Starting phenix.real_space_refine on Wed May 6 13:42:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y4a_72476/05_2026/9y4a_72476.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y4a_72476/05_2026/9y4a_72476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y4a_72476/05_2026/9y4a_72476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y4a_72476/05_2026/9y4a_72476.map" model { file = "/net/cci-nas-00/data/ceres_data/9y4a_72476/05_2026/9y4a_72476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y4a_72476/05_2026/9y4a_72476.cif" } resolution = 3.1 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= 0.002 sd= 0.034 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 192 5.16 5 C 25476 2.51 5 N 6660 2.21 5 O 7548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 148 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39876 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3323 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 390} Chain breaks: 3 Chain: "B" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3323 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 390} Chain breaks: 3 Chain: "C" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3323 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 390} Chain breaks: 3 Chain: "D" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3323 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 390} Chain breaks: 3 Chain: "E" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3323 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 390} Chain breaks: 3 Chain: "F" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3323 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 390} Chain breaks: 3 Chain: "G" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3323 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 390} Chain breaks: 3 Chain: "H" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3323 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 390} Chain breaks: 3 Chain: "I" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3323 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 390} Chain breaks: 3 Chain: "J" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3323 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 390} Chain breaks: 3 Chain: "K" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3323 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 390} Chain breaks: 3 Chain: "L" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3323 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 390} Chain breaks: 3 Time building chain proxies: 8.85, per 1000 atoms: 0.22 Number of scatterers: 39876 At special positions: 0 Unit cell: (158.14, 159.887, 123.192, 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 192 16.00 O 7548 8.00 N 6660 7.00 C 25476 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=0, symmetry=0 Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.6 seconds 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9312 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 49 sheets defined 40.7% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 109 through 123 Processing helix chain 'A' and resid 167 through 181 Processing helix chain 'A' and resid 205 through 227 Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.807A pdb=" N SER A 331 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 332 " --> pdb=" O GLY A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 332' Processing helix chain 'A' and resid 344 through 363 Processing helix chain 'A' and resid 393 through 403 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 411 through 431 removed outlier: 4.031A pdb=" N ILE A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 442 removed outlier: 3.607A pdb=" N ARG A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 109 through 123 Processing helix chain 'B' and resid 167 through 181 Processing helix chain 'B' and resid 205 through 227 Processing helix chain 'B' and resid 270 through 283 Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 344 through 363 Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 405 through 412 removed outlier: 3.541A pdb=" N LYS B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 Processing helix chain 'B' and resid 435 through 442 Processing helix chain 'C' and resid 8 through 19 Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 109 through 123 Processing helix chain 'C' and resid 167 through 181 Processing helix chain 'C' and resid 205 through 227 Processing helix chain 'C' and resid 270 through 283 Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 328 through 332 removed outlier: 3.811A pdb=" N SER C 331 " --> pdb=" O ARG C 328 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR C 332 " --> pdb=" O GLY C 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 328 through 332' Processing helix chain 'C' and resid 344 through 363 Processing helix chain 'C' and resid 393 through 403 Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 411 through 432 removed outlier: 4.007A pdb=" N ILE C 415 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR C 416 " --> pdb=" O GLY C 412 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 442 removed outlier: 3.509A pdb=" N ARG C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 19 Processing helix chain 'D' and resid 40 through 42 No H-bonds generated for 'chain 'D' and resid 40 through 42' Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 109 through 123 Processing helix chain 'D' and resid 167 through 181 Processing helix chain 'D' and resid 205 through 227 Processing helix chain 'D' and resid 270 through 283 Processing helix chain 'D' and resid 287 through 292 Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 344 through 363 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 412 removed outlier: 3.526A pdb=" N LYS D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 432 removed outlier: 3.867A pdb=" N THR D 432 " --> pdb=" O ASP D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 442 Processing helix chain 'E' and resid 8 through 19 Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 109 through 123 Processing helix chain 'E' and resid 167 through 181 Processing helix chain 'E' and resid 205 through 227 Processing helix chain 'E' and resid 270 through 283 Processing helix chain 'E' and resid 287 through 292 Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 328 through 332 removed outlier: 3.815A pdb=" N SER E 331 " --> pdb=" O ARG E 328 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR