r_work: 0.3221 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 44580 Z= 0.129 Angle : 0.571 10.786 60255 Z= 0.295 Chirality : 0.044 0.184 6663 Planarity : 0.004 0.051 7815 Dihedral : 9.218 86.916 6600 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.59 % Allowed : 14.34 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.11), residues: 5586 helix: 1.37 (0.12), residues: 2139 sheet: 0.39 (0.15), residues: 1131 loop : -1.10 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 268 TYR 0.018 0.001 TYR B 457 PHE 0.020 0.001 PHE G 323 TRP 0.010 0.001 TRP L 276 HIS 0.019 0.001 HIS G 255 Details of bonding type rmsd covalent geometry : bond 0.00291 (44574) covalent geometry : angle 0.57125 (60255) hydrogen bonds : bond 0.04061 ( 2064) hydrogen bonds : angle 4.55025 ( 5823) Misc. bond : bond 0.00018 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 451 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8308 (mt-10) REVERT: A 522 MET cc_start: 0.7525 (ttp) cc_final: 0.7274 (ttm) REVERT: A 556 LYS cc_start: 0.7556 (mtpp) cc_final: 0.6935 (mmmt) REVERT: A 561 ASN cc_start: 0.8297 (m-40) cc_final: 0.8000 (m110) REVERT: A 675 MET cc_start: 0.4258 (mtt) cc_final: 0.3769 (mpt) REVERT: A 683 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6522 (pm20) REVERT: B 36 ASP cc_start: 0.8086 (t0) cc_final: 0.7867 (t70) REVERT: B 58 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: B 326 LYS cc_start: 0.7399 (mmmt) cc_final: 0.6554 (mptt) REVERT: B 353 ASP cc_start: 0.8280 (p0) cc_final: 0.7965 (p0) REVERT: B 377 PHE cc_start: 0.7889 (m-80) cc_final: 0.7624 (m-80) REVERT: B 408 MET cc_start: 0.5532 (tpt) cc_final: 0.4660 (tpp) REVERT: D 64 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.8066 (tmmt) REVERT: D 141 LYS cc_start: 0.8046 (tptt) cc_final: 0.7648 (mmmm) REVERT: D 234 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6825 (ptp90) REVERT: D 235 LYS cc_start: 0.7844 (mttt) cc_final: 0.7618 (pptt) REVERT: D 276 TRP cc_start: 0.8630 (t60) cc_final: 0.8396 (t60) REVERT: D 299 LYS cc_start: 0.8565 (pttm) cc_final: 0.8226 (mtpp) REVERT: D 327 ARG cc_start: 0.7325 (mtt180) cc_final: 0.7087 (mtt180) REVERT: D 393 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: D 412 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.7015 (pm20) REVERT: D 563 MET cc_start: 0.7874 (mmt) cc_final: 0.7573 (mmt) REVERT: F 57 HIS cc_start: 0.7999 (t-170) cc_final: 0.6804 (m90) REVERT: F 61 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: F 69 GLU cc_start: 0.6216 (pp20) cc_final: 0.5978 (tm-30) REVERT: F 189 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.6919 (m-30) REVERT: F 235 LYS cc_start: 0.7177 (mptt) cc_final: 0.6659 (pptt) REVERT: F 353 ASP cc_start: 0.8600 (p0) cc_final: 0.8356 (p0) REVERT: F 425 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8349 (ttt) REVERT: F 476 GLU cc_start: 0.5706 (mt-10) cc_final: 0.5214 (pp20) REVERT: G 86 SER cc_start: 0.2577 (t) cc_final: 0.2211 (p) REVERT: G 114 ILE cc_start: 0.5400 (mm) cc_final: 0.5194 (tp) REVERT: G 284 LYS cc_start: 0.4781 (mttt) cc_final: 0.4317 (mmtm) REVERT: G 287 GLU cc_start: 0.3316 (OUTLIER) cc_final: 0.2693 (tp30) REVERT: G 336 MET cc_start: 0.3638 (OUTLIER) cc_final: 0.3287 (tmt) REVERT: G 406 SER cc_start: 0.7187 (t) cc_final: 0.6636 (m) REVERT: G 457 GLN cc_start: 0.4715 (mt0) cc_final: 0.4392 (mt0) REVERT: G 614 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7531 (tp) REVERT: G 683 GLU cc_start: 0.4629 (OUTLIER) cc_final: 0.4050 (pm20) REVERT: H 44 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: H 48 GLN cc_start: 0.8401 (mt0) cc_final: 0.7929 (mt0) REVERT: H 269 LYS cc_start: 0.7641 (mmmt) cc_final: 0.7194 (mmmt) REVERT: H 297 GLN cc_start: 0.8448 (tp40) cc_final: 0.8245 (tt0) REVERT: H 471 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8694 (p) REVERT: H 480 ASN cc_start: 0.6777 (m-40) cc_final: 0.6572 (m110) REVERT: H 511 LYS cc_start: 0.7530 (tttm) cc_final: 0.6874 (ttpt) REVERT: H 515 GLU cc_start: 0.8124 (tt0) cc_final: 0.7820 (tm-30) REVERT: I 160 MET cc_start: 0.1155 (mmm) cc_final: 0.0756 (tpt) REVERT: I 339 ARG cc_start: 0.1627 (ptt-90) cc_final: 0.1306 (pmt170) REVERT: I 361 ARG cc_start: 0.3674 (mtt-85) cc_final: 0.3460 (ttm170) REVERT: I 378 GLN cc_start: 0.3503 (mt0) cc_final: 0.3000 (mm-40) REVERT: I 396 MET cc_start: 0.4437 (OUTLIER) cc_final: 0.3731 (ttp) REVERT: I 464 HIS cc_start: 0.4565 (m170) cc_final: 0.3963 (t-170) REVERT: I 630 ASP cc_start: 0.8178 (t0) cc_final: 0.7534 (m-30) REVERT: I 680 MET cc_start: 0.6434 (mmm) cc_final: 0.5998 (tpp) REVERT: J 34 GLN cc_start: 0.7233 (tp40) cc_final: 0.6970 (mm-40) REVERT: J 48 GLN cc_start: 0.8552 (mt0) cc_final: 0.8306 (mt0) REVERT: J 61 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: J 130 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8510 (mt-10) REVERT: J 213 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8344 (mtt) REVERT: J 324 ASN cc_start: 0.8365 (t0) cc_final: 0.8062 (t0) REVERT: J 511 LYS cc_start: 0.6627 (tttm) cc_final: 0.5999 (ttmt) REVERT: J 514 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7032 (pp20) REVERT: K 69 LYS cc_start: 0.3628 (mttm) cc_final: 0.3106 (tmmm) REVERT: K 94 GLU cc_start: 0.4957 (mm-30) cc_final: 0.3746 (tm-30) REVERT: K 136 MET cc_start: 0.1980 (ptt) cc_final: 0.0729 (tmt) REVERT: K 285 ILE cc_start: 0.3564 (OUTLIER) cc_final: 0.3352 (mm) REVERT: K 415 ARG cc_start: 0.3143 (tpp80) cc_final: 0.2814 (mtt180) REVERT: K 635 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7936 (mtmt) REVERT: L 64 LYS cc_start: 0.8349 (tttt) cc_final: 0.8063 (ttpm) REVERT: L 69 GLU cc_start: 0.7107 (tp30) cc_final: 0.6600 (tp30) REVERT: L 99 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: L 234 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6829 (ppp80) REVERT: L 235 LYS cc_start: 0.7502 (mttt) cc_final: 0.6825 (tmtt) REVERT: L 408 MET cc_start: 0.5817 (tpt) cc_final: 0.5544 (tpt) REVERT: L 515 GLU cc_start: 0.7804 (tt0) cc_final: 0.7365 (tm-30) outliers