Starting phenix.real_space_refine on Wed Aug 27 01:04:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xl6_38439/08_2025/8xl6_38439.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xl6_38439/08_2025/8xl6_38439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xl6_38439/08_2025/8xl6_38439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xl6_38439/08_2025/8xl6_38439.map" model { file = "/net/cci-nas-00/data/ceres_data/8xl6_38439/08_2025/8xl6_38439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xl6_38439/08_2025/8xl6_38439.cif" } resolution = 2.29 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= -0.001 sd= 0.107 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: 4 Type Number sf(0) Gaussians S 248 5.16 5 C 28211 2.51 5 N 7777 2.21 5 O 8376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44612 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5121 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 28, 'TRANS': 631} 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: 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: "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: 5121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5121 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 28, 'TRANS': 631} 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: 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: "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: 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: "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: 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: "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: "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: "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: "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: "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: "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 Time building chain proxies: 9.92, per 1000 atoms: 0.22 Number of scatterers: 44612 At special positions: 0 Unit cell: (149.745, 161.595, 190.682, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 248 16.00 O 8376 8.00 N 7777 7.00 C 28211 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: 3.07 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 715.3 nanoseconds 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10544 Finding SS restraints... Secondary structure from input PDB file: 219 helices and 59 sheets defined 41.0% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 57 through 72 removed outlier: 3.752A pdb=" N ALA A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 removed outlier: 4.044A pdb=" N ASP A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 109 through 120 removed outlier: 3.947A pdb=" N ILE A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 153 through 159 removed outlier: 4.083A pdb=" N ASP A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.528A pdb=" N SER A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 313 Processing helix chain 'A' and resid 343 through 352 removed outlier: 4.250A pdb=" N THR A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET A 349 " --> pdb=" O PRO A 345 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.904A pdb=" N ILE A 375 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 493 through 496 Processing helix chain 'A' and resid 504 through 529 removed outlier: 3.771A 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: 4.064A pdb=" N LEU B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 4.265A 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 144 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: 3.702A 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: 3.628A 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: 4.003A 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 57 through 72 removed outlier: 3.754A pdb=" N ALA C 61 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 removed outlier: 4.043A pdb=" N ASP C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 109 through 120 removed outlier: 3.947A pdb=" N ILE C 113 " --> pdb=" O SER C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 153 through 159 removed outlier: 4.082A pdb=" N ASP C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 172 Processing helix chain 'C' and resid 295 through 313 Processing helix chain 'C' and resid 343 through 352 removed outlier: 4.251A pdb=" N THR C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 364 Processing helix chain 'C' and resid 371 through 375 removed outlier: 3.903A pdb=" N ILE C 375 " --> pdb=" O GLN C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 394 Processing helix chain 'C' and resid 443 through 456 Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 482 Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 493 through 496 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: 4.065A pdb=" N LEU D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 4.267A 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 144 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: 3.589A 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: 3.816A 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: 3.627A pdb=" N TYR D 457 " --> pdb=" O GLY D 454 " (cutoff:3.500A) removed outlier: 3.586A 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: 4.003A 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 57 through 72 removed outlier: 3.753A pdb=" N ALA E 61 " --> pdb=" O ARG E 57 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 92 removed outlier: 4.044A pdb=" N ASP E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'E' and resid 109 through 120 removed outlier: 3.947A pdb=" N ILE E 113 " --> pdb=" O SER E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 146 Processing helix chain 'E' and resid 153 through 159 removed outlier: 4.081A pdb=" N ASP E 159 " --> pdb=" O SER E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 172 Processing helix chain 'E' and resid 187 through 199 Processing helix chain 'E' and resid 223 through 234 Processing helix chain 'E' and resid 234 through 239 removed outlier: 3.527A pdb=" N SER E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 313 Processing helix chain 'E' and resid 343 through 352 removed outlier: 4.250A pdb=" N THR E 347 " --> pdb=" O GLU E 343 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET E 349 " --> pdb=" O PRO E 345 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 364 Processing helix chain 'E' and resid 371 through 375 removed outlier: 3.904A pdb=" N ILE E 375 " --> pdb=" O GLN E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 394 Processing helix chain 'E' and resid 443 through 456 Processing helix chain 'E' and resid 466 through 475 Processing helix chain 'E' and resid 476 through 482 Processing helix chain 'E' and resid 487 through 492 Processing helix chain 'E' and resid 493 through 496 Processing helix chain 'E' and resid 504 through 529 removed outlier: 3.772A 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: 4.065A pdb=" N LEU F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 4.267A 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 144 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: 4.044A 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: 3.588A 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: 3.816A 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: 3.628A pdb=" N TYR F 457 " --> pdb=" O GLY F 454 " (cutoff:3.500A) removed outlier: 3.586A 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: 4.002A 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 504 through 529 removed outlier: 3.771A 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: 4.267A 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 144 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: 4.044A pdb=" N ARG H 337 " --> pdb=" O GLU H 333 " (cutoff:3.500A) removed outlier: 3.701A 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: 3.816A 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: 3.627A pdb=" N TYR H 457 " --> pdb=" O GLY H 454 " (cutoff:3.500A) removed outlier: 3.586A 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 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: 4.267A 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 144 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: 3.589A 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: 3.816A 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: 3.587A 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 504 through 529 removed outlier: 3.772A 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: 4.065A 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 144 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: 4.044A pdb=" N ARG L 337 " --> pdb=" O GLU L 333 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL L 339 " --> pdb=" O ILE L 335 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 343 removed outlier: 3.588A 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: 3.627A pdb=" N TYR L 457 " --> pdb=" O GLY L 454 " (cutoff:3.500A) removed outlier: 3.586A 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: 4.003A 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 148 through 149 removed outlier: 4.023A pdb=" N VAL A 78 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR A 75 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N TYR A 96 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA A 77 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 95 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY C 625 " --> pdb=" O SER C 622 " (cutoff:3.500A) 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) Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 218 Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 275 removed outlier: 5.477A pdb=" N TYR A 270 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE A 261 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE A 272 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN A 259 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE A 324 " --> pdb=" O PHE A 333 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N PHE A 333 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 279 through 280 Processing sheet with id=AA5, first strand: chain 'A' and resid 286 through 288 removed outlier: 6.726A pdb=" N HIS A 380 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP A 440 " --> pdb=" O HIS A 380 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE A 382 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL A 438 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA A 384 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS A 436 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE A 386 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 390 removed outlier: 3.670A pdb=" N MET A 396 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 404 through 406 Processing sheet with id=AA8, first strand: chain 'E' and resid 148 through 149 removed outlier: 4.024A pdb=" N VAL E 78 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR E 75 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N TYR E 96 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA E 77 " --> pdb=" O TYR E 96 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E 95 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY A 625 " --> pdb=" O SER A 622 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR A 549 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing sheet with id=AA9, 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: 6.866A pdb=" N VAL A 676 " --> pdb=" O GLU A 658 " (cutoff:3.500A) Processing sheet with id=AB1, 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=AB2, 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: 