E 332 " --> pdb=" O GLY E 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 328 through 332' Processing helix chain 'E' and resid 344 through 363 Processing helix chain 'E' and resid 393 through 403 Processing helix chain 'E' and resid 406 through 411 Processing helix chain 'E' and resid 413 through 431 Processing helix chain 'E' and resid 435 through 442 Processing helix chain 'F' and resid 8 through 19 Processing helix chain 'F' and resid 40 through 42 No H-bonds generated for 'chain 'F' and resid 40 through 42' Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 109 through 123 Processing helix chain 'F' and resid 167 through 181 Processing helix chain 'F' and resid 205 through 227 Processing helix chain 'F' and resid 270 through 283 Processing helix chain 'F' and resid 287 through 292 Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 344 through 363 Processing helix chain 'F' and resid 393 through 403 Processing helix chain 'F' and resid 405 through 432 removed outlier: 3.544A pdb=" N LYS F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN F 413 " --> pdb=" O LYS F 409 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N HIS F 414 " --> pdb=" O ALA F 410 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE F 415 " --> pdb=" O LEU F 411 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR F 416 " --> pdb=" O GLY F 412 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR F 432 " --> pdb=" O ASP F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 442 Processing helix chain 'G' and resid 8 through 19 Processing helix chain 'G' and resid 43 through 49 Processing helix chain 'G' and resid 109 through 123 Processing helix chain 'G' and resid 167 through 181 Processing helix chain 'G' and resid 205 through 227 Processing helix chain 'G' and resid 270 through 283 Processing helix chain 'G' and resid 287 through 292 Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 328 through 332 removed outlier: 3.804A pdb=" N SER G 331 " --> pdb=" O ARG G 328 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR G 332 " --> pdb=" O GLY G 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 328 through 332' Processing helix chain 'G' and resid 344 through 363 Processing helix chain 'G' and resid 393 through 403 Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 413 through 431 Processing helix chain 'G' and resid 435 through 442 removed outlier: 3.618A pdb=" N ARG G 439 " --> pdb=" O SER G 435 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 19 Processing helix chain 'H' and resid 40 through 42 No H-bonds generated for 'chain 'H' and resid 40 through 42' Processing helix chain 'H' and resid 43 through 49 Processing helix chain 'H' and resid 109 through 123 Processing helix chain 'H' and resid 167 through 181 Processing helix chain 'H' and resid 205 through 227 Processing helix chain 'H' and resid 270 through 283 Processing helix chain 'H' and resid 287 through 292 Processing helix chain 'H' and resid 296 through 301 Processing helix chain 'H' and resid 344 through 363 Processing helix chain 'H' and resid 393 through 403 Processing helix chain 'H' and resid 405 through 412 Processing helix chain 'H' and resid 413 through 431 Processing helix chain 'H' and resid 435 through 442 Processing helix chain 'I' and resid 8 through 19 Processing helix chain 'I' and resid 43 through 49 Processing helix chain 'I' and resid 109 through 123 Processing helix chain 'I' and resid 167 through 181 Processing helix chain 'I' and resid 205 through 227 Processing helix chain 'I' and resid 270 through 283 Processing helix chain 'I' and resid 287 through 292 Processing helix chain 'I' and resid 296 through 301 Processing helix chain 'I' and resid 328 through 332 removed outlier: 3.811A pdb=" N SER I 331 " --> pdb=" O ARG I 328 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR I 332 " --> pdb=" O GLY I 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 328 through 332' Processing helix chain 'I' and resid 344 through 363 Processing helix chain 'I' and resid 393 through 403 Processing helix chain 'I' and resid 406 through 411 Processing helix chain 'I' and resid 411 through 432 removed outlier: 4.006A pdb=" N ILE I 415 " --> pdb=" O LEU I 411 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR I 416 " --> pdb=" O GLY I 412 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR I 432 " --> pdb=" O ASP I 428 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 442 removed outlier: 3.532A pdb=" N ARG I 439 " --> pdb=" O SER I 435 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 19 Processing helix chain 'J' and resid 40 through 42 No H-bonds generated for 'chain 'J' and resid 40 through 42' Processing helix chain 'J' and resid 43 through 49 Processing helix chain 'J' and resid 109 through 123 Processing helix chain 'J' and resid 167 through 181 Processing helix chain 'J' and resid 205 through 227 Processing helix chain 'J' and resid 270 through 283 Processing helix chain 'J' and resid 287 through 292 Processing helix chain 'J' and resid 296 through 301 Processing helix chain 'J' and resid 328 through 332 removed outlier: 3.760A pdb=" N SER J 331 " --> pdb=" O ARG J 328 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR J 332 " --> pdb=" O GLY J 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 328 through 332' Processing helix chain 'J' and resid 344 through 363 Processing helix chain 'J' and resid 393 through 403 Processing helix chain 'J' and resid 405 through 412 removed outlier: 3.539A pdb=" N LYS J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 413 through 432 removed outlier: 3.867A pdb=" N THR J 432 " --> pdb=" O ASP J 428 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 442 Processing helix chain 'K' and resid 8 through 19 Processing helix chain 'K' and resid 43 through 49 Processing helix chain 'K' and resid 109 through 123 Processing helix chain 'K' and resid 167 through 181 Processing helix chain 'K' and resid 205 through 227 Processing helix chain 'K' and resid 270 through 283 Processing helix chain 'K' and resid 287 through 292 Processing helix chain 'K' and resid 296 through 301 Processing helix chain 'K' and resid 328 through 332 removed outlier: 3.819A pdb=" N SER K 331 " --> pdb=" O ARG K 328 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR K 332 " --> pdb=" O GLY K 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 328 through 332' Processing helix chain 'K' and resid 344 through 363 Processing helix chain 'K' and resid 393 through 403 