start: 119 outliers final: 50 residues processed: 529 average time/residue: 0.7894 time to fit residues: 505.1602 Evaluate side-chains 503 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 430 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 412 GLU Chi-restraints excluded: chain E residue 554 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 425 MET Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 683 GLU Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 471 SER Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 396 MET Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 635 LYS Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 213 MET Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 514 GLU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 285 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain K residue 635 LYS Chi-restraints excluded: chain K residue 653 MET Chi-restraints excluded: chain L residue 58 GLU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 161 MET Chi-restraints excluded: chain L residue 234 ARG Chi-restraints excluded: chain L residue 272 VAL Chi-restraints excluded: chain L residue 557 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 533 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 263 optimal weight: 0.9980 chunk 271 optimal weight: 2.9990 chunk 441 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN D 236 GLN D 297 GLN F 297 GLN G 255 HIS G 259 GLN ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN J 297 GLN K 459 ASN K 464 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.213889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122356 restraints weight = 46778.762| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.53 r_work: 0.3206 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 44580 Z= 0.214 Angle : 0.657 11.078 60255 Z= 0.342 Chirality : 0.048 0.229 6663 Planarity : 0.005 0.054 7815 Dihedral : 9.282 89.770 6600 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.96 % Allowed : 14.26 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.11), residues: 5586 helix: 1.27 (0.11), residues: 2109 sheet: 0.42 (0.15), residues: 1101 loop : -1.08 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 525 TYR 0.027 0.002 TYR J 457 PHE 0.019 0.002 PHE D 347 TRP 0.009 0.001 TRP L 276 HIS 0.009 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00508 (44574) covalent geometry : angle 0.65708 (60255) hydrogen bonds : bond 0.05259 ( 2064) hydrogen bonds : angle 4.75345 ( 5823) Misc. bond : bond 0.00032 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 449 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.7400 (ttp) cc_final: 0.7148 (ttm) REVERT: A 556 LYS cc_start: 0.7408 (mtpp) cc_final: 0.6824 (mmmt) REVERT: A 559 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6506 (tptp) REVERT: A 561 ASN cc_start: 0.8337 (m-40) cc_final: 0.7930 (m110) REVERT: A 675 MET cc_start: 0.4321 (mtt) cc_final: 0.3736 (mpt) REVERT: B 36 ASP cc_start: 0.7993 (t0) cc_final: 0.7771 (t70) REVERT: B 58 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: B 326 LYS cc_start: 0.7404 (mmmt) cc_final: 0.6485 (mptt) REVERT: C 556 LYS cc_start: 0.6972 (tttt) cc_final: 0.6544 (mtmt) REVERT: D 61 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7126 (tm-30) REVERT: D 141 LYS cc_start: 0.8013 (tptt) cc_final: 0.7589 (mmmm) REVERT: D 234 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6319 (ptp90) REVERT: D 235 LYS cc_start: 0.8091 (mttt) cc_final: 0.7696 (pptt) REVERT: D 276 TRP cc_start: 0.8627 (t60) cc_final: 0.8083 (t60) REVERT: D 299 LYS cc_start: 0.8581 (pttm) cc_final: 0.8215 (mtpp) REVERT: D 393 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8450 (tt0) REVERT: D 563 MET cc_start: 0.7823 (mmt) cc_final: 0.7605 (mmt) REVERT: F 57 HIS cc_start: 0.8002 (t-170) cc_final: 0.6831 (m90) REVERT: F 61 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: F 189 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7136 (m-30) REVERT: F 353 ASP cc_start: 0.8532 (p0) cc_final: 0.8268 (p0) REVERT: F 476 GLU cc_start: 0.5849 (mt-10) cc_final: 0.5355 (pm20) REVERT: F 563 MET cc_start: 0.7998 (mmt) cc_final: 0.7721 (mmt) REVERT: G 86 SER cc_start: 0.2511 (t) cc_final: 0.2118 (p) REVERT: G 114 ILE cc_start: 0.5512 (mm) cc_final: 0.5246 (tp) REVERT: G 261 PHE cc_start: 0.3891 (OUTLIER) cc_final: 0.3666 (m-80) REVERT: G 284 LYS cc_start: 0.4366 (mttt) cc_final: 0.3958 (mmtm) REVERT: G 287 GLU cc_start: 0.3415 (OUTLIER) cc_final: 0.2625 (tp30) REVERT: G 406 SER cc_start: 0.7249 (t) cc_final: 0.6674 (m) REVERT: G 457 GLN cc_start: 0.4916 (mt0) cc_final: 0.4612 (mt0) REVERT: G 614 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7525 (tp) REVERT: H 269 LYS cc_start: 0.7546 (mmmt) cc_final: 0.7105 (mmmt) REVERT: H 297 GLN cc_start: 0.8403 (tp40) cc_final: 0.8187 (tt0) REVERT: H 299 LYS cc_start: 0.8360 (mmpt) cc_final: 0.8067 (mppt) REVERT: H 471 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8710 (p) REVERT: H 511 LYS cc_start: 0.7399 (tttm) cc_final: 0.6711 (ttpt) REVERT: H 515 GLU cc_start: 0.7895 (tt0) cc_final: 0.7616 (tm-30) REVERT: I 160 MET cc_start: 0.1016 (mmm) cc_final: 0.0473 (tpt) REVERT: I 336 MET cc_start: 0.2013 (ttt) cc_final: 0.1635 (tpp) REVERT: I 339 ARG cc_start: 0.1703 (ptt-90) cc_final: 0.1263 (ptp90) REVERT: I 378 GLN cc_start: 0.3681 (mt0) cc_final: 0.3087 (mm-40) REVERT: I 382 PHE cc_start: 0.5191 (m-80) cc_final: 0.4935 (m-80) REVERT: I 396 MET cc_start: 0.4621 (OUTLIER) cc_final: 0.3896 (ttp) REVERT: I 630 ASP cc_start: 0.8196 (t0) cc_final: 0.7590 (m-30) REVERT: I 680 MET cc_start: 0.6364 (mmm) cc_final: 0.5924 (tpp) REVERT: J 34 GLN cc_start: 0.7360 (tp40) cc_final: 0.6937 (mm-40) REVERT: J 61 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: J 130 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8448 (mt-10) REVERT: J 213 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8495 (mtt) REVERT: J 259 ASP cc_start: 0.7844 (m-30) cc_final: 0.6843 (p0) REVERT: J 324 ASN