8.493A pdb=" N ILE B 168 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N MET B 132 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.814A 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: 3.512A pdb=" N VAL B 233 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.844A 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: 6.481A pdb=" N ILE B 232 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AB3, 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=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 345 through 347 removed outlier: 4.722A pdb=" N THR B 357 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 7.565A 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: 7.589A pdb=" N LEU B 401 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL B 370 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE B 461 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing sheet with id=AB5, 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=AB6, first strand: chain 'C' and resid 148 through 149 removed outlier: 4.023A pdb=" N VAL C 78 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR C 75 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N TYR C 96 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA C 77 " --> pdb=" O TYR C 96 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 95 " --> pdb=" O ALA E 606 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY E 625 " --> pdb=" O SER E 622 " (cutoff:3.500A) removed outlier: 4.620A 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) Processing sheet with id=AB7, first strand: chain 'C' and resid 268 through 275 removed outlier: 5.477A pdb=" N TYR C 270 " --> pdb=" O PHE C 261 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE C 261 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE C 272 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN C 259 " --> pdb=" O PHE C 272 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE C 324 " --> pdb=" O PHE C 333 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N PHE C 333 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 279 through 280 Processing sheet with id=AB9, first strand: chain 'C' and resid 286 through 288 removed outlier: 6.726A pdb=" N HIS C 380 " --> pdb=" O TRP C 440 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP C 440 " --> pdb=" O HIS C 380 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE C 382 " --> pdb=" O VAL C 438 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL C 438 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA C 384 " --> pdb=" O LYS C 436 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS C 436 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE C 386 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 389 through 390 removed outlier: 3.670A pdb=" N MET C 396 " --> pdb=" O ASP C 390 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 404 through 406 Processing sheet with id=AC3, first strand: chain 'C' and resid 683 through 686 removed outlier: 4.308A pdb=" N MET C 675 " --> pdb=" O ILE C 686 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 676 " --> pdb=" O GLU C 658 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 694 through 697 removed outlier: 6.903A pdb=" N GLU C 713 " --> pdb=" O LYS C 695 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.662A pdb=" N THR D 121 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 8.493A 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: 7.815A 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: 3.616A 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: 6.844A 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=AC6, 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=AC6 Processing sheet with id=AC7, 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: 7.564A pdb=" N LEU D 399 " --> pdb=" O PRO D 366 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLY D 368 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU D 401 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL D 370 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE D 461 " --> pdb=" O LYS D 436 " (cutoff:3.500A) Processing sheet with id=AC8, 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=AC9, first strand: chain 'E' and resid 216 through 218 Processing sheet with id=AD1, first strand: chain 'E' and resid 268 through 275 removed outlier: 5.478A pdb=" N TYR E 270 " --> pdb=" O PHE E 261 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE E 261 " --> pdb=" O TYR E 270 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE E 272 " --> pdb=" O GLN E 259 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN E 259 " --> pdb=" O PHE E 272 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE E 324 " --> pdb=" O PHE E 333 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N PHE E 333 " --> pdb=" O ILE E 324 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 279 through 280 Processing sheet with id=AD3, first strand: chain 'E' and resid 286 through 288 removed outlier: 6.726A pdb=" N HIS E 380 " --> pdb=" O TRP E 440 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP E 440 " --> pdb=" O HIS E 380 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE E 382 " --> pdb=" O VAL E 438 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL E 438 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA E 384 " --> pdb=" O LYS E 436 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS E 436 " --> pdb=" O ALA E 384 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE E 386 " --> pdb=" O ILE E 434 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 389 through 390 removed outlier: 3.670A pdb=" N MET E 396 " --> pdb=" O ASP E 390 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 404 through 406 Processing sheet with id=AD6, first strand: chain 'E' and resid 683 through 686 removed outlier: 4.309A pdb=" N MET E 675 " --> pdb=" O ILE E 686 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL E 676 " --> pdb=" O GLU E 658 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 694 through 697 removed outlier: 6.902A pdb=" N GLU E 713 " --> pdb=" O LYS E 695 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 98 through 100 removed outlier: 4.663A pdb=" N THR F 121 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ILE F 168 " --> pdb=" O GLU F 130 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N MET F 132 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 7.814A 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: 3.616A pdb=" N ALA F 210 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL F 233 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 6.844A 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: 6.480A pdb=" N ILE F 232 " --> pdb=" O ALA F 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 215 through 217 removed outlier: 6.662A pdb=" N CYS F 216 " --> pdb=" O PHE F 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, 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: 7.565A 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=AE2, first strand: chain 'F' and resid 443 through 445 removed outlier: 3.511A pdb=" N SER F 471 " --> pdb=" O SER F 444 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 549 through 557 removed outlier: 4.619A pdb=" N TYR G 549 " --> pdb=" O TYR G 568 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR G 596 " --> pdb=" O LEU G 611 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY G 625 " --> pdb=" O SER G 622 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 683 through 686 removed outlier: 4.310A pdb=" N MET G 675 " --> pdb=" O ILE G 686 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL G 676 " --> pdb=" O GLU G 658 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 694 through 697 removed outlier: 6.902A pdb=" N GLU G 713 " --> pdb=" O LYS G 695 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 98 through 100 removed outlier: 4.663A pdb=" N THR H 121 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ILE H 168 " --> pdb=" O GLU H 130 " (cutoff:3.500A) removed outlier: 6.292A 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: 3.616A 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: 6.844A pdb=" N ASN H 230 " --> pdb=" O HIS H 275 " (cutoff:3.500A) removed outlier: 8.031A 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=AE7, first strand: chain 'H' and resid 215 through 217 removed outlier: 6.661A pdb=" N CYS H 216 " --> pdb=" O PHE H 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, 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: 6.312A pdb=" N GLY H 368 " --> pdb=" O LEU H 399 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU H 401 " --> pdb=" O GLY H 368 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL H 370 " --> pdb=" O LEU H 401 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE H 461 " --> pdb=" O LYS H 436 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 443 through 445 removed outlier: 3.510A pdb=" N SER H 471 " --> pdb=" O SER H 444 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 549 through 557 removed outlier: 4.619A 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) removed outlier: 3.758A pdb=" N GLY I 625 " --> pdb=" O SER I 622 " (cutoff:3.500A) Processing sheet with id=AF2, 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=AF3, 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=AF4, first strand: chain 'J' and resid 98 through 100 removed outlier: 4.664A 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: 6.292A pdb=" N MET J 132 " --> pdb=" O ILE J 168 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU J 170 " --> pdb=" O MET J 132 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE J 134 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA J 210 " --> pdb=" O GLU J 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL J 233 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN J 230 " --> pdb=" O HIS J 275 " (cutoff:3.500A) removed outlier: 8.030A 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=AF5, 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=AF5 Processing sheet with id=AF6, first strand: chain 'J' and resid 345 through 347 removed outlier: 4.720A 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=AF7, first strand: chain 'J' and resid 443 through 445 removed outlier: 3.510A pdb=" N SER J 471 " --> pdb=" O SER J 444 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 549 through 557 removed outlier: 4.619A pdb=" N TYR K 549 " --> pdb=" O TYR K 568 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR K 596 " --> pdb=" O LEU K 611 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY K 625 " --> pdb=" O SER K 622 " (cutoff:3.500A) Processing sheet with id=AF9, 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: 6.868A pdb=" N VAL K 676 " --> pdb=" O GLU K 658 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 694 through 697 removed outlier: 6.902A pdb=" N GLU K 713 " --> pdb=" O LYS K 695 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 98 through 100 removed outlier: 4.663A pdb=" N THR L 121 " --> pdb=" O LEU L 100 " (cutoff:3.500A) removed outlier: 8.493A 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: 7.814A pdb=" N LEU L 170 " --> pdb=" O MET L 132 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE L 134 " --> pdb=" O LEU L 170 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA L 210 " --> pdb=" O GLU L 229 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL L 233 " --> pdb=" O VAL L 212 " (cutoff:3.500A) removed outlier: 6.843A 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=AG3, first strand: chain 'L' and resid 215 through 217 removed outlier: 6.662A pdb=" N CYS L 216 " --> pdb=" O PHE L 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'L' and resid 345 through 347 removed outlier: 4.720A 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: 6.312A pdb=" N GLY L 368 " --> pdb=" O LEU L 399 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU L 401 " --> pdb=" O GLY L 368 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL L 370 " --> pdb=" O LEU L 401 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE L 461 " --> pdb=" O LYS L 436 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 443 through 445 removed outlier: 3.510A pdb=" N SER L 471 " --> pdb=" O SER L 444 " (cutoff:3.500A) 2119 hydrogen bonds defined for protein. 