cc_start: 0.8426 (t0) cc_final: 0.8073 (t0) REVERT: J 511 LYS cc_start: 0.6698 (tttm) cc_final: 0.5972 (ttmt) REVERT: J 514 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6936 (pp20) REVERT: K 69 LYS cc_start: 0.3677 (mttm) cc_final: 0.3116 (tmmm) REVERT: K 136 MET cc_start: 0.1853 (ptt) cc_final: 0.0630 (tmt) REVERT: K 415 ARG cc_start: 0.3290 (tpp80) cc_final: 0.2867 (mtt180) REVERT: K 635 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7717 (pmtt) REVERT: L 64 LYS cc_start: 0.8404 (tttt) cc_final: 0.8119 (ttpm) REVERT: L 69 GLU cc_start: 0.7102 (tp30) cc_final: 0.6601 (tp30) REVERT: L 99 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8307 (mt-10) REVERT: L 234 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6675 (ppp80) REVERT: L 235 LYS cc_start: 0.7366 (mttt) cc_final: 0.6848 (tmtt) REVERT: L 268 ARG cc_start: 0.6832 (mpt-90) cc_final: 0.5607 (mpt-90) REVERT: L 297 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: L 473 MET cc_start: 0.8148 (ptp) cc_final: 0.7830 (ptm) REVERT: L 515 GLU cc_start: 0.7761 (tt0) cc_final: 0.7529 (tm-30) outliers start: 136 outliers final: 57 residues processed: 531 average time/residue: 0.6495 time to fit residues: 420.7052 Evaluate side-chains 514 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 437 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 554 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 555 LYS Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 471 SER Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 396 MET Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 635 LYS Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 213 MET Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 514 GLU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain K residue 628 GLU Chi-restraints excluded: chain K residue 635 LYS Chi-restraints excluded: chain K residue 653 MET Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 58 GLU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 161 MET Chi-restraints excluded: chain L residue 234 ARG Chi-restraints excluded: chain L residue 272 VAL Chi-restraints excluded: chain L residue 297 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 431 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 424 optimal weight: 0.8980 chunk 542 optimal weight: 3.9990 chunk 349 optimal weight: 20.0000 chunk 245 optimal weight: 2.9990 chunk 533 optimal weight: 0.7980 chunk 552 optimal weight: 7.9990 chunk 345 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A 616 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN D 297 GLN F 297 GLN ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 457 GLN J 297 GLN K 464 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.213937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123806 restraints weight = 46666.767| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.63 r_work: 0.3219 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 44580 Z= 0.177 Angle : 0.617 9.674 60255 Z= 0.321 Chirality : 0.046 0.190 6663 Planarity : 0.004 0.057 7815 Dihedral : 9.103 87.980 6600 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.66 % Allowed : 14.98 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.11), residues: 5586 helix: 1.29 (0.11), residues: 2142 sheet: 0.44 (0.15), residues: 1101 loop : -1.07 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 525 TYR 0.021 0.002 TYR B 457 PHE 0.020 0.002 PHE G 395 TRP 0.008 0.001 TRP B 276 HIS 0.006 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00416 (44574) covalent geometry : angle 0.61704 (60255) hydrogen bonds : bond 0.04712 ( 2064) hydrogen bonds : angle 4.67411 ( 5823) Misc. bond : bond 0.00019 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 446 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.7441 (ttp) cc_final: 0.7189 (ttm) REVERT: A 556 LYS cc_start: 0.7330 (mtpp) cc_final: 0.6752 (mmmt) REVERT: A 559 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6519 (tptp) REVERT: A 561 ASN cc_start: 0.8327 (m-40) cc_final: 0.7936 (m110) REVERT: A 675 MET cc_start: 0.4425 (mtt) cc_final: 0.3899 (mpt) REVERT: B 36 ASP cc_start: 0.8004 (t0) cc_final: 0.7802 (t70) REVERT: B 58 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: B 326 LYS cc_start: 0.7382 (mmmt) cc_final: 0.6482 (mptt) REVERT: B 377 PHE cc_start: 0.7880 (m-80) cc_final: 0.7675 (m-80) REVERT: C 556 LYS cc_start: 0.6943 (tttt) cc_final: 0.6443 (ptpt) REVERT: D 61 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: D 141 LYS cc_start: 0.8035 (tptt) cc_final: 0.7626 (mmmm) REVERT: D 226 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8364 (mtp) REVERT: D 234 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6495 (ptp90) REVERT: D 235 LYS cc_start: 0.8115 (mttt) cc_final: 0.7714 (pptt) REVERT: D 276 TRP cc_start: 0.8597 (t60) cc_final: 0.8131 (t60) REVERT: D 299 LYS cc_start: 0.8660 (pttm) cc_final: 0.8276 (mmpt) REVERT: D 393 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: D 563 MET cc_start: 0.7836 (mmt) cc_final: 0.7592 (mmt) REVERT: F 57 HIS cc_start: 0.8118 (t-170) cc_final: 0.6909 (m90) REVERT: F 61 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: F 88 ASP cc_start: 0.8219 (p0) cc_final: 0.7976 (p0) REVERT: F 189 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7097 (m-30) REVERT: F 353 ASP cc_start: 0.8539 (p0) cc_final: 0.8280 (p0) REVERT: F 425 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8349 (ttt) REVERT: F 476 GLU cc_start: 0.5720 (mt-10) cc_final: 0.5180 (pm20) REVERT: F 563 MET cc_start: 0.7979 (mmt) cc_final: 0.7685 (mmt) REVERT: G 86 SER cc_start: 0.2441 (t) cc_final: 0.2052 (p) REVERT: G 114 ILE cc_start: 0.5466 (mm) cc_final: 0.5260 (tp) REVERT: G 255 HIS cc_start: 0.1679 (OUTLIER) cc_final: 0.0949 (m-70) REVERT: G 261 PHE cc_start: 0.3710 (OUTLIER) cc_final: 0.3396 (m-80) REVERT: G 284 LYS cc_start: 0.4296 (mttt) cc_final: 0.3911 (mmtm) REVERT: G 287 GLU cc_start: 0.3632 (OUTLIER) cc_final: 0.2796 (tp30) REVERT: G 406 SER cc_start: 0.6997 (t) cc_final: 0.6591 (m) REVERT: G 457 GLN cc_start: 0.4804 (mt0) cc_final: 0.4510 (mt0) REVERT: G 614 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7503 (tp) REVERT: G 635 LYS cc_start: 0.8135 (mttt) cc_final: 0.7681 (tptp) REVERT: H 44 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: H 297 GLN cc_start: 0.8432 (tp40) cc_final: 0.8227 (tt0) REVERT: H 299 LYS cc_start: 0.8372 (mmpt) cc_final: 0.8090 (mppt) REVERT: H 471 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8758 (p) REVERT: H 473 MET cc_start: 0.8379 (mtt) cc_final: 0.8073 (mtt) REVERT: H 511 LYS cc_start: 0.7413 (tttm) cc_final: 0.6752 (ttpp) REVERT: H 515 GLU cc_start: 0.7904 (tt0) cc_final: 0.7619 (tm-30) REVERT: I 136 MET cc_start: 0.3201 (ptp) cc_final: 0.2766 (pmm) REVERT: I 160 MET cc_start: 0.1182 (mmm) cc_final: 0.0530 (tpt) REVERT: I 336 MET cc_start: 0.1849 (ttt) cc_final: 0.1541 (tpp) REVERT: I 339 ARG cc_start: 0.1339 (ptt-90) cc_final: 0.0923 (tmm-80) REVERT: I 378 GLN cc_start: 0.3625 (mt0) cc_final: 0.3040 (mm-40) REVERT: I 396 MET cc_start: 0.4583 (OUTLIER) cc_final: 0.3888 (ttp) REVERT: I 630 ASP cc_start: 0.8250 (t0) cc_final: 0.7568 (m-30) REVERT: I 653 MET cc_start: 0.5392 (OUTLIER) cc_final: 0.4967 (mmm) REVERT: I 677 MET cc_start: 0.4552 (OUTLIER) cc_final: 0.4013 (ppp) REVERT: I 680 MET cc_start: 0.6292 (mmm) cc_final: 0.5911 (tpp) REVERT: J 34 GLN cc_start: 0.7495 (tp40) cc_final: 0.7273 (tp-100) REVERT: J 61 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: J 130 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8509 (mt-10) REVERT: J 213 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8403 (mtt) REVERT: J 259 ASP cc_start: 0.7813 (m-30) cc_final: 0.6834 (p0) REVERT: J 324 ASN cc_start: 0.8416 (t0) cc_final: 0.8159 (t0) REVERT: J 511 LYS cc_start: 0.6603 (tttm) cc_final: 0.6367 (ttmt) REVERT: J 514 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6924 (tm-30) REVERT: J 515 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7044 (mm-30) REVERT: K 69 LYS cc_start: 0.3642 (mttm) cc_final: 0.3086 (tmmm) REVERT: K 136 MET cc_start: 0.1668 (ptt) cc_final: 0.0436 (tmt) REVERT: K 415 ARG cc_start: 0.3265 (tpp80) cc_final: 0.2827 (mtt180) REVERT: K 635 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7738 (pmtt) REVERT: K 653 MET cc_start: 0.1750 (OUTLIER) cc_final: 0.0999 (ttp) REVERT: K 675 MET cc_start: 0.2953 (ttp) cc_final: 0.2747 (ttp) REVERT: L 64 LYS cc_start: 0.8401 (tttt) cc_final: 0.8116 (ttpm) REVERT: L 69 GLU cc_start: 0.7153 (tp30) cc_final: 0.6640 (tp30) REVERT: L 99 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8316 (mt-10) REVERT: L 188 ARG cc_start: 0.7781 (tmm160) cc_final: 0.7550 (tmm160) REVERT: L 234 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6738 (ppp80) REVERT: L 235 LYS cc_start: 0.7397 (mttt) cc_final: 0.6889 (tmtt) REVERT: L 268 ARG cc_start: 0.6898 (mpt-90) cc_final: 0.5752 (mpt-90) REVERT: L 297 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: L 515 GLU cc_start: 0.7741 (tt0) cc_final: 0.7522 (tm-30) outliers start: 122 outliers final: 58 residues processed: 524 average time/residue: 0.5226 time to fit residues: 334.7309 Evaluate side-chains 511 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 426 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 554 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 425 MET Chi-restraints excluded: chain F residue 555 LYS Chi-restraints excluded: chain G residue 255 HIS Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 683 GLU Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 471 SER Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 396 MET Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 635 LYS Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 677 MET Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 213 MET Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 514 GLU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain K residue 628 GLU Chi-restraints excluded: chain K residue 635 LYS Chi-restraints excluded: chain K residue 653 MET Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 58 GLU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 161 MET Chi-restraints excluded: chain L residue 234 ARG Chi-restraints excluded: chain L residue 272 VAL Chi-restraints excluded: chain L residue 297 GLN Chi-restraints excluded: chain L residue 557 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 428 optimal weight: 0.0010 chunk 512 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 438 optimal weight: 0.8980 chunk 178 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 478 optimal weight: 20.0000 chunk 301 optimal weight: 1.9990 chunk 339 optimal weight: 0.9980 chunk 373 optimal weight: 9.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A 616 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 HIS D 297 GLN F 297 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN H 480 ASN I 265 HIS J 297 GLN K 464 HIS L 75 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.216137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127425 restraints weight = 47316.528| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.73 r_work: 0.3250 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 44580 Z= 0.113 Angle : 0.562 12.161 60255 Z= 0.290 Chirality : 0.044 0.174 6663 Planarity : 0.004 0.052 7815 Dihedral : 8.769 86.913 6600 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.18 % Allowed : 15.70 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.11), residues: 5586 helix: 1.66 (0.12), residues: 2106 sheet: 0.50 (0.15), residues: 1101 loop : -0.97 (0.13), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 234 TYR 0.013 0.001 TYR B 457 PHE 0.021 0.001 PHE G 323 TRP 0.013 0.001 TRP F 276 HIS 0.008 0.001 HIS G 344 Details of bonding type rmsd covalent geometry : bond 0.00246 (44574) covalent geometry : angle 0.56150 (60255) hydrogen bonds : bond 0.03707 ( 2064) hydrogen bonds : angle 4.47619 ( 5823) Misc. bond : bond 0.00013 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 452 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.7380 (ttp) cc_final: 0.7123 (ttm) REVERT: A 556 LYS cc_start: 0.7344 (mtpp) cc_final: 0.6763 (mmmt) REVERT: A 559 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6339 (tptp) REVERT: A 561 ASN cc_start: 0.8303 (m-40) cc_final: 0.7949 (m110) REVERT: A 675 MET cc_start: 0.4434 (mtt) cc_final: 0.3946 (mpt) REVERT: A 682 MET cc_start: 0.6688 (tpt) cc_final: 0.6121 (tpp) REVERT: B 36 ASP cc_start: 0.8000 (t0) cc_final: 0.7759 (t70) REVERT: B 58 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: B 74 LEU cc_start: 0.8243 (tp) cc_final: 0.7954 (tp) REVERT: B 326 LYS cc_start: 0.7347 (mmmt) cc_final: 0.6497 (mptt) REVERT: B 408 MET cc_start: 0.5596 (tpt) cc_final: 0.4830 (tpp) REVERT: C 556 LYS cc_start: 0.6809 (tttt) cc_final: 0.6294 (ptpt) REVERT: D 48 GLN cc_start: 0.8627 (mt0) cc_final: 0.8354 (mm-40) REVERT: D 141 LYS cc_start: 0.8005 (tptt) cc_final: 0.7605 (mmmm) REVERT: D 234 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6366 (ptp90) REVERT: D 235 LYS cc_start: 0.8068 (mttt) cc_final: 0.7687 (pptt) REVERT: D 276 TRP cc_start: 0.8563 (t60) cc_final: 0.8140 (t60) REVERT: D 299 LYS cc_start: 0.8661 (pttm) cc_final: 0.8279 (mmpt) REVERT: D 393 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: D 563 MET cc_start: 0.7832 (mmt) cc_final: 0.7588 (mmt) REVERT: F 57 HIS cc_start: 0.8093 (t-170) cc_final: 0.6829 (m90) REVERT: F 69 GLU cc_start: 0.6126 (pp20) cc_final: 0.5880 (tm-30) REVERT: F 178 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7537 (mm) REVERT: F 353 ASP cc_start: 0.8614 (p0) cc_final: 0.8394 (p0) REVERT: F 425 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8367 (ttt) REVERT: F 476 GLU cc_start: 0.5682 (mt-10) cc_final: 0.5153 (pm20) REVERT: F 563 MET cc_start: 0.7985 (mmt) cc_final: 0.7696 (mmt) REVERT: G 86 SER cc_start: 0.2381 (t) cc_final: 0.1976 (p) REVERT: G 261 PHE cc_start: 0.3433 (OUTLIER) cc_final: 0.3134 (m-80) REVERT: G 287 GLU cc_start: 0.3506 (OUTLIER) cc_final: 0.2325 (tp30) REVERT: G 334 MET cc_start: 0.3340 (mtp) cc_final: 0.2963 (ppp) REVERT: G 336 MET cc_start: 0.3460 (OUTLIER) cc_final: 0.2843 (tmm) REVERT: G 406 SER cc_start: 0.7045 (t) cc_final: 0.6579 (m) REVERT: G 457 GLN cc_start: 0.4878 (mt0) cc_final: 0.4544 (mt0) REVERT: G 579 GLU cc_start: 0.8121 (tt0) cc_final: 0.7499 (tp30) REVERT: G 614 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7491 (tp) REVERT: G 635 LYS cc_start: 0.8134 (mttt) cc_final: 0.7669 (tptp) REVERT: H 44 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: H 297 GLN cc_start: 0.8421 (tp40) cc_final: 0.8216 (tt0) REVERT: H 299 LYS cc_start: 0.8375 (mmpt) cc_final: 0.8107 (mppt) REVERT: H 471 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8722 (p) REVERT: H 511 LYS cc_start: 0.7369 (tttm) cc_final: 0.6719 (ttpp) REVERT: H 515 GLU cc_start: 0.7885 (tt0) cc_final: 0.7598 (tm-30) REVERT: I 160 MET cc_start: 0.1451 (mmm) cc_final: 0.0683 (tpt) REVERT: I 339 ARG cc_start: 0.1263 (ptt-90) cc_final: 0.1045 (ptp90) REVERT: I 378 GLN cc_start: 0.3617 (mt0) cc_final: 0.3058 (mm-40) REVERT: I 396 MET cc_start: 0.4547 (OUTLIER) cc_final: 0.3864 (ttp) REVERT: I 464 HIS cc_start: 0.4419 (m170) cc_final: 0.3888 (t-170) REVERT: I 476 HIS cc_start: 0.1129 (t-90) cc_final: 0.0832 (t70) REVERT: I 630 ASP cc_start: 0.8152 (t0) cc_final: 0.7557 (m-30) REVERT: I 653 MET cc_start: 0.5242 (OUTLIER) cc_final: 0.4799 (mmm) REVERT: I 677 MET cc_start: 0.4498 (OUTLIER) cc_final: 0.4182 (ppp) REVERT: I 680 MET cc_start: 0.6351 (mmm) cc_final: 0.5954 (tpp) REVERT: J 34 GLN cc_start: 0.7548 (tp40) cc_final: 0.7323 (tp-100) REVERT: J 61 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: J 130 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8542 (mt-10) REVERT: J 213 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8226 (mtt) REVERT: J 259 ASP cc_start: 0.7749 (m-30) cc_final: 0.6783 (p0) REVERT: J 308 GLU cc_start: 0.8422 (tt0) cc_final: 0.8191 (tt0) REVERT: J 324 ASN cc_start: 0.8316 (t0) cc_final: 0.8039 (t0) REVERT: J 511 LYS cc_start: 0.6579 (tttm) cc_final: 0.6351 (ttmt) REVERT: J 514 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: J 515 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7102 (mm-30) REVERT: K 69 LYS cc_start: 0.3615 (mttm) cc_final: 0.3065 (tmmm) REVERT: K 136 MET cc_start: 0.1740 (ptt) cc_final: 0.0529 (tmt) REVERT: K 274 ARG cc_start: 0.2809 (OUTLIER) cc_final: 0.2445 (ptt-90) REVERT: K 415 ARG cc_start: 0.3047 (tpp80) cc_final: 0.2758 (mtt180) REVERT: K 635 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7787 (pmtt) REVERT: K 650 LEU cc_start: 0.3295 (OUTLIER) cc_final: 0.2356 (pt) REVERT: K 653 MET cc_start: 0.2260 (OUTLIER) cc_final: 0.1591 (ttp) REVERT: K 675 MET cc_start: 0.3321 (ttp) cc_final: 0.3105 (ttp) REVERT: L 47 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7821 (mptt) REVERT: L 64 LYS cc_start: 0.8344 (tttt) cc_final: 0.8035 (ttpt) REVERT: L 69 GLU cc_start: 0.7141 (tp30) cc_final: 0.6659 (tp30) REVERT: L 99 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: L 234 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6761 (ppp80) REVERT: L 235 LYS cc_start: 0.7458 (mttt) cc_final: 0.6865 (tmtt) REVERT: L 268 ARG cc_start: 0.6879 (mpt-90) cc_final: 0.5773 (mpt-90) REVERT: L 297 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8081 (tt0) outliers start: 100 outliers final: 48 residues processed: 513 average time/residue: 0.4616 time to fit residues: 290.0017 Evaluate side-chains 508 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 434 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 425 MET Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 683 GLU Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 471 SER Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 396 MET Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 635 LYS Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 677 MET Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 