5940 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: 11.38 Time building geometry restraints manager: 4.24 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: 7704 1.31 - 1.44: 11408 1.44 - 1.56: 25953 1.56 - 1.69: 6 1.69 - 1.81: 407 Bond restraints: 45478 Sorted by residual: bond pdb=" C3 BTN C 801 " pdb=" O3 BTN C 801 " ideal model delta sigma weight residual 1.220 1.404 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" C3 BTN G 801 " pdb=" O3 BTN G 801 " ideal model delta sigma weight residual 1.220 1.404 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" C3 BTN A 801 " pdb=" O3 BTN A 801 " ideal model delta sigma weight residual 1.220 1.404 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" C3 BTN K 801 " pdb=" O3 BTN K 801 " ideal model delta sigma weight residual 1.220 1.404 -0.184 2.00e-02 2.50e+03 8.46e+01 bond pdb=" C3 BTN E 801 " pdb=" O3 BTN E 801 " ideal model delta sigma weight residual 1.220 1.404 -0.184 2.00e-02 2.50e+03 8.43e+01 ... (remaining 45473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 59504 2.48 - 4.97: 1669 4.97 - 7.45: 173 7.45 - 9.93: 60 9.93 - 12.41: 9 Bond angle restraints: 61415 Sorted by residual: angle pdb=" N PHE E 395 " pdb=" CA PHE E 395 " pdb=" C PHE E 395 " ideal model delta sigma weight residual 111.52 123.93 -12.41 1.40e+00 5.10e-01 7.86e+01 angle pdb=" N PHE C 395 " pdb=" CA PHE C 395 " pdb=" C PHE C 395 " ideal model delta sigma weight residual 111.52 123.93 -12.41 1.40e+00 5.10e-01 7.85e+01 angle pdb=" N PHE A 395 " pdb=" CA PHE A 395 " pdb=" C PHE A 395 " ideal model delta sigma weight residual 111.52 123.88 -12.36 1.40e+00 5.10e-01 7.79e+01 angle pdb=" C ASN A 394 " pdb=" N PHE A 395 " pdb=" CA PHE A 395 " ideal model delta sigma weight residual 122.34 131.10 -8.76 1.39e+00 5.18e-01 3.97e+01 angle pdb=" C ASN C 394 " pdb=" N PHE C 395 " pdb=" CA PHE C 395 " ideal model delta sigma weight residual 122.34 131.09 -8.75 1.39e+00 5.18e-01 3.96e+01 ... (remaining 61410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 25269 17.81 - 35.62: 1810 35.62 - 53.43: 351 53.43 - 71.23: 77 71.23 - 89.04: 33 Dihedral angle restraints: 27540 sinusoidal: 11024 harmonic: 16516 Sorted by residual: 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 -153.52 -26.48 0 5.00e+00 4.00e-02 2.81e+01 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 -153.52 -26.48 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 ... (remaining 27537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4651 0.059 - 0.118: 1624 0.118 - 0.178: 436 0.178 - 0.237: 65 0.237 - 0.296: 21 Chirality restraints: 6797 Sorted by residual: chirality pdb=" CA PHE E 395 " pdb=" N PHE E 395 " pdb=" C PHE E 395 " pdb=" CB PHE E 395 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA PHE C 395 " pdb=" N PHE C 395 " pdb=" C PHE C 395 " pdb=" CB PHE C 395 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA PHE A 395 " pdb=" N PHE A 395 " pdb=" C PHE A 395 " pdb=" CB PHE A 395 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 6794 not shown) Planarity restraints: 8015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTN A 801 " 0.020 2.00e-02 2.50e+03 5.05e-02 3.82e+01 pdb=" C4 BTN A 801 " 0.015 2.00e-02 2.50e+03 pdb=" C5 BTN A 801 " -0.078 2.00e-02 2.50e+03 pdb=" N1 BTN A 801 " 0.078 2.00e-02 2.50e+03 pdb=" N2 BTN A 801 " 0.012 2.00e-02 2.50e+03 pdb=" O3 BTN A 801 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTN E 801 " 0.019 2.00e-02 2.50e+03 5.02e-02 3.79e+01 pdb=" C4 BTN E 801 " 0.015 2.00e-02 2.50e+03 pdb=" C5 BTN E 801 " -0.078 2.00e-02 2.50e+03 pdb=" N1 BTN E 801 " 0.078 2.00e-02 2.50e+03 pdb=" N2 BTN E 801 " 0.013 2.00e-02 2.50e+03 pdb=" O3 BTN E 801 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTN C 801 " -0.019 2.00e-02 2.50e+03 5.02e-02 3.78e+01 pdb=" C4 BTN C 801 " -0.015 2.00e-02 2.50e+03 pdb=" C5 BTN C 801 " 0.078 2.00e-02 2.50e+03 pdb=" N1 BTN C 801 " -0.078 2.00e-02 2.50e+03 pdb=" N2 BTN C 801 " -0.013 2.00e-02 2.50e+03 pdb=" O3 BTN C 801 " 0.047 2.00e-02 2.50e+03 ... (remaining 8012 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 9212 2.78 - 3.31: 38756 3.31 - 3.84: 73296 3.84 - 4.37: 86870 4.37 - 4.90: 153120 Nonbonded interactions: 361254 Sorted by model distance: nonbonded pdb=" OH TYR A 590 " pdb=" CD LYS A 608 " model vdw 2.245 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 nonbonded pdb=" OH TYR C 590 " pdb=" CD LYS C 608 " model vdw 2.245 3.440 nonbonded pdb=" OH TYR G 590 " pdb=" CD LYS G 608 " model vdw 2.245 3.440 ... (remaining 361249 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 49 through 174 or resid 251 through 801)) selection = chain 'C' selection = (chain 'E' and (resid 49 through 174 or resid 251 through 801)) } 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: 9.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 39.720 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.150 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:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.184 45484 Z= 0.549 Angle : 0.997 12.414 61415 Z= 0.588 Chirality : 0.064 0.296 6797 Planarity : 0.008 0.068 8015 Dihedral : 13.276 89.042 16996 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.74 % Favored : 95.05 % Rotamer: Outliers : 0.51 % Allowed : 4.88 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.10), residues: 5742 helix: -1.68 (0.10), residues: 2061 sheet: -0.01 (0.15), residues: 1118 loop : -2.06 (0.11), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 525 TYR 0.017 0.002 TYR H 457 PHE 0.024 0.002 PHE L 344 TRP 0.017 0.003 TRP J 276 HIS 0.008 0.001 HIS J 57 Details of bonding type rmsd covalent geometry : bond 0.01144 (45478) covalent geometry : angle 0.99703 (61415) hydrogen bonds : bond 0.17840 ( 2119) hydrogen bonds : angle 7.22239 ( 5940) Misc. bond : bond 0.11631 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 1021 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7810 (ttpt) cc_final: 0.7604 (tmmt) REVERT: A 148 ILE cc_start: 0.6656 (mt) cc_final: 0.6312 (mt) REVERT: A 215 MET cc_start: 0.0143 (mtp) cc_final: -0.0074 (pmt) REVERT: A 658 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6194 (mp0) REVERT: A 659 LYS cc_start: 0.6488 (mttt) cc_final: 0.6068 (pttt) REVERT: A 677 MET cc_start: 0.6482 (ttp) cc_final: 0.5750 (ppp) REVERT: B 228 ASP cc_start: 0.7605 (m-30) cc_final: 0.7363 (m-30) REVERT: B 409 VAL cc_start: 0.8573 (p) cc_final: 0.8271 (t) REVERT: B 425 MET cc_start: 0.7822 (ttt) cc_final: 0.7577 (ttp) REVERT: B 452 MET cc_start: 0.8699 (mmm) cc_final: 0.8149 (mmm) REVERT: C 323 PHE cc_start: 0.5066 (m-80) cc_final: 0.4862 (m-10) REVERT: C 336 MET cc_start: 0.4626 (ttt) cc_final: 0.4212 (ttp) REVERT: C 659 LYS cc_start: 0.6155 (mttt) cc_final: 0.5852 (tttp) REVERT: C 683 GLU cc_start: 0.6161 (mt-10) cc_final: 0.5783 (mp0) REVERT: D 217 THR cc_start: 0.7705 (m) cc_final: 0.7491 (t) REVERT: E 110 MET cc_start: 0.6179 (mtp) cc_final: 0.5731 (ttp) REVERT: E 270 TYR cc_start: 0.7744 (p90) cc_final: 0.7030 (p90) REVERT: E 275 ASP cc_start: 0.6943 (t0) cc_final: 0.6724 (t0) REVERT: E 437 LEU cc_start: 0.8506 (tp) cc_final: 0.8134 (tp) REVERT: E 576 MET cc_start: 0.8672 (mtt) cc_final: 0.8374 (mtt) REVERT: F 140 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8495 (m) REVERT: F 253 GLU cc_start: 0.6212 (tt0) cc_final: 0.5469 (pt0) REVERT: F 452 MET cc_start: 0.8365 (mmm) cc_final: 0.8064 (mmm) REVERT: F 511 LYS cc_start: 0.7785 (tttm) cc_final: 0.7195 (tttp) REVERT: G 576 MET cc_start: 0.8793 (mtt) cc_final: 0.8342 (mtp) REVERT: G 615 GLU cc_start: 0.6503 (mt-10) cc_final: 0.6203 (mm-30) REVERT: H 49 MET cc_start: 0.8583 (tpp) cc_final: 0.8315 (tpt) REVERT: I 576 MET cc_start: 0.8105 (mtt) cc_final: 0.7547 (mtt) REVERT: J 338 ILE cc_start: 0.8567 (pt) cc_final: 0.8363 (mp) REVERT: J 408 MET cc_start: 0.6965 (tpt) cc_final: 0.6378 (tpt) REVERT: J 452 MET cc_start: 0.8395 (mmm) cc_final: 0.7898 (mmm) REVERT: K 619 TYR cc_start: 0.8078 (m-80) cc_final: 0.7854 (m-80) REVERT: K 674 LEU cc_start: 0.6540 (mt) cc_final: 0.6331 (mm) REVERT: K 682 MET cc_start: 0.6871 (tpp) cc_final: 0.6282 (tpp) REVERT: L 473 MET cc_start: 0.8684 (ptp) cc_final: 0.8461 (ptp) outliers start: 24 outliers final: 1 residues processed: 1034 average time/residue: 0.8681 time to fit residues: 1075.8957 Evaluate side-chains 554 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 552 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain G residue 678 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 394 optimal weight: 3.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 0.8980 chunk 497 optimal weight: 0.9980 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 8.9990 chunk 223 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 483 ASN A 531 HIS A 684 HIS B 89 ASN B 198 GLN B 230 ASN B 285 HIS B 297 GLN B 386 HIS B 389 GLN B 393 GLN B 477 GLN C 126 HIS C 283 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 HIS C 588 ASN C 684 HIS D 102 GLN D 389 GLN D 480 ASN E 126 HIS E 464 HIS E 529 GLN E 531 HIS E 684 HIS F 198 GLN F 324 ASN F 386 HIS F 389 GLN G 684 HIS H 57 HIS H 389 GLN H 477 GLN J 198 GLN J 208 GLN J 295 ASN J 386 HIS J 389 GLN K 531 HIS L 75 HIS L 102 GLN L 107 GLN L 136 ASN L 198 GLN L 389 GLN ** L 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 477 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.182413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124654 restraints weight = 50461.113| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.11 r_work: 0.3294 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 45484 Z= 0.204 Angle : 0.698 11.125 61415 Z= 0.370 Chirality : 0.047 0.194 6797 Planarity : 0.006 0.062 8015 Dihedral : 5.922 58.284 6385 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.72 % Allowed : 12.54 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.11), residues: 5742 helix: 0.24 (0.11), residues: 2128 sheet: 0.27 (0.14), residues: 1106 loop : -1.35 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 525 TYR 0.037 0.002 TYR H 457 PHE 0.024 0.002 PHE A 537 TRP 0.017 0.002 TRP J 465 HIS 0.010 0.002 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00444 (45478) covalent geometry : angle 0.69792 (61415) hydrogen bonds : bond 0.05630 ( 2119) hydrogen bonds : angle 5.21375 ( 5940) Misc. bond : bond 0.00074 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 599 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7909 (ttpt) cc_final: 0.7434 (ttmt) REVERT: A 134 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5588 (mp0) REVERT: A 148 ILE cc_start: 0.6833 (mt) cc_final: 0.6603 (mt) REVERT: A 170 MET cc_start: 0.3464 (OUTLIER) cc_final: 0.3212 (mmt) REVERT: A 244 MET cc_start: -0.0009 (mmm) cc_final: -0.0802 (tpt) REVERT: A 357 GLU cc_start: 0.6966 (tt0) cc_final: 0.6394 (tm-30) REVERT: A 366 GLU cc_start: 0.6174 (mt-10) cc_final: 0.5968 (mp0) REVERT: A 436 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7252 (mtmm) REVERT: A 579 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7610 (mm-30) REVERT: A 677 MET cc_start: 0.5961 (ttp) cc_final: 0.5299 (ppp) REVERT: A 683 GLU cc_start: 0.6455 (mt-10) cc_final: 0.6158 (mp0) REVERT: B 228 ASP cc_start: 0.8157 (m-30) cc_final: 0.7915 (m-30) REVERT: B 409 VAL cc_start: 0.8529 (p) cc_final: 0.8321 (t) REVERT: B 452 MET cc_start: 0.9307 (mmm) cc_final: 0.8918 (mmm) REVERT: C 285 ILE cc_start: 0.7382 (tp) cc_final: 0.7067 (pt) REVERT: C 288 GLU cc_start: 0.6354 (mt-10) cc_final: 0.5978 (tt0) REVERT: C 334 MET cc_start: 0.6107 (tmt) cc_final: 0.5783 (tmm) REVERT: C 390 ASP cc_start: 0.4578 (t0) cc_final: 0.4369 (t0) REVERT: C 411 ASP cc_start: 0.4837 (m-30) cc_final: 0.4416 (m-30) REVERT: C 433 MET cc_start: 0.7585 (ttp) cc_final: 0.7204 (ttt) REVERT: C 683 GLU cc_start: 0.5980 (mt-10) cc_final: 0.5642 (mp0) REVERT: D 37 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8394 (mp) REVERT: D 299 LYS cc_start: 0.8876 (mptm) cc_final: 0.8576 (mmtm) REVERT: D 476 GLU cc_start: 0.6943 (mp0) cc_final: 0.6675 (pm20) REVERT: E 110 MET cc_start: 0.6808 (mtp) cc_final: 0.6528 (mtp) REVERT: E 270 TYR cc_start: 0.7459 (p90) cc_final: 0.6841 (p90) REVERT: E 275 ASP cc_start: 0.7024 (t0) cc_final: 0.6794 (t0) REVERT: E 415 ARG cc_start: 0.7539 (ttm170) cc_final: 0.7282 (mtp180) REVERT: E 706 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6903 (m110) REVERT: F 140 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8643 (m) REVERT: F 178 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8553 (mp) REVERT: F 213 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8511 (mtt) REVERT: F 253 GLU cc_start: 0.6541 (tt0) cc_final: 0.6023 (pt0) REVERT: F 452 MET cc_start: 0.8949 (mmm) cc_final: 0.8718 (mmm) REVERT: F 555 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8438 (ttmt) REVERT: G 577 GLN cc_start: 0.8826 (tp40) cc_final: 0.8542 (tp-100) REVERT: G 675 MET cc_start: 0.8080 (ttm) cc_final: 0.7827 (mtm) REVERT: G 684 HIS cc_start: 0.7784 (m-70) cc_final: 0.7448 (m-70) REVERT: H 58 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: H 376 LEU cc_start: 0.9127 (mt) cc_final: 0.8872 (tp) REVERT: H 377 PHE cc_start: 0.8613 (m-80) cc_final: 0.8377 (m-80) REVERT: H 394 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8682 (mtp180) REVERT: H 408 MET cc_start: 0.7095 (tpt) cc_final: 0.6792 (tpp) REVERT: I 518 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.7979 (mptt) REVERT: I 529 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7701 (pp30) REVERT: I 623 LYS cc_start: 0.6611 (tppt) cc_final: 0.6134 (tptt) REVERT: J 408 MET cc_start: 0.7234 (tpt) cc_final: 0.6969 (tpt) REVERT: J 425 MET cc_start: 0.8811 (ttp) cc_final: 0.8576 (tpt) REVERT: J 452 MET cc_start: 0.8987 (mmm) cc_final: 0.8616 (mmm) REVERT: J 476 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6845 (pm20) REVERT: K 520 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8450 (ttpp) REVERT: K 522 MET cc_start: 0.8192 (tpt) cc_final: 0.7889 (tpt) REVERT: K 623 LYS cc_start: 0.6778 (mmmt) cc_final: 0.6246 (mmmt) REVERT: K 653 MET cc_start: 0.6138 (mtp) cc_final: 0.5372 (mmt) REVERT: K 674 LEU cc_start: 0.5505 (mt) cc_final: 0.5191 (mm) REVERT: K 677 MET cc_start: 0.5977 (ptm) cc_final: 0.5454 (ptp) REVERT: K 682 MET cc_start: 0.6699 (tpp) cc_final: 0.6085 (tpp) REVERT: L 43 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7448 (mp10) REVERT: L 234 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8126 (ptt90) REVERT: L 240 PHE cc_start: 0.7968 (p90) cc_final: 0.7747 (p90) REVERT: L 452 MET cc_start: 0.9122 (mmm) cc_final: 0.8884 (mmm) outliers start: 128 outliers final: 36 residues processed: 672 average time/residue: 0.6898 time to fit residues: 560.5577 Evaluate side-chains 528 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 476 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 706 ASN Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 555 LYS Chi-restraints excluded: chain G residue 529 GLN Chi-restraints excluded: chain G residue 600 CYS Chi-restraints excluded: chain G residue 656 THR Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 518 LYS Chi-restraints excluded: chain I residue 529 GLN Chi-restraints excluded: chain I residue 562 VAL Chi-restraints excluded: chain I residue 582 THR Chi-restraints excluded: chain I residue 617 THR Chi-restraints excluded: chain I residue 627 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 512 LYS Chi-restraints excluded: chain K residue 520 LYS Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain L residue 234 ARG Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 315 ASP Chi-restraints excluded: chain L residue 482 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 65 optimal weight: 8.9990 chunk 431 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 326 optimal weight: 0.8980 chunk 470 optimal weight: 7.9990 chunk 376 optimal weight: 0.9990 chunk 534 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 327 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 528 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 HIS A 483 ASN B 477 GLN C 264 HIS C 283 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 ASN E 255 HIS E 279 GLN F 48 GLN F 285 HIS H 198 GLN H 477 GLN I 561 ASN K 531 HIS L 136 ASN L 236 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.182756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126003 restraints weight = 50616.917| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.07 r_work: 0.3321 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 45484 Z= 0.126 Angle : 0.585 10.297 61415 Z= 0.309 Chirality : 0.044 0.180 6797 Planarity : 0.004 0.050 8015 Dihedral : 5.448 55.576 6383 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.61 % Allowed : 14.24 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.11), residues: 5742 helix: 1.05 (0.11), residues: 2128 sheet: 0.50 (0.14), residues: 1085 loop : -1.16 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 707 TYR 0.019 0.001 TYR H 457 PHE 0.016 0.001 PHE A 537 TRP 0.013 0.001 TRP D 276 HIS 0.006 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00273 (45478) covalent geometry : angle 0.58535 (61415) hydrogen bonds : bond 0.04353 ( 2119) hydrogen bonds : angle 4.80351 ( 5940) Misc. bond : bond 0.00029 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 526 time to evaluate : 1.605 Fit side-chains revert: symmetry clash REVERT: A 134 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5488 (mp0) REVERT: A 148 ILE cc_start: 0.6843 (mt) cc_final: 0.6625 (mt) REVERT: A 160 MET cc_start: 0.4615 (mmp) cc_final: 0.4150 (mmp) REVERT: A 244 MET cc_start: 0.0641 (mmm) cc_final: -0.0518 (tpt) REVERT: A 421 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.6901 (mtp180) REVERT: A 436 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7323 (mtmm) REVERT: A 677 MET cc_start: 0.5736 (ttp) cc_final: 0.4961 (ppp) REVERT: A 683 GLU cc_start: 0.6511 (mt-10) cc_final: 0.6259 (mp0) REVERT: B 330 ASP cc_start: 0.8740 (t70) cc_final: 0.8498 (t70) REVERT: B 416 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6532 (tt0) REVERT: B 452 MET cc_start: 0.9344 (mmm) cc_final: 0.8840 (mmm) REVERT: C 267 ASN cc_start: 0.3850 (m-40) cc_final: 0.3152 (m110) REVERT: C 269 VAL cc_start: 0.6593 (OUTLIER) cc_final: 0.6217 (p) REVERT: C 285 ILE cc_start: 0.7357 (tp) cc_final: 0.7072 (pt) REVERT: C 288 GLU cc_start: 0.6202 (mt-10) cc_final: 0.5845 (mt-10) REVERT: C 390 ASP cc_start: 0.4629 (t0) cc_final: 0.4392 (t0) REVERT: C 411 ASP cc_start: 0.5014 (m-30) cc_final: 0.4570 (m-30) REVERT: C 433 MET cc_start: 0.7504 (ttp) cc_final: 0.7147 (ttt) REVERT: C 529 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8031 (pp30) REVERT: C 683 GLU cc_start: 0.5938 (mt-10) cc_final: 0.5544 (mp0) REVERT: C 704 GLN cc_start: 0.5667 (tp40) cc_final: 0.5103 (mp-120) REVERT: D 299 LYS cc_start: 0.8837 (mptm) cc_final: 0.8532 (mmtp) REVERT: D 476 GLU cc_start: 0.6916 (mp0) cc_final: 0.6641 (pm20) REVERT: E 136 MET cc_start: 0.6387 (mtm) cc_final: 0.6171 (mtm) REVERT: E 275 ASP cc_start: 0.7136 (t0) cc_final: 0.6888 (t0) REVERT: E 276 CYS cc_start: 0.6546 (m) cc_final: 0.6332 (p) REVERT: E 279 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7265 (pt0) REVERT: E 700 ARG cc_start: 0.6532 (ptm160) cc_final: 0.6317 (mtp-110) REVERT: E 706 ASN cc_start: 0.7251 (m110) cc_final: 0.7038 (m110) REVERT: F 140 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8622 (m) REVERT: F 178 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8520 (mp) REVERT: F 452 MET cc_start: 0.8956 (mmm) cc_final: 0.8711 (mmm) REVERT: F 515 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7068 (mm-30) REVERT: G 577 GLN cc_start: 0.8865 (tp40) cc_final: 0.8577 (tp-100) REVERT: G 623 LYS cc_start: 0.7099 (mmtp) cc_final: 0.6844 (ptmm) REVERT: G 675 MET cc_start: 0.7985 (ttm) cc_final: 0.7762 (mtm) REVERT: G 677 MET cc_start: 0.8355 (ptm) cc_final: 0.7888 (ptm) REVERT: G 684 HIS cc_start: 0.7878 (m-70) cc_final: 0.7669 (m-70) REVERT: H 58 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: H 253 GLU cc_start: 0.7166 (tt0) cc_final: 0.6747 (mm-30) REVERT: H 376 LEU cc_start: 0.9126 (mt) cc_final: 0.8916 (tp) REVERT: H 394 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8683 (mtp180) REVERT: H 408 MET cc_start: 0.7087 (tpt) cc_final: 0.6695 (tpp) REVERT: H 515 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7723 (pp20) REVERT: I 529 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7539 (pp30) REVERT: J 201 MET cc_start: 0.9295 (mtm) cc_final: 0.9008 (mtm) REVERT: J 511 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8047 (tttm) REVERT: J 554 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: J 557 ASP cc_start: 0.8440 (p0) cc_final: 0.8214 (p0) REVERT: K 577 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7796 (tp40) REVERT: K 623 LYS cc_start: 0.6721 (mmmt) cc_final: 0.6396 (ptpt) REVERT: K 653 MET cc_start: 0.5866 (OUTLIER) cc_final: 0.5072 (mmt) REVERT: K 674 LEU cc_start: 0.5596 (mt) cc_final: 0.5312 (mm) REVERT: K 682 MET cc_start: 0.6244 (tpp) cc_final: 0.5880 (tpp) REVERT: L 43 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: L 421 ASP cc_start: 0.7943 (m-30) cc_final: 0.7663 (m-30) outliers start: 123 outliers final: 31 residues processed: 607 average time/residue: 0.8186 time to fit residues: 603.4519 Evaluate side-chains 505 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 457 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 659 LYS Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 529 GLN Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain I residue 529 GLN Chi-restraints excluded: chain I residue 562 VAL Chi-restraints excluded: chain I residue 582 THR Chi-restraints excluded: chain I residue 611 LEU Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain K residue 528 LEU Chi-restraints excluded: chain K residue 577 GLN Chi-restraints excluded: chain K residue 653 MET Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 315 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 241 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 341 optimal weight: 4.9990 chunk 310 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN B 477 GLN B 518 ASN C 264 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN D 433 GLN E 259 GLN G 706 ASN H 43 GLN H 477 GLN I 531 HIS I 561 ASN K 531 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.178297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117964 restraints weight = 49961.834| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.03 r_work: 0.3200 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 45484 Z= 0.240 Angle : 0.707 10.034 61415 Z= 0.374 Chirality : 0.049 0.202 6797 Planarity : 0.005 0.062 8015 Dihedral : 5.716 56.173 6383 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.86 % Allowed : 15.17 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.11), residues: 5742 helix: 1.01 (0.11), residues: 2134 sheet: 0.48 (0.14), residues: 1077 loop : -1.05 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 525 TYR 0.033 0.002 TYR H 457 PHE 0.022 0.002 PHE L 407 TRP 0.014 0.002 TRP D 276 HIS 0.009 