213 MET Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 514 GLU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 274 ARG Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain K residue 448 LEU Chi-restraints excluded: chain K residue 628 GLU Chi-restraints excluded: chain K residue 635 LYS Chi-restraints excluded: chain K residue 650 LEU Chi-restraints excluded: chain K residue 653 MET Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 58 GLU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 234 ARG Chi-restraints excluded: chain L residue 297 GLN Chi-restraints excluded: chain L residue 557 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 444 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 378 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 175 optimal weight: 7.9990 chunk 245 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 363 optimal weight: 3.9990 chunk 234 optimal weight: 20.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A 616 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN D 236 GLN D 297 GLN F 297 GLN ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 493 HIS H 230 ASN H 480 ASN I 265 HIS K 464 HIS L 75 HIS L 324 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.215164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123336 restraints weight = 46482.455| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.08 r_work: 0.3263 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 44580 Z= 0.130 Angle : 0.578 12.703 60255 Z= 0.299 Chirality : 0.045 0.183 6663 Planarity : 0.004 0.052 7815 Dihedral : 8.691 89.131 6600 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.11 % Allowed : 15.96 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.11), residues: 5586 helix: 1.65 (0.12), residues: 2106 sheet: 0.53 (0.15), residues: 1101 loop : -0.95 (0.13), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 158 TYR 0.018 0.001 TYR H 457 PHE 0.021 0.001 PHE G 395 TRP 0.017 0.001 TRP L 276 HIS 0.006 0.001 HIS G 344 Details of bonding type rmsd covalent geometry : bond 0.00294 (44574) covalent geometry : angle 0.57797 (60255) hydrogen bonds : bond 0.04068 ( 2064) hydrogen bonds : angle 4.48432 ( 5823) Misc. bond : bond 0.00014 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 439 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.7420 (ttp) cc_final: 0.7159 (ttm) REVERT: A 556 LYS cc_start: 0.7545 (mtpp) cc_final: 0.6966 (mmmt) REVERT: A 559 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6377 (tptp) REVERT: A 561 ASN cc_start: 0.8285 (m-40) cc_final: 0.8027 (m110) REVERT: A 675 MET cc_start: 0.4455 (mtt) cc_final: 0.3951 (mpt) REVERT: B 58 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: B 74 LEU cc_start: 0.8313 (tp) cc_final: 0.8047 (tp) REVERT: B 326 LYS cc_start: 0.7420 (mmmt) cc_final: 0.6555 (mptt) REVERT: B 353 ASP cc_start: 0.8209 (p0) cc_final: 0.7890 (p0) REVERT: B 408 MET cc_start: 0.5606 (tpt) cc_final: 0.4837 (tpp) REVERT: C 556 LYS cc_start: 0.6847 (tttt) cc_final: 0.6376 (ptpt) REVERT: D 43 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7834 (mt0) REVERT: D 141 LYS cc_start: 0.8046 (tptt) cc_final: 0.7643 (mmmm) REVERT: D 234 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6383 (ptp90) REVERT: D 235 LYS cc_start: 0.8063 (mttt) cc_final: 0.7708 (pptt) REVERT: D 276 TRP cc_start: 0.8529 (t60) cc_final: 0.8065 (t60) REVERT: D 299 LYS cc_start: 0.8690 (pttm) cc_final: 0.8342 (mmpt) REVERT: D 393 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: D 414 GLU cc_start: 0.6308 (mm-30) cc_final: 0.6025 (mm-30) REVERT: D 563 MET cc_start: 0.7842 (mmt) cc_final: 0.7582 (mmt) REVERT: F 57 HIS cc_start: 0.8139 (t-170) cc_final: 0.6931 (m90) REVERT: F 69 GLU cc_start: 0.6177 (pp20) cc_final: 0.5935 (tm-30) REVERT: F 178 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7741 (mm) REVERT: F 189 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.6887 (m-30) REVERT: F 425 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8397 (ttt) REVERT: F 476 GLU cc_start: 0.5683 (mt-10) cc_final: 0.5165 (pm20) REVERT: F 563 MET cc_start: 0.7977 (mmt) cc_final: 0.7712 (mmt) REVERT: G 84 ARG cc_start: 0.6002 (ttm170) cc_final: 0.5649 (mtm180) REVERT: G 86 SER cc_start: 0.2291 (t) cc_final: 0.1892 (p) REVERT: G 158 ARG cc_start: 0.5194 (mtt-85) cc_final: 0.4735 (tmm-80) REVERT: G 160 MET cc_start: 0.1573 (ptt) cc_final: 0.1367 (ptt) REVERT: G 287 GLU cc_start: 0.3751 (OUTLIER) cc_final: 0.2717 (tp30) REVERT: G 406 SER cc_start: 0.7003 (t) cc_final: 0.6604 (m) REVERT: G 457 GLN cc_start: 0.4976 (mt0) cc_final: 0.4622 (mt0) REVERT: G 579 GLU cc_start: 0.8000 (tt0) cc_final: 0.7462 (tp30) REVERT: G 614 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7536 (tp) REVERT: G 635 LYS cc_start: 0.8155 (mttt) cc_final: 0.7685 (tptp) REVERT: H 44 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: H 299 LYS cc_start: 0.8372 (mmpt) cc_final: 0.8118 (mppt) REVERT: H 471 SER cc_start: 0.9012 (OUTLIER) cc_final: 0.8792 (p) REVERT: H 511 LYS cc_start: 0.7413 (tttm) cc_final: 0.6741 (ttpp) REVERT: H 515 GLU cc_start: 0.7911 (tt0) cc_final: 0.7640 (tm-30) REVERT: I 136 MET cc_start: 0.2915 (ptp) cc_final: 0.2658 (pmm) REVERT: I 160 MET cc_start: 0.1543 (mmm) cc_final: 0.0880 (tpt) REVERT: I 325 MET cc_start: 0.4574 (ppp) cc_final: 0.3858 (pmm) REVERT: I 339 ARG cc_start: 0.1430 (ptt-90) cc_final: 0.1187 (ptp90) REVERT: I 378 GLN cc_start: 0.3756 (mt0) cc_final: 0.3094 (mm-40) REVERT: I 396 MET cc_start: 0.4483 (OUTLIER) cc_final: 0.3811 (ttp) REVERT: I 464 HIS cc_start: 0.4519 (m170) cc_final: 0.3926 (t70) REVERT: I 630 ASP cc_start: 0.8216 (t0) cc_final: 0.7623 (m-30) REVERT: I 653 MET cc_start: 0.5370 (OUTLIER) cc_final: 0.4888 (mmm) REVERT: I 677 MET cc_start: 0.4738 (OUTLIER) cc_final: 0.4339 (ppp) REVERT: I 680 MET cc_start: 0.6412 (mmm) cc_final: 0.6004 (tpp) REVERT: J 34 GLN cc_start: 0.7593 (tp40) cc_final: 0.7380 (tp-100) REVERT: J 43 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7425 (mt0) REVERT: J 61 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: J 130 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8485 (mt-10) REVERT: J 213 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8268 (mtt) REVERT: J 259 ASP cc_start: 0.7773 (m-30) cc_final: 0.6746 (p0) REVERT: J 308 GLU cc_start: 0.8347 (tt0) cc_final: 0.8094 (tt0) REVERT: J 324 ASN cc_start: 0.8452 (t0) cc_final: 0.8221 (t0) REVERT: J 511 LYS cc_start: 0.6684 (tttm) cc_final: 0.6451 (ttmt) REVERT: J 514 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6935 (tm-30) REVERT: J 515 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7117 (mm-30) REVERT: K 136 MET cc_start: 0.1747 (ptt) cc_final: 0.0457 (tmt) REVERT: K 274 ARG cc_start: 0.2922 (OUTLIER) cc_final: 0.2532 (ptt-90) REVERT: K 402 LEU cc_start: 0.4347 (mp) cc_final: 0.4107 (mp) REVERT: K 415 ARG cc_start: 0.3121 (tpp80) cc_final: 0.2809 (mtt180) REVERT: K 635 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7743 (pmtt) REVERT: K 650 LEU cc_start: 0.3359 (OUTLIER) cc_final: 0.2424 (pt) REVERT: K 653 MET cc_start: 0.2214 (OUTLIER) cc_final: 0.1564 (ttp) REVERT: K 675 MET cc_start: 0.3378 (ttp) cc_final: 0.3164 (ttp) REVERT: L 64 LYS cc_start: 0.8337 (tttt) cc_final: 0.8060 (ttpm) REVERT: L 69 GLU cc_start: 0.7198 (tp30) cc_final: 0.6709 (tp30) REVERT: L 99 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: L 234 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6793 (ppp80) REVERT: L 235 LYS cc_start: 0.7398 (mttt) cc_final: 0.6787 (tmtt) REVERT: L 268 ARG cc_start: 0.6908 (mpt-90) cc_final: 0.5858 (mpt-90) REVERT: L 297 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8100 (tt0) outliers start: 97 outliers final: 51 residues processed: 499 average time/residue: 0.4787 time to fit residues: 290.2550 Evaluate side-chains 498 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 422 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 425 MET Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 683 GLU Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 471 SER Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 396 MET Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 635 LYS Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 677 MET Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 213 MET Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 514 GLU Chi-restraints excluded: chain K residue 87 MET Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 274 ARG Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain K residue 448 LEU Chi-restraints excluded: chain K residue 628 GLU Chi-restraints excluded: chain K residue 635 LYS Chi-restraints excluded: chain K residue 650 LEU Chi-restraints excluded: chain K residue 653 MET Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 58 GLU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 234 ARG Chi-restraints excluded: chain L residue 297 GLN Chi-restraints excluded: chain L residue 557 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 302 optimal weight: 4.9990 chunk 487 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 539 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 243 optimal weight: 20.0000 chunk 403 optimal weight: 3.9990 chunk 413 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 246 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A 616 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN D 236 GLN D 297 GLN F 297 GLN ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN I 265 HIS I 485 HIS ** K 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.213771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119919 restraints weight = 46780.208| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.17 r_work: 0.3236 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 44580 Z= 0.177 Angle : 0.623 12.587 60255 Z= 0.323 Chirality : 0.046 0.198 6663 Planarity : 0.005 0.054 7815 Dihedral : 8.757 85.227 6600 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.92 % Allowed : 16.20 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.11), residues: 5586 helix: 1.42 (0.11), residues: 2142 sheet: 0.50 (0.15), residues: 1101 loop : -1.01 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 525 TYR 0.023 0.002 TYR D 296 PHE 0.019 0.002 PHE G 323 TRP 0.014 0.001 TRP L 276 HIS 0.006 0.001 HIS G 88 Details of bonding type rmsd covalent geometry : bond 0.00415 (44574) covalent geometry : angle 0.62283 (60255) hydrogen bonds : bond 0.04736 ( 2064) hydrogen bonds : angle 4.62374 ( 5823) Misc. bond : bond 0.00022 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 441 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LYS cc_start: 0.7416 (mtpp) cc_final: 0.6866 (mmmt) REVERT: A 559 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6460 (tptp) REVERT: A 561 ASN cc_start: 0.8277 (m-40) cc_final: 0.7959 (m110) REVERT: A 675 MET cc_start: 0.4421 (mtt) cc_final: 0.3872 (mpt) REVERT: B 36 ASP cc_start: 0.7934 (t70) cc_final: 0.7600 (t70) REVERT: B 58 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: B 377 PHE cc_start: 0.7955 (m-80) cc_final: 0.7629 (m-80) REVERT: B 408 MET cc_start: 0.5587 (tpt) cc_final: 0.4833 (tpp) REVERT: B 480 ASN cc_start: 0.7004 (m-40) cc_final: 0.6796 (m-40) REVERT: C 556 LYS cc_start: 0.6956 (tttt) cc_final: 0.6460 (ptpt) REVERT: D 43 GLN cc_start: 0.8357 (mm-40) cc_final: 0.7862 (mt0) REVERT: D 141 LYS cc_start: 0.8047 (tptt) cc_final: 0.7641 (mmmm) REVERT: D 234 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.6389 (ptp90) REVERT: D 235 LYS cc_start: 0.8088 (mttt) cc_final: 0.7735 (pptt) REVERT: D 276 TRP cc_start: 0.8551 (t60) cc_final: 0.8051 (t60) REVERT: D 299 LYS cc_start: 0.8716 (pttm) cc_final: 0.8383 (mmpt) REVERT: D 393 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: D 414 GLU cc_start: 0.6355 (mm-30) cc_final: 0.6101 (mm-30) REVERT: D 563 MET cc_start: 0.7848 (mmt) cc_final: 0.7595 (mmt) REVERT: F 57 HIS cc_start: 0.8134 (t-170) cc_final: 0.6992 (m90) REVERT: F 69 GLU cc_start: 0.6152 (OUTLIER) cc_final: 