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00559 (45478) covalent geometry : angle 0.70721 (61415) hydrogen bonds : bond 0.06092 ( 2119) hydrogen bonds : angle 5.10843 ( 5940) Misc. bond : bond 0.00054 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 488 time to evaluate : 1.758 Fit side-chains revert: symmetry clash REVERT: A 134 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5434 (mt-10) REVERT: A 160 MET cc_start: 0.4559 (mmp) cc_final: 0.4179 (mmp) REVERT: A 261 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: A 396 MET cc_start: 0.5508 (OUTLIER) cc_final: 0.4873 (tpt) REVERT: A 421 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7178 (mtp180) REVERT: A 677 MET cc_start: 0.5815 (ttp) cc_final: 0.4953 (ppp) REVERT: A 683 GLU cc_start: 0.6466 (mt-10) cc_final: 0.6162 (mp0) REVERT: B 234 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8179 (ptt-90) REVERT: B 414 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6861 (tp30) REVERT: B 416 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6649 (tt0) REVERT: B 452 MET cc_start: 0.9332 (mmm) cc_final: 0.8809 (mmm) REVERT: C 66 ARG cc_start: 0.6783 (mtm-85) cc_final: 0.6273 (ttp-110) REVERT: C 287 GLU cc_start: 0.6916 (tp30) cc_final: 0.6705 (tp30) REVERT: C 288 GLU cc_start: 0.6387 (mt-10) cc_final: 0.6129 (mt-10) REVERT: C 334 MET cc_start: 0.6659 (OUTLIER) cc_final: 0.5985 (tmt) REVERT: C 357 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6601 (pp20) REVERT: C 433 MET cc_start: 0.7655 (ttp) cc_final: 0.7375 (ttt) REVERT: C 529 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8174 (pp30) REVERT: C 683 GLU cc_start: 0.5963 (mt-10) cc_final: 0.5566 (mp0) REVERT: C 704 GLN cc_start: 0.5747 (tp40) cc_final: 0.5048 (mp-120) REVERT: D 33 THR cc_start: 0.8712 (m) cc_final: 0.8450 (p) REVERT: D 172 ASP cc_start: 0.8566 (t0) cc_final: 0.8336 (t0) REVERT: D 189 ASP cc_start: 0.8406 (p0) cc_final: 0.8160 (m-30) REVERT: D 259 ASP cc_start: 0.6709 (m-30) cc_final: 0.6362 (t0) REVERT: D 476 GLU cc_start: 0.7109 (mp0) cc_final: 0.6811 (pm20) REVERT: E 83 ASP cc_start: 0.8326 (m-30) cc_final: 0.7949 (m-30) REVERT: E 136 MET cc_start: 0.6299 (mtm) cc_final: 0.6037 (mtm) REVERT: E 215 MET cc_start: 0.1740 (mmm) cc_final: 0.1198 (mpt) REVERT: E 335 GLU cc_start: 0.2385 (OUTLIER) cc_final: 0.2037 (tm-30) REVERT: E 366 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.6092 (mm-30) REVERT: E 378 GLN cc_start: 0.7255 (pm20) cc_final: 0.6981 (pm20) REVERT: E 576 MET cc_start: 0.9043 (mtt) cc_final: 0.8833 (mtt) REVERT: E 683 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: E 700 ARG cc_start: 0.6642 (ptm160) cc_final: 0.6390 (mtp-110) REVERT: E 706 ASN cc_start: 0.7599 (m110) cc_final: 0.7305 (m110) REVERT: F 140 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8625 (m) REVERT: F 178 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8703 (mp) REVERT: F 213 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8609 (mtt) REVERT: F 452 MET cc_start: 0.9068 (mmm) cc_final: 0.8814 (mmm) REVERT: F 515 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7161 (mm-30) REVERT: G 553 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8290 (ptm) REVERT: G 577 GLN cc_start: 0.8866 (tp40) cc_final: 0.8652 (tp40) REVERT: G 684 HIS cc_start: 0.8212 (m-70) cc_final: 0.7901 (m-70) REVERT: H 253 GLU cc_start: 0.7424 (tt0) cc_final: 0.6921 (mm-30) REVERT: H 376 LEU cc_start: 0.9206 (mt) cc_final: 0.8993 (tp) REVERT: H 394 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8783 (mtp180) REVERT: H 408 MET cc_start: 0.7074 (tpt) cc_final: 0.6641 (tpp) REVERT: I 507 SER cc_start: 0.8252 (m) cc_final: 0.7721 (p) REVERT: I 529 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7564 (pp30) REVERT: I 571 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7651 (p0) REVERT: I 616 ASN cc_start: 0.7352 (m-40) cc_final: 0.7133 (m-40) REVERT: I 623 LYS cc_start: 0.6471 (tppt) cc_final: 0.6261 (tptt) REVERT: J 511 LYS cc_start: 0.8464 (ttmt) cc_final: 0.8161 (tttm) REVERT: J 554 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: J 557 ASP cc_start: 0.8585 (p0) cc_final: 0.8367 (p0) REVERT: K 556 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7756 (ttmm) REVERT: K 623 LYS cc_start: 0.6851 (mmmt) cc_final: 0.6625 (ptpt) REVERT: K 653 MET cc_start: 0.5897 (OUTLIER) cc_final: 0.5281 (mmm) REVERT: K 674 LEU cc_start: 0.5016 (mt) cc_final: 0.4707 (mm) REVERT: K 682 MET cc_start: 0.6445 (tpp) cc_final: 0.6079 (tpp) REVERT: L 43 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: L 70 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8397 (mmmm) outliers start: 135 outliers final: 46 residues processed: 571 average time/residue: 0.8446 time to fit residues: 583.5207 Evaluate side-chains 522 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 451 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 683 GLU Chi-restraints excluded: chain E residue 698 PHE Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 529 GLN Chi-restraints excluded: chain G residue 553 MET Chi-restraints excluded: chain G residue 556 LYS Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 656 THR Chi-restraints excluded: chain G residue 663 LYS Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 529 GLN Chi-restraints excluded: chain I residue 562 VAL Chi-restraints excluded: chain I residue 571 ASP Chi-restraints excluded: chain I residue 582 THR Chi-restraints excluded: chain I residue 611 LEU Chi-restraints excluded: chain I residue 617 THR Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain K residue 501 LYS Chi-restraints excluded: chain K residue 556 LYS Chi-restraints excluded: chain K residue 653 MET Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain L residue 70 LYS Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 315 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 546 optimal weight: 0.0670 chunk 485 optimal weight: 0.8980 chunk 534 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 223 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 439 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 540 optimal weight: 0.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 85 ASN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 ASN E 255 HIS E 279 GLN G 706 ASN H 477 GLN I 531 HIS I 561 ASN I 584 GLN K 531 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.178917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118610 restraints weight = 49725.875| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.05 r_work: 0.3212 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 45484 Z= 0.175 Angle : 0.631 9.796 61415 Z= 0.333 Chirality : 0.046 0.198 6797 Planarity : 0.005 0.053 8015 Dihedral : 5.591 57.972 6383 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.78 % Allowed : 15.64 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.11), residues: 5742 helix: 1.18 (0.11), residues: 2166 sheet: 0.56 (0.15), residues: 1062 loop : -1.04 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 525 TYR 0.028 0.002 TYR H 457 PHE 0.017 0.002 PHE B 407 TRP 0.014 0.002 TRP D 276 HIS 0.006 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00404 (45478) covalent geometry : angle 0.63056 (61415) hydrogen bonds : bond 0.05083 ( 2119) hydrogen bonds : angle 4.87701 ( 5940) Misc. bond : bond 0.00040 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 485 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.5886 (OUTLIER) cc_final: 0.5342 (mt-10) REVERT: A 244 MET cc_start: 0.0732 (mmm) cc_final: 0.0022 (tpt) REVERT: A 259 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.6153 (tp40) REVERT: A 261 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: A 298 VAL cc_start: 0.4842 (t) cc_final: 0.4550 (p) REVERT: A 333 PHE cc_start: 0.5697 (t80) cc_final: 0.5485 (t80) REVERT: A 336 MET cc_start: 0.5169 (OUTLIER) cc_final: 0.4158 (mtp) REVERT: A 421 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7095 (mtp180) REVERT: A 422 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: A 683 GLU cc_start: 0.6416 (mt-10) cc_final: 0.6149 (mp0) REVERT: B 235 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7577 (tmmt) REVERT: B 414 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6813 (tp30) REVERT: B 452 MET cc_start: 0.9376 (mmm) cc_final: 0.8984 (mmm) REVERT: C 66 ARG cc_start: 0.6681 (mtm-85) cc_final: 0.6332 (ttp-110) REVERT: C 279 GLN cc_start: 0.6609 (OUTLIER) cc_final: 0.6230 (mt0) REVERT: C 304 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6481 (mp0) REVERT: C 357 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6765 (pp20) REVERT: C 433 MET cc_start: 0.7631 (ttp) cc_final: 0.7166 (ttt) REVERT: C 529 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7973 (pp30) REVERT: C 556 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8307 (mtmm) REVERT: C 683 GLU cc_start: 0.6009 (mt-10) cc_final: 0.5580 (mp0) REVERT: C 704 GLN cc_start: 0.5712 (tp40) cc_final: 0.4992 (mp-120) REVERT: D 33 THR cc_start: 0.8669 (m) cc_final: 0.8433 (p) REVERT: D 259 ASP cc_start: 0.6653 (m-30) cc_final: 0.6314 (t0) REVERT: D 476 GLU cc_start: 0.7048 (mp0) cc_final: 0.6671 (pm20) REVERT: E 134 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6176 (mm-30) REVERT: E 136 MET cc_start: 0.6333 (mtm) cc_final: 0.6108 (mtm) REVERT: E 215 MET cc_start: 0.1156 (mmm) cc_final: 0.0676 (mpp) REVERT: E 366 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.6181 (mm-30) REVERT: E 367 LYS cc_start: 0.6348 (mttt) cc_final: 0.5857 (pttt) REVERT: E 374 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.5977 (mp0) REVERT: E 378 GLN cc_start: 0.7270 (pm20) cc_final: 0.6946 (pm20) REVERT: E 700 ARG cc_start: 0.6665 (ptm160) cc_final: 0.6394 (mtp-110) REVERT: E 706 ASN cc_start: 0.7577 (m110) cc_final: 0.7264 (m110) REVERT: F 69 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7518 (pt0) REVERT: F 140 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8620 (m) REVERT: F 178 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8631 (mp) REVERT: F 213 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8585 (mtt) REVERT: F 452 MET cc_start: 0.9026 (mmm) cc_final: 0.8763 (mmm) REVERT: F 515 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7128 (mm-30) REVERT: G 577 GLN cc_start: 0.8845 (tp40) cc_final: 0.8645 (tp40) REVERT: G 684 HIS cc_start: 0.8188 (m-70) cc_final: 0.7838 (m-70) REVERT: H 376 LEU cc_start: 0.9105 (mt) cc_final: 0.8888 (tp) REVERT: H 394 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8729 (mtp180) REVERT: H 408 MET cc_start: 0.7032 (tpt) cc_final: 0.6684 (tpp) REVERT: I 507 SER cc_start: 0.8225 (m) cc_final: 0.7715 (p) REVERT: I 529 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7611 (pp30) REVERT: I 623 LYS cc_start: 0.6461 (tppt) cc_final: 0.6209 (tptp) REVERT: I 635 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7964 (tmtm) REVERT: I 674 LEU cc_start: 0.4383 (mt) cc_final: 0.4051 (tt) REVERT: J 178 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8339 (tp) REVERT: J 511 LYS cc_start: 0.8431 (ttmt) cc_final: 0.8121 (tttm) REVERT: J 554 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: K 522 MET cc_start: 0.8206 (tpt) cc_final: 0.7931 (tpt) REVERT: K 571 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8321 (p0) REVERT: K 653 MET cc_start: 0.5613 (OUTLIER) cc_final: 0.5391 (mtm) REVERT: K 682 MET cc_start: 0.6380 (tpp) cc_final: 0.6010 (tpp) REVERT: L 43 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7473 (mp10) REVERT: L 70 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8434 (mmmm) REVERT: L 482 LEU cc_start: 0.8124 (tp) cc_final: 0.7873 (tp) REVERT: L 554 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7316 (pm20) outliers start: 131 outliers final: 45 residues processed: 569 average time/residue: 0.7986 time to fit residues: 546.5764 Evaluate side-chains 