0.5898 (tm-30) REVERT: F 88 ASP cc_start: 0.8323 (p0) cc_final: 0.8037 (p0) REVERT: F 563 MET cc_start: 0.7970 (mmt) cc_final: 0.7714 (mmt) REVERT: G 84 ARG cc_start: 0.5868 (ttm170) cc_final: 0.5501 (mtm-85) REVERT: G 86 SER cc_start: 0.2452 (t) cc_final: 0.2026 (p) REVERT: G 261 PHE cc_start: 0.3755 (OUTLIER) cc_final: 0.3401 (m-80) REVERT: G 287 GLU cc_start: 0.3712 (OUTLIER) cc_final: 0.2715 (tp30) REVERT: G 406 SER cc_start: 0.6944 (t) cc_final: 0.6497 (m) REVERT: G 433 MET cc_start: 0.3547 (ttm) cc_final: 0.3270 (tmm) REVERT: G 579 GLU cc_start: 0.8112 (tt0) cc_final: 0.7524 (tp30) REVERT: G 614 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7422 (tp) REVERT: G 635 LYS cc_start: 0.8165 (mttt) cc_final: 0.7686 (tptp) REVERT: H 44 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: H 299 LYS cc_start: 0.8355 (mmpt) cc_final: 0.8115 (mppt) REVERT: H 473 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8281 (mtt) REVERT: H 511 LYS cc_start: 0.7386 (tttm) cc_final: 0.6704 (ttpp) REVERT: H 515 GLU cc_start: 0.7941 (tt0) cc_final: 0.7657 (tm-30) REVERT: I 136 MET cc_start: 0.2896 (ptp) cc_final: 0.2621 (pmm) REVERT: I 339 ARG cc_start: 0.1614 (ptt-90) cc_final: 0.1381 (ptp90) REVERT: I 378 GLN cc_start: 0.3877 (mt0) cc_final: 0.3167 (mm-40) REVERT: I 396 MET cc_start: 0.4457 (OUTLIER) cc_final: 0.3794 (ttp) REVERT: I 459 ASN cc_start: 0.3122 (m-40) cc_final: 0.2803 (m-40) REVERT: I 595 CYS cc_start: 0.6539 (m) cc_final: 0.6336 (m) REVERT: I 630 ASP cc_start: 0.8184 (t0) cc_final: 0.7598 (m-30) REVERT: I 653 MET cc_start: 0.5554 (OUTLIER) cc_final: 0.5047 (mmm) REVERT: I 680 MET cc_start: 0.6450 (mmm) cc_final: 0.5858 (mmm) REVERT: J 61 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: J 130 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8492 (mt-10) REVERT: J 213 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8430 (mtt) REVERT: J 259 ASP cc_start: 0.7796 (m-30) cc_final: 0.6766 (p0) REVERT: J 324 ASN cc_start: 0.8486 (t0) cc_final: 0.8238 (t0) REVERT: J 511 LYS cc_start: 0.6589 (tttm) cc_final: 0.6357 (ttmt) REVERT: J 514 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6921 (tm-30) REVERT: J 515 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7107 (mm-30) REVERT: K 136 MET cc_start: 0.1708 (ptt) cc_final: 0.0420 (tmt) REVERT: K 635 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7715 (pmtt) REVERT: K 650 LEU cc_start: 0.3276 (OUTLIER) cc_final: 0.2348 (pt) REVERT: K 653 MET cc_start: 0.2334 (OUTLIER) cc_final: 0.1659 (ttp) REVERT: K 675 MET cc_start: 0.3406 (ttp) cc_final: 0.3177 (ttp) REVERT: L 64 LYS cc_start: 0.8402 (tttt) cc_final: 0.8138 (ttpm) REVERT: L 69 GLU cc_start: 0.7244 (tp30) cc_final: 0.6742 (tp30) REVERT: L 99 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: L 234 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6856 (ppp80) REVERT: L 235 LYS cc_start: 0.7389 (mttt) cc_final: 0.6861 (tmtt) REVERT: L 268 ARG cc_start: 0.6908 (mpt-90) cc_final: 0.5859 (mpt-90) REVERT: L 297 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: L 473 MET cc_start: 0.8246 (ptp) cc_final: 0.7947 (ptm) REVERT: L 511 LYS cc_start: 0.7241 (tttm) cc_final: 0.6599 (tmtt) outliers start: 88 outliers final: 56 residues processed: 494 average time/residue: 0.5015 time to fit residues: 300.6877 Evaluate side-chains 505 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 427 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 554 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 473 MET Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 396 MET Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 635 LYS Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 213 MET Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 514 GLU Chi-restraints excluded: chain K residue 87 MET Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 274 ARG Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain K residue 448 LEU Chi-restraints excluded: chain K residue 628 GLU Chi-restraints excluded: chain K residue 635 LYS Chi-restraints excluded: chain K residue 650 LEU Chi-restraints excluded: chain K residue 653 MET Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 58 GLU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 234 ARG Chi-restraints excluded: chain L residue 297 GLN Chi-restraints excluded: chain L residue 557 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 247 optimal weight: 0.7980 chunk 223 optimal weight: 3.9990 chunk 380 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 453 optimal weight: 5.9990 chunk 177 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 548 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A 616 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 480 ASN D 236 GLN D 297 GLN F 297 GLN ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN J 34 GLN ** K 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.214950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122135 restraints weight = 46933.319| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.12 r_work: 0.3254 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 44580 Z= 0.141 Angle : 0.587 12.309 60255 Z= 0.304 Chirality : 0.045 0.211 6663 Planarity : 0.004 0.052 7815 Dihedral : 8.608 81.542 6600 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.90 % Allowed : 16.31 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.11), residues: 5586 helix: 1.64 (0.12), residues: 2088 sheet: 0.59 (0.15), residues: 1095 loop : -0.93 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 234 TYR 0.019 0.001 TYR B 457 PHE 0.019 0.001 PHE G 323 TRP 0.015 0.001 TRP L 276 HIS 0.005 0.001 HIS I 464 Details of bonding type rmsd covalent geometry : bond 0.00325 (44574) covalent geometry : angle 0.58689 (60255) hydrogen bonds : bond 0.04155 ( 2064) hydrogen bonds : angle 4.51875 ( 5823) Misc. bond : bond 0.00023 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22732.56 seconds wall clock time: 384 minutes 17.18 seconds (23057.18 seconds total)