521 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 447 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 698 PHE Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 656 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 529 GLN Chi-restraints excluded: chain I residue 582 THR Chi-restraints excluded: chain I residue 611 LEU Chi-restraints excluded: chain I residue 617 THR Chi-restraints excluded: chain I residue 635 LYS Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 653 MET Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain L residue 70 LYS Chi-restraints excluded: chain L residue 213 MET Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 315 ASP Chi-restraints excluded: chain L residue 490 ARG Chi-restraints excluded: chain L residue 554 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 420 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 293 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 263 optimal weight: 7.9990 chunk 251 optimal weight: 8.9990 chunk 223 optimal weight: 3.9990 chunk 382 optimal weight: 0.8980 chunk 559 optimal weight: 0.9990 chunk 195 optimal weight: 0.6980 chunk 359 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN D 230 ASN D 297 GLN D 480 ASN G 706 ASN H 477 GLN I 531 HIS I 561 ASN I 584 GLN J 480 ASN K 531 HIS L 386 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.180258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.121252 restraints weight = 50093.932| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.09 r_work: 0.3237 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 45484 Z= 0.126 Angle : 0.575 9.456 61415 Z= 0.302 Chirality : 0.044 0.181 6797 Planarity : 0.004 0.047 8015 Dihedral : 5.377 58.052 6383 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.42 % Allowed : 16.25 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.11), residues: 5742 helix: 1.54 (0.12), residues: 2136 sheet: 0.62 (0.15), residues: 1084 loop : -0.99 (0.12), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 268 TYR 0.020 0.001 TYR I 590 PHE 0.017 0.001 PHE C 323 TRP 0.013 0.001 TRP D 276 HIS 0.004 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00281 (45478) covalent geometry : angle 0.57531 (61415) hydrogen bonds : bond 0.04229 ( 2119) hydrogen bonds : angle 4.64312 ( 5940) Misc. bond : bond 0.00022 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 472 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.1870 (tpp) cc_final: 0.0439 (ttt) REVERT: A 259 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.6189 (tp40) REVERT: A 261 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: A 298 VAL cc_start: 0.4894 (OUTLIER) cc_final: 0.4661 (p) REVERT: A 373 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7450 (pp20) REVERT: A 396 MET cc_start: 0.5426 (OUTLIER) cc_final: 0.4858 (tpt) REVERT: A 677 MET cc_start: 0.5639 (OUTLIER) cc_final: 0.4137 (ppp) REVERT: A 683 GLU cc_start: 0.6138 (mt-10) cc_final: 0.5904 (mp0) REVERT: B 33 THR cc_start: 0.8524 (m) cc_final: 0.8181 (p) REVERT: B 235 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7599 (tmmt) REVERT: B 414 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6789 (tp30) REVERT: B 452 MET cc_start: 0.9355 (mmm) cc_final: 0.9084 (mmm) REVERT: C 66 ARG cc_start: 0.6705 (mtm-85) cc_final: 0.6360 (ttp-110) REVERT: C 301 LYS cc_start: 0.6372 (mmtm) cc_final: 0.5755 (tmmt) REVERT: C 334 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.5831 (tmt) REVERT: C 380 HIS cc_start: 0.6930 (OUTLIER) cc_final: 0.6473 (t70) REVERT: C 433 MET cc_start: 0.7590 (ttp) cc_final: 0.7145 (ttt) REVERT: C 529 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: C 556 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8284 (mtmm) REVERT: C 683 GLU cc_start: 0.5961 (mt-10) cc_final: 0.5473 (mp0) REVERT: C 704 GLN cc_start: 0.5635 (tp40) cc_final: 0.4948 (mp-120) REVERT: D 33 THR cc_start: 0.8667 (m) cc_final: 0.8447 (p) REVERT: D 259 ASP cc_start: 0.6660 (m-30) cc_final: 0.6313 (t0) REVERT: D 476 GLU cc_start: 0.7032 (mp0) cc_final: 0.6674 (pm20) REVERT: E 134 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.6201 (mm-30) REVERT: E 215 MET cc_start: 0.1284 (mmm) cc_final: 0.0597 (mpp) REVERT: E 366 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.6007 (mm-30) REVERT: E 378 GLN cc_start: 0.7377 (pm20) cc_final: 0.7025 (pm20) REVERT: E 396 MET cc_start: 0.4773 (tmm) cc_final: 0.4038 (ppp) REVERT: E 700 ARG cc_start: 0.6690 (ptm160) cc_final: 0.6409 (mtp-110) REVERT: F 69 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7489 (pt0) REVERT: F 140 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8593 (m) REVERT: F 178 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8515 (mp) REVERT: F 213 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8555 (mtt) REVERT: F 408 MET cc_start: 0.6871 (tpt) cc_final: 0.6237 (mmm) REVERT: F 452 MET cc_start: 0.9012 (mmm) cc_final: 0.8749 (mmm) REVERT: F 515 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7168 (mm-30) REVERT: G 677 MET cc_start: 0.8236 (ptm) cc_final: 0.7849 (ptm) REVERT: G 684 HIS cc_start: 0.8042 (m-70) cc_final: 0.7698 (m-70) REVERT: H 58 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: H 158 GLU cc_start: 0.8889 (pt0) cc_final: 0.8679 (pt0) REVERT: H 229 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7902 (tp30) REVERT: H 376 LEU cc_start: 0.9086 (mt) cc_final: 0.8876 (tp) REVERT: H 394 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8724 (mtp180) REVERT: H 408 MET cc_start: 0.7088 (tpt) cc_final: 0.6726 (tpp) REVERT: I 507 SER cc_start: 0.8206 (m) cc_final: 0.7708 (p) REVERT: I 529 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7376 (pp30) REVERT: I 571 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7658 (p0) REVERT: I 623 LYS cc_start: 0.6652 (tppt) cc_final: 0.6286 (tptt) REVERT: I 674 LEU cc_start: 0.4293 (mt) cc_final: 0.4004 (tt) REVERT: J 511 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8106 (tttm) REVERT: J 515 GLU cc_start: 0.8240 (tp30) cc_final: 0.7862 (tp30) REVERT: K 522 MET cc_start: 0.8229 (tpt) cc_final: 0.7960 (tpt) REVERT: K 682 MET cc_start: 0.6303 (tpp) cc_final: 0.5937 (tpp) REVERT: L 43 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7377 (mp10) REVERT: L 421 ASP cc_start: 0.8066 (m-30) cc_final: 0.7767 (m-30) REVERT: L 482 LEU cc_start: 0.8122 (tp) cc_final: 0.7886 (tp) REVERT: L 554 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7183 (pm20) outliers start: 114 outliers final: 43 residues processed: 539 average time/residue: 0.5164 time to fit residues: 339.3757 Evaluate side-chains 515 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 448 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 683 GLU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 529 GLN Chi-restraints excluded: chain I residue 562 VAL Chi-restraints excluded: chain I residue 571 ASP Chi-restraints excluded: chain I residue 611 LEU Chi-restraints excluded: chain I residue 617 THR Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain L residue 213 MET Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 315 ASP Chi-restraints excluded: chain L residue 486 THR Chi-restraints excluded: chain L residue 490 ARG Chi-restraints excluded: chain L residue 554 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 419 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 435 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 547 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 161 optimal weight: 0.8980 chunk 463 optimal weight: 0.9990 chunk 169 optimal weight: 0.0980 chunk 110 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN A 483 ASN B 75 HIS C 457 GLN D 48 GLN D 297 GLN D 480 ASN E 279 GLN G 706 ASN H 477 GLN I 561 ASN I 584 GLN J 480 ASN K 531 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.178977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120741 restraints weight = 49703.851| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.01 r_work: 0.3245 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 45484 Z= 0.162 Angle : 0.614 9.663 61415 Z= 0.323 Chirality : 0.046 0.190 6797 Planarity : 0.004 0.049 8015 Dihedral : 5.432 58.940 6383 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.55 % Allowed : 16.51 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.11), residues: 5742 helix: 1.49 (0.11), residues: 2138 sheet: 0.59 (0.15), residues: 1086 loop : -0.95 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 268 TYR 0.026 0.002 TYR H 457 PHE 0.018 0.002 PHE C 323 TRP 0.011 0.001 TRP F 276 HIS 0.007 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00370 (45478) covalent geometry : angle 0.61427 (61415) hydrogen bonds : bond 0.04906 ( 2119) hydrogen bonds : angle 4.74239 ( 5940) Misc. bond : bond 0.00026 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 456 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7669 (tmmt) REVERT: A 215 MET cc_start: 0.1842 (tpp) cc_final: 0.0373 (ttt) REVERT: A 244 MET cc_start: 0.0735 (mmm) cc_final: 0.0171 (tpt) REVERT: A 259 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6383 (tp40) REVERT: A 261 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7489 (m-80) REVERT: A 298 VAL cc_start: 0.5008 (OUTLIER) cc_final: 0.4784 (p) REVERT: A 396 MET cc_start: 0.5475 (OUTLIER) cc_final: 0.4837 (tpt) REVERT: A 677 MET cc_start: 0.5822 (OUTLIER) cc_final: 0.4297 (ppp) REVERT: A 683 GLU cc_start: 0.6157 (mt-10) cc_final: 0.5934 (mp0) REVERT: B 33 THR cc_start: 0.8587 (m) cc_final: 0.8272 (p) REVERT: B 235 LYS cc_start: 0.7882 (mtmt) cc_final: 0.7541 (tmmt) REVERT: B 414 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6733 (tp30) REVERT: B 452 MET cc_start: 0.9344 (mmm) cc_final: 0.8950 (mmm) REVERT: B 509 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8414 (mp) REVERT: C 66 ARG cc_start: 0.6670 (mtm-85) cc_final: 0.6297 (ttp-110) REVERT: C 279 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.6166 (mt0) REVERT: C 334 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.5981 (tmt) REVERT: C 380 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.6384 (t70) REVERT: C 433 MET cc_start: 0.7616 (ttp) cc_final: 0.7195 (ttt) REVERT: C 529 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7880 (pp30) REVERT: C 556 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8277 (mtmm) REVERT: C 683 GLU cc_start: 0.5851 (mt-10) cc_final: 0.5428 (mp0) REVERT: C 704 GLN cc_start: 0.5790 (tp40) cc_final: 0.5102 (mp-120) REVERT: D 259 ASP cc_start: 0.6642 (m-30) cc_final: 0.6341 (t0) REVERT: D 407 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.7047 (t80) REVERT: D 452 MET cc_start: 0.8946 (mmm) cc_final: 0.8612 (mmm) REVERT: D 476 GLU cc_start: 0.6992 (mp0) cc_final: 0.6654 (pm20) REVERT: E 134 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6205 (mm-30) REVERT: E 215 MET cc_start: 0.1160 (mmm) cc_final: 0.0687 (mpp) REVERT: E 272 PHE cc_start: 0.6292 (m-80) cc_final: 0.6083 (m-80) REVERT: E 313 VAL cc_start: 0.5031 (OUTLIER) cc_final: 0.4580 (m) REVERT: E 366 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.6096 (mm-30) REVERT: E 367 LYS cc_start: 0.6451 (mttt) cc_final: 0.6006 (ptpt) REVERT: E 396 MET cc_start: 0.4675 (tmm) cc_final: 0.3987 (ppp) REVERT: E 484 VAL cc_start: 0.6789 (t) cc_final: 0.6545 (m) REVERT: E 680 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7969 (mmt) REVERT: E 700 ARG cc_start: 0.6704 (ptm160) cc_final: 0.6421 (mtp-110) REVERT: F 69 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7420 (pt0) REVERT: F 140 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8628 (m) REVERT: F 178 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8618 (mp) REVERT: F 213 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8537 (mtt) REVERT: F 408 MET cc_start: 0.6703 (tpt) cc_final: 0.6100 (mmm) REVERT: F 452 MET cc_start: 0.9006 (mmm) cc_final: 0.8743 (mmm) REVERT: G 553 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8110 (ptm) REVERT: G 677 MET cc_start: 0.8207 (ptm) cc_final: 0.7830 (ptm) REVERT: G 684 HIS cc_start: 0.8124 (m-70) cc_final: 0.7797 (m-70) REVERT: H 33 THR cc_start: 0.8594 (m) cc_final: 0.8307 (p) REVERT: H 229 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7810 (tp30) REVERT: H 376 LEU cc_start: 0.9079 (mt) cc_final: 0.8864 (tp) REVERT: H 394 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8717 (mtp180) REVERT: H 408 MET cc_start: 0.7010 (tpt) cc_final: 0.6575 (tpp) REVERT: I 507 SER cc_start: 0.8299 (m) cc_final: 0.7784 (p) REVERT: I 529 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7281 (pp30) REVERT: I 571 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7638 (p0) REVERT: I 623 LYS cc_start: 0.6590 (tppt) cc_final: 0.6263 (tptt) REVERT: I 674 LEU cc_start: 0.4389 (mt) cc_final: 0.4105 (tt) REVERT: J 511 LYS cc_start: 0.8441 (ttmt) cc_final: 0.8138 (tttm) REVERT: J 515 GLU cc_start: 0.8152 (tp30) cc_final: 0.7828 (tp30) REVERT: J 554 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: K 522 MET cc_start: 0.8146 (tpt) cc_final: 0.7880 (tpt) REVERT: K 653 MET cc_start: 0.6465 (mtm) cc_final: 0.5471 (mtt) REVERT: K 682 MET cc_start: 0.6405 (tpp) cc_final: 0.6072 (tpp) REVERT: L 43 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7423 (mp10) REVERT: L 482 LEU cc_start: 0.8171 (tp) cc_final: 0.7914 (tp) REVERT: L 554 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7263 (pm20) outliers start: 120 outliers final: 57 residues processed: 527 average time/residue: 0.4783 time to fit residues: 309.4570 Evaluate side-chains 530 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 444 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 282 HIS Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 529 GLN Chi-restraints excluded: chain G residue 553 MET Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 656 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 529 GLN Chi-restraints excluded: chain I residue 562 VAL Chi-restraints excluded: chain I residue 571 ASP Chi-restraints excluded: chain I residue 582 THR Chi-restraints excluded: chain I residue 611 LEU Chi-restraints excluded: chain I residue 617 THR Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 408 MET Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain K residue 608 LYS Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain L residue 213 MET Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 315 ASP Chi-restraints excluded: chain L residue 486 THR Chi-restraints excluded: chain L residue 490 ARG Chi-restraints excluded: chain L residue 554 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 455 optimal weight: 0.0980 chunk 79 optimal weight: 0.9990 chunk 388 optimal weight: 0.9990 chunk 277 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 221 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 370 optimal weight: 0.0370 chunk 449 optimal weight: 0.9980 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN B 75 HIS ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN D 297 GLN D 480 ASN H 477 GLN I 561 ASN I 584 GLN J 480 ASN K 531 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.180873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123491 restraints weight = 49941.343| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.08 r_work: 0.3288 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 45484 Z= 0.109 Angle : 0.557 12.524 61415 Z= 0.291 Chirality : 0.044 0.176 6797 Planarity : 0.004 0.047 8015 Dihedral : 5.187 59.440 6383 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.89 % Allowed : 17.19 % Favored : 80.93 % 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 aren not related in a simple way. whole: 0.59 (0.11), residues: 5742 helix: 1.72 (0.12), residues: 2146 sheet: 0.73 (0.15), residues: 1044 loop : -0.92 (0.12), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 308 TYR 0.019 0.001 TYR I 590 PHE 0.020 0.001 PHE C 323 TRP 0.013 0.001 TRP L 276 HIS 0.003 0.001 HIS F 285 Details of bonding type rmsd covalent geometry : bond 0.00236 (45478) covalent geometry : angle 0.55688 (61415) hydrogen bonds : bond 0.03783 ( 2119) hydrogen bonds : angle 4.49331 ( 5940) Misc. bond : bond 0.00013 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 449 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.1877 (tpp) cc_final: 0.0515 (ttt) REVERT: A 244 MET cc_start: 0.0893 (mmm) cc_final: 0.0264 (tpt) REVERT: A 261 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7275 (m-80) REVERT: A 298 VAL cc_start: 0.4982 (OUTLIER) cc_final: 0.4759 (p) REVERT: A 393 ASN cc_start: 0.4916 (OUTLIER) cc_final: 0.4534 (m110) REVERT: A 396 MET cc_start: 0.5467 (OUTLIER) cc_final: 0.4867 (tpt) REVERT: A 683 GLU cc_start: 0.6139 (mt-10) cc_final: 0.5880 (mp0) REVERT: B 33 THR cc_start: 0.8509 (m) cc_final: 0.8181 (p) REVERT: B 235 LYS cc_start: 0.7867 (mtmt) cc_final: 0.7604 (tmmt) REVERT: B 414 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6769 (tp30) REVERT: B 452 MET cc_start: 0.9359 (mmm) cc_final: 0.8972 (mmm) REVERT: C 66 ARG cc_start: 0.6583 (mtm-85) cc_final: 0.6308 (ttp-110) REVERT: C 267 ASN cc_start: 0.4351 (m-40) cc_final: 0.3822 (m110) REVERT: C 301 LYS cc_start: 0.6474 (tppt) cc_final: 0.6144 (tmmt) REVERT: C 380 HIS cc_start: 0.6820 (OUTLIER) cc_final: 0.6514 (t70) REVERT: C 396 MET cc_start: 0.5462 (mmt) cc_final: 0.4806 (tmm) REVERT: C 433 MET cc_start: 0.7547 (ttp) cc_final: 0.7049 (ttt) REVERT: C 529 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: C 683 GLU cc_start: 0.5892 (mt-10) cc_final: 0.5484 (mp0) REVERT: C 704 GLN cc_start: 0.5728 (tp40) cc_final: 0.5064 (mp-120) REVERT: D 259 ASP cc_start: 0.6677 (m-30) cc_final: 0.6320 (t0) REVERT: D 407 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.7051 (t80) REVERT: D 452 MET cc_start: 0.8965 (mmm) cc_final: 0.8489 (mmm) REVERT: D 476 GLU cc_start: 0.6941 (mp0) cc_final: 0.6637 (pm20) REVERT: E 215 MET cc_start: 0.1160 (mmm) cc_final: 0.0431 (mpp) REVERT: E 313 VAL cc_start: 0.4564 (OUTLIER) cc_final: 0.4194 (m) REVERT: E 366 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5897 (mm-30) REVERT: E 396 MET cc_start: 0.4648 (tmm) cc_final: 0.3908 (ppp) REVERT: E 436 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8236 (ptmt) REVERT: E 484 VAL cc_start: 0.6806 (t) cc_final: 0.6567 (m) REVERT: E 677 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7741 (ptp) REVERT: E 680 MET cc_start: 0.8317 (mtt) cc_final: 0.7970 (mmt) REVERT: E 700 ARG cc_start: 0.6675 (ptm160) cc_final: 0.6400 (mtp-110) REVERT: F 178 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8484 (mp) REVERT: F 213 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8357 (mtt) REVERT: F 408 MET cc_start: 0.6829 (tpt) cc_final: 0.6236 (mmm) REVERT: G 677 MET cc_start: 0.8108 (ptm) cc_final: 0.7790 (ptm) REVERT: G 684 HIS cc_start: 0.7950 (m-70) cc_final: 0.7610 (m-70) REVERT: H 58 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: H 158 GLU cc_start: 0.8809 (pt0) cc_final: 0.8584 (pt0) REVERT: H 376 LEU cc_start: 0.9075 (mt) cc_final: 0.8868 (tp) REVERT: H 394 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8705 (mtp180) REVERT: H 408 MET cc_start: 0.7058 (tpt) cc_final: 0.6671 (tpp) REVERT: I 507 SER cc_start: 0.8118 (m) cc_final: 0.7621 (p) REVERT: I 522 MET cc_start: 0.8492 (mtp) cc_final: 0.8272 (mtm) REVERT: I 674 LEU cc_start: 0.4366 (mt) cc_final: 0.4115 (tt) REVERT: J 353 ASP cc_start: 0.8599 (p0) cc_final: 0.8375 (p0) REVERT: J 511 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8140 (tttm) REVERT: J 515 GLU cc_start: 0.8166 (tp30) cc_final: 0.7787 (tp30) REVERT: J 554 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: K 522 MET cc_start: 0.8138 (tpt) cc_final: 0.7907 (tpt) REVERT: K 560 ASN cc_start: 0.7395 (m-40) cc_final: 0.7169 (m-40) REVERT: K 653 MET cc_start: 0.6590 (mtm) cc_final: 0.5591 (mtt) REVERT: K 682 MET cc_start: 0.6342 (tpp) cc_final: 0.6030 (tpp) REVERT: L 43 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: L 421 ASP cc_start: 0.7944 (m-30) cc_final: 0.7656 (m-30) REVERT: L 482 LEU cc_start: 0.8139 (tp) cc_final: 0.7880 (tp) REVERT: L 554 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7244 (pm20) outliers start: 89 outliers final: 39 residues processed: 501 average time/residue: 0.4948 time to fit residues: 303.0292 Evaluate side-chains 493 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 435 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain E residue 282 HIS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 436 LYS Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 677 MET Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 656 THR Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 529 GLN Chi-restraints excluded: chain I residue 582 THR Chi-restraints excluded: chain I residue 611 LEU Chi-restraints excluded: chain I residue 617 THR Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain K residue 628 GLU Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 315 ASP Chi-restraints excluded: chain L residue 490 ARG Chi-restraints excluded: chain L residue 554 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 142 optimal weight: 4.9990 chunk 525 optimal weight: 3.9990 chunk 336 optimal weight: 7.9990 chunk 398 optimal weight: 0.0870 chunk 73 optimal weight: 1.9990 chunk 450 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 366 optimal weight: 6.9990 chunk 503 optimal weight: 0.9980 chunk 299 optimal weight: 3.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN B 75 HIS D 48 GLN D 297 GLN D 480 ASN H 477 GLN I 561 ASN I 584 GLN J 480 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.175920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116124 restraints weight = 48113.684| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.17 r_work: 0.3134 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 45484 Z= 0.224 Angle : 0.681 10.528 61415 Z= 0.359 Chirality : 0.048 0.198 6797 Planarity : 0.005 0.059 8015 Dihedral : 5.530 56.155 6382 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.36 % Allowed : 17.02 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.11), residues: 5742 helix: 1.38 (0.11), residues: 2132 sheet: 0.69 (0.15), residues: 1056 loop : -0.96 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 525 TYR 0.033 0.002 TYR L 457 PHE 0.020 0.002 PHE F 103 TRP 0.010 0.002 TRP F 276 HIS 0.009 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00526 (45478) covalent geometry : angle 0.68095 (61415) hydrogen bonds : bond 0.05685 ( 2119) hydrogen bonds : angle 4.87576 ( 5940) Misc. bond : bond 0.00050 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 458 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.1927 (tpp) cc_final: 0.0523 (ttt) REVERT: A 244 MET cc_start: 0.1010 (mmm) cc_final: 0.0361 (tpt) REVERT: A 261 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: A 298 VAL cc_start: 0.5089 (OUTLIER) cc_final: 0.4878 (p) REVERT: A 366 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6076 (mt-10) REVERT: A 396 MET cc_start: 0.5514 (OUTLIER) cc_final: 0.4909 (tpt) REVERT: A 683 GLU cc_start: 0.6190 (mt-10) cc_final: 0.5981 (mp0) REVERT: A 701 GLU cc_start: 0.5701 (tt0) cc_final: 0.4829 (tm-30) REVERT: B 33 THR cc_start: 0.8665 (m) cc_final: 0.8337 (p) REVERT: B 234 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8170 (ptt-90) REVERT: B 235 LYS cc_start: 0.7979 (mtmt) cc_final: 0.7573 (tmmt) REVERT: B 414 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6796 (tp30) REVERT: B 452 MET cc_start: 0.9313 (mmm) cc_final: 0.8770 (mmm) REVERT: C 66 ARG cc_start: 0.6557 (mtm-85) cc_final: 0.6266 (ttp-110) REVERT: C 301 LYS cc_start: 0.6609 (tppt) cc_final: 0.6181 (tmmt) REVERT: C 334 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.6012 (tmt) REVERT: C 433 MET cc_start: 0.7643 (ttp) cc_final: 0.7244 (ttt) REVERT: C 529 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7921 (pp30) REVERT: C 683 GLU cc_start: 0.5941 (mt-10) cc_final: 0.5515 (mp0) REVERT: C 704 GLN cc_start: 0.5878 (tp40) cc_final: 0.5154 (mp-120) REVERT: D 259 ASP cc_start: 0.6629 (m-30) cc_final: 0.6312 (t0) REVERT: D 407 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.7186 (t80) REVERT: D 476 GLU cc_start: 0.6947 (mp0) cc_final: 0.6662 (pm20) REVERT: E 215 MET cc_start: 0.1395 (mmm) cc_final: 0.0917 (mpp) REVERT: E 283 GLN cc_start: 0.5972 (OUTLIER) cc_final: 0.5771 (mp10) REVERT: E 313 VAL cc_start: 0.5098 (OUTLIER) cc_final: 0.4810 (m) REVERT: E 367 LYS cc_start: 0.6659 (mttt) cc_final: 0.6199 (ptpt) REVERT: E 436 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8184 (ptmt) REVERT: E 484 VAL cc_start: 0.6826 (t) cc_final: 0.6581 (m) REVERT: E 674 LEU cc_start: 0.7205 (mp) cc_final: 0.6992 (mp) REVERT: E 677 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7839 (ptp) REVERT: E 680 MET cc_start: 0.8288 (mtt) cc_final: 0.7925 (mmt) REVERT: E 700 ARG cc_start: 0.6559 (ptm160) cc_final: 0.6281 (mtp-110) REVERT: F 178 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8704 (mp) REVERT: F 213 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8667 (mtt) REVERT: F 229 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8152 (mt-10) REVERT: F 408 MET cc_start: 0.6708 (tpt) cc_final: 0.6134 (mmm) REVERT: G 677 MET cc_start: 0.8201 (ptm) cc_final: 0.7890 (ptm) REVERT: G 684 HIS cc_start: 0.8146 (m-70) cc_final: 0.7835 (m-70) REVERT: H 33 THR cc_start: 0.8651 (m) cc_final: 0.8385 (p) REVERT: H 229 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7787 (tp30) REVERT: H 376 LEU cc_start: 0.9077 (mt) cc_final: 0.8867 (tp) REVERT: H 394 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8719 (mtp180) REVERT: H 408 MET cc_start: 0.7012 (tpt) cc_final: 0.6599 (tpp) REVERT: I 507 SER cc_start: 0.8163 (m) cc_final: 0.7667 (p) REVERT: J 178 LEU cc_start: 0.8797 (mm) cc_final: 0.8391 (tp) REVERT: J 511 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8173 (tttm) REVERT: J 554 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: K 682 MET cc_start: 0.6326 (tpp) cc_final: 0.5939 (tpp) REVERT: L 43 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7516 (mp10) REVERT: L 554 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7281 (pm20) outliers start: 111 outliers final: 50 residues processed: 521 average time/residue: 0.4910 time to fit residues: 312.0039 Evaluate side-chains 515 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 444 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain E residue 282 HIS Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 436 LYS Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 677 MET Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 229 GLU Chi-restraints excluded: chain F residue 557 ASP Chi-restraints excluded: chain G residue 529 GLN Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain G residue 656 THR Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 529 GLN Chi-restraints excluded: chain I residue 562 VAL Chi-restraints excluded: chain I residue 582 THR Chi-restraints excluded: chain I residue 611 LEU Chi-restraints excluded: chain I residue 617 THR Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain K residue 525 THR Chi-restraints excluded: chain K residue 628 GLU Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain L residue 213 MET Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 315 ASP Chi-restraints excluded: chain L residue 490 ARG Chi-restraints excluded: chain L residue 554 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 48 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 161 optimal weight: 0.4980 chunk 287 optimal weight: 0.5980 chunk 45 optimal weight: 0.0980 chunk 228 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 410 optimal weight: 0.8980 chunk 200 optimal weight: 0.0570 chunk 138 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN B 75 HIS ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN D 297 GLN D 480 ASN E 227 GLN H 34 GLN H 48 GLN H 477 GLN I 531 HIS I 584 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.179183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121135 restraints weight = 48935.605| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.23 r_work: 0.3199 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 45484 Z= 0.106 Angle : 0.565 11.059 61415 Z= 0.294 Chirality : 0.044 0.175 6797 Planarity : 0.004 0.049 8015 Dihedral : 5.177 53.059 6382 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.49 % Allowed : 18.06 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.11), residues: 5742 helix: 1.69 (0.12), residues: 2145 sheet: 0.79 (0.15), residues: 1030 loop : -0.88 (0.12), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 308 TYR 0.017 0.001 TYR I 590 PHE 0.016 0.001 PHE C 333 TRP 0.014 0.001 TRP D 276 HIS 0.003 0.001 HIS F 285 Details of bonding type rmsd covalent geometry : bond 0.00222 (45478) covalent geometry : angle 0.56486 (61415) hydrogen bonds : bond 0.03754 ( 2119) hydrogen bonds : angle 4.49873 ( 5940) Misc. bond : bond 0.00016 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11484 Ramachandran restraints generated. 5742 Oldfield, 0 Emsley, 5742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 450 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.1990 (tpp) cc_final: 0.0642 (ttt) REVERT: A 244 MET cc_start: 0.0892 (mmm) cc_final: 0.0244 (tpt) REVERT: A 261 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7195 (m-80) REVERT: A 298 VAL cc_start: 0.5152 (OUTLIER) cc_final: 0.4903 (p) REVERT: A 313 VAL cc_start: 0.5554 (t) cc_final: 0.5290 (p) REVERT: A 393 ASN cc_start: 0.4846 (OUTLIER) cc_final: 0.4418 (m110) REVERT: A 396 MET cc_start: 0.5451 (OUTLIER) cc_final: 0.4853 (tpt) REVERT: A 683 GLU cc_start: 0.6191 (mt-10) cc_final: 0.5955 (mp0) REVERT: B 33 THR cc_start: 0.8516 (m) cc_final: 0.8184 (p) REVERT: B 235 LYS cc_start: 0.7906 (mtmt) cc_final: 0.7630 (tmmt) REVERT: B 414 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6738 (tp30) REVERT: B 452 MET cc_start: 0.9365 (mmm) cc_final: 0.8979 (mmm) REVERT: C 66 ARG cc_start: 0.6545 (mtm-85) cc_final: 0.6268 (ttp-110) REVERT: C 380 HIS cc_start: 0.6832 (OUTLIER) cc_final: 0.6498 (t70) REVERT: C 389 GLU cc_start: 0.6501 (pt0) cc_final: 0.6285 (pt0) REVERT: C 396 MET cc_start: 0.5501 (mmt) cc_final: 0.4880 (tmm) REVERT: C 433 MET cc_start: 0.7621 (ttp) cc_final: 0.7108 (ttt) REVERT: C 529 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: C 683 GLU cc_start: 0.5918 (mt-10) cc_final: 0.5527 (mp0) REVERT: C 704 GLN cc_start: 0.5752 (tp40) cc_final: 0.5120 (mp-120) REVERT: D 259 ASP cc_start: 0.6582 (m-30) cc_final: 0.6232 (t0) REVERT: D 407 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.7052 (t80) REVERT: D 452 MET cc_start: 0.8832 (mmm) cc_final: 0.8521 (mmm) REVERT: D 476 GLU cc_start: 0.6951 (mp0) cc_final: 0.6644 (pm20) REVERT: E 215 MET cc_start: 0.1383 (mmm) cc_final: 0.0648 (mpp) REVERT: E 313 VAL cc_start: 0.4917 (OUTLIER) cc_final: 0.4545 (m) REVERT: E 336 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.5619 (ttp) REVERT: E 367 LYS cc_start: 0.6441 (mttt) cc_final: 0.6007 (ptpt) REVERT: E 396 MET cc_start: 0.4617 (tmm) cc_final: 0.3911 (ppp) REVERT: E 436 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8154 (ptmt) REVERT: E 484 VAL cc_start: 0.6792 (t) cc_final: 0.6556 (m) REVERT: E 677 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7832 (ptp) REVERT: E 680 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7948 (mmt) REVERT: E 700 ARG cc_start: 0.6557 (ptm160) cc_final: 0.6289 (mtp-110) REVERT: F 178 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8492 (mp) REVERT: F 213 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8304 (mtt) REVERT: F 229 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: F 408 MET cc_start: 0.6695 (tpt) cc_final: 0.6112 (mmm) REVERT: G 677 MET cc_start: 0.8083 (ptm) cc_final: 0.7750 (ptm) REVERT: G 680 MET cc_start: 0.7858 (mtt) cc_final: 0.7586 (mtm) REVERT: G 684 HIS cc_start: 0.7961 (m-70) cc_final: 0.7583 (m-70) REVERT: H 58 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: H 110 ASP cc_start: 0.7782 (p0) cc_final: 0.7434 (p0) REVERT: H 158 GLU cc_start: 0.8842 (pt0) cc_final: 0.8616 (pt0) REVERT: H 376 LEU cc_start: 0.9066 (mt) cc_final: 0.8863 (tp) REVERT: H 394 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8679 (mtp180) REVERT: H 408 MET cc_start: 0.6923 (tpt) cc_final: 0.6544 (tpp) REVERT: I 507 SER cc_start: 0.8132 (m) cc_final: 0.7614 (p) REVERT: I 522 MET cc_start: 0.8470 (mtp) cc_final: 0.8249 (mtm) REVERT: J 511 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8156 (tttm) REVERT: J 515 GLU cc_start: 0.8138 (tp30) cc_final: 0.7828 (tp30) REVERT: K 653 MET cc_start: 0.5955 (mtm) cc_final: 0.5386 (mtt) REVERT: K 682 MET cc_start: 0.6265 (tpp) cc_final: 0.5850 (tpp) REVERT: L 43 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: L 421 ASP cc_start: 0.7937 (m-30) cc_final: 0.7667 (m-30) REVERT: L 482 LEU cc_start: 0.8143 (tp) cc_final: 0.7835 (tp) REVERT: L 554 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7278 (pm20) outliers start: 70 outliers final: 31 residues processed: 486 average time/residue: 0.5110 time to fit residues: 306.9379 Evaluate side-chains 481 residues out of total 4713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 430 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain E residue 282 HIS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 436 LYS Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 677 MET Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 229 GLU Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 656 THR Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 529 GLN Chi-restraints excluded: chain I residue 582 THR Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 315 ASP Chi-restraints excluded: chain L residue 490 ARG Chi-restraints excluded: chain L residue 554 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 526 optimal weight: 0.6980 chunk 417 optimal weight: 0.0980 chunk 494 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 480 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 222 optimal weight: 1.9990 chunk 471 optimal weight: 1.9990 chunk 171 optimal weight: 0.2980 chunk 459 optimal weight: 0.8980 chunk 474 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN B 75 HIS C 267 ASN ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN D 297 GLN D 480 ASN F 324 ASN H 477 GLN I 584 GLN J 480 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.180779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.120934 restraints weight = 49969.886| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.02 r_work: 0.3289 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 45484 Z= 0.110 Angle : 0.570 11.525 61415 Z= 0.295 Chirality : 0.044 0.175 6797 Planarity : 0.004 0.057 8015 Dihedral : 5.078 53.504 6382 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.53 % Allowed : 18.10 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.11), residues: 5742 helix: 1.78 (0.12), residues: 2139 sheet: 0.82 (0.15), residues: 1052 loop : -0.85 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 84 TYR 0.027 0.001 TYR E 270 PHE 0.029 0.001 PHE C 333 TRP 0.012 0.001 TRP D 276 HIS 0.004 0.001 HIS F 285 Details of bonding type rmsd covalent geometry : bond 0.00239 (45478) covalent geometry : angle 0.57041 (61415) hydrogen bonds : bond 0.03770 ( 2119) hydrogen bonds : angle 4.44656 ( 5940) Misc. bond : bond 0.00013 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20043.09 seconds wall clock time: 340 minutes 9.77 seconds (20409.77 seconds total)