Processing helix chain 'K' and resid 406 through 411 Processing helix chain 'K' and resid 413 through 431 Processing helix chain 'K' and resid 435 through 442 Processing helix chain 'L' and resid 8 through 19 Processing helix chain 'L' and resid 40 through 42 No H-bonds generated for 'chain 'L' and resid 40 through 42' Processing helix chain 'L' and resid 43 through 49 Processing helix chain 'L' and resid 109 through 123 Processing helix chain 'L' and resid 167 through 181 Processing helix chain 'L' and resid 205 through 227 Processing helix chain 'L' and resid 270 through 283 Processing helix chain 'L' and resid 287 through 292 Processing helix chain 'L' and resid 296 through 301 Processing helix chain 'L' and resid 344 through 363 Processing helix chain 'L' and resid 393 through 403 Processing helix chain 'L' and resid 405 through 412 removed outlier: 3.576A pdb=" N LYS L 409 " --> pdb=" O GLU L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 432 removed outlier: 3.798A pdb=" N THR L 432 " --> pdb=" O ASP L 428 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 442 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.279A pdb=" N GLN A 26 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL A 98 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N THR A 28 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N VAL A 91 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N TRP A 79 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ARG A 93 " --> pdb=" O ASP A 77 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASP A 77 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE A 95 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET A 70 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET A 52 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 134 removed outlier: 3.717A pdb=" N HIS A 247 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.461A pdb=" N ASP A 200 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER A 188 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLU A 198 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N HIS A 190 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLN A 196 " --> pdb=" O HIS A 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 310 through 311 removed outlier: 3.700A pdb=" N GLN A 388 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 34 through 37 removed outlier: 6.241A pdb=" N GLN B 26 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL B 98 " --> pdb=" O GLN B 26 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N THR B 28 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 11.746A pdb=" N VAL B 91 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 10.389A pdb=" N TRP B 79 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N ARG B 93 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ASP B 77 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE B 95 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET B 52 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 134 removed outlier: 3.774A pdb=" N HIS B 247 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 152 removed outlier: 5.294A pdb=" N GLU B 151 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLN B 196 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N HIS B 190 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLU B 198 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER B 188 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASP B 200 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 148 through 152 removed outlier: 5.294A pdb=" N GLU B 151 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 22 through 23 Processing sheet with id=AB2, first strand: chain 'C' and resid 34 through 36 removed outlier: 6.265A pdb=" N GLN C 26 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL C 98 " --> pdb=" O GLN C 26 " (cutoff:3.500A) removed outlier: 9.671A pdb=" N THR C 28 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 11.739A pdb=" N VAL C 91 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 10.443A pdb=" N TRP C 79 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N ARG C 93 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ASP C 77 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE C 95 " --> pdb=" O ASP C 75 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET C 70 " --> pdb=" O PHE C 54 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET C 52 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 128 through 134 removed outlier: 3.711A pdb=" N HIS C 247 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 185 through 190 removed outlier: 6.482A pdb=" N ASP C 200 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER C 188 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLU C 198 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N HIS C 190 " --> pdb=" O GLN C 196 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN C 196 " --> pdb=" O HIS C 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 310 through 311 removed outlier: 3.742A pdb=" N GLN C 388 " --> pdb=" O ILE C 311 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 34 through 37 removed outlier: 6.253A pdb=" N GLN D 26 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL D 98 " --> pdb=" O GLN D 26 " (cutoff:3.500A) removed outlier: 9.685A pdb=" N THR D 28 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 11.641A pdb=" N VAL D 91 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 10.352A pdb=" N TRP D 79 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N ARG D 93 " --> pdb=" O ASP D 77 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ASP D 77 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE D 95 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET D 52 " --> pdb=" O LEU D 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 128 through 134 removed outlier: 3.805A pdb=" N HIS D 247 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 250 " --> pdb=" O ILE D 334 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 185 through 190 removed outlier: 6.479A pdb=" N ASP D 200 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER D 188 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLU D 198 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N HIS D 190 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLN D 196 " --> pdb=" O HIS D 190 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 34 through 40 removed outlier: 6.986A pdb=" N TYR E 22 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU E 94 " --> pdb=" O TYR E 22 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG E 24 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N CYS E 96 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN E 26 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL E 98 " --> pdb=" O GLN E 26 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N THR E 28 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N VAL E 91 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 10.489A pdb=" N TRP E 79 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N ARG E 93 " --> pdb=" O ASP E 77 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ASP E 77 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE E 95 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET E 70 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N MET E 52 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 128 through 134 removed outlier: 3.729A pdb=" N HIS E 247 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 185 through 190 removed outlier: 6.514A pdb=" N ASP E 200 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER E 188 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLU E 198 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N HIS E 190 " --> pdb=" O GLN E 196 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLN E 196 " --> pdb=" O HIS E 190 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 310 through 311 removed outlier: 3.804A pdb=" N GLN E 388 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 34 through 37 removed outlier: 6.259A pdb=" N GLN F 26 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL F 98 " --> pdb=" O GLN F 26 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N THR F 28 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 11.659A pdb=" N VAL F 91 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N TRP F 79 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 9.649A pdb=" N ARG F 93 " --> pdb=" O ASP F 77 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ASP F 77 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE F 95 " --> pdb=" O ASP F 75 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET F 70 " --> pdb=" O PHE F 54 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET F 52 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 128 through 134 removed outlier: 3.729A pdb=" N HIS F 247 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 185 through 190 removed outlier: 6.455A pdb=" N ASP F 200 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER F 188 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLU F 198 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N HIS F 190 " --> pdb=" O GLN F 196 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLN F 196 " --> pdb=" O HIS F 190 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 22 through 23 Processing sheet with id=AC8, first strand: chain 'G' and resid 34 through 36 removed outlier: 6.248A pdb=" N GLN G 26 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL G 98 " --> pdb=" O GLN G 26 " (cutoff:3.500A) removed outlier: 9.700A pdb=" N THR G 28 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 11.842A pdb=" N VAL G 91 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 10.476A pdb=" N TRP G 79 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N ARG G 93 " --> pdb=" O ASP G 77 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASP G 77 " --> pdb=" O ARG G 93 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE G 95 " --> pdb=" O ASP G 75 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET G 70 " --> pdb=" O PHE G 54 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N MET G 52 " --> pdb=" O LEU G 72 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 128 through 134 removed outlier: 3.722A pdb=" N HIS G 247 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 185 through 190 removed outlier: 6.467A pdb=" N ASP G 200 " --> pdb=" O GLU G 186 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER G 188 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU G 198 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N HIS G 190 " --> pdb=" O GLN G 196 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLN G 196 " --> pdb=" O HIS G 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 310 through 311 removed outlier: 3.711A pdb=" N GLN G 388 " --> pdb=" O ILE G 311 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 34 through 37 removed outlier: 6.237A pdb=" N GLN H 26 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL H 98 " --> pdb=" O GLN H 26 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N THR H 28 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 11.637A pdb=" N VAL H 91 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N TRP H 79 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ARG H 93 " --> pdb=" O ASP H 77 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ASP H 77 " --> pdb=" O ARG H 93 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE H 95 " --> pdb=" O ASP H 75 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET H 70 " --> pdb=" O PHE H 54 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET H 52 " --> pdb=" O LEU H 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 128 through 134 removed outlier: 3.756A pdb=" N HIS H 247 " --> pdb=" O GLU H 134 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 148 through 152 removed outlier: 4.462A pdb=" N LYS H 141 " --> pdb=" O THR H 149 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLU H 151 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU H 139 " --> pdb=" O GLU H 151 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLN H 196 " --> pdb=" O HIS H 190 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N HIS H 190 " --> pdb=" O GLN H 196 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLU H 198 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER H 188 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP H 200 " --> pdb=" O GLU H 186 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 148 through 152 removed outlier: 4.462A pdb=" N LYS H 141 " --> pdb=" O THR H 149 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLU H 151 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU H 139 " --> pdb=" O GLU H 151 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 22 through 23 Processing sheet with id=AD8, first strand: chain 'I' and resid 34 through 36 removed outlier: 6.265A pdb=" N GLN I 26 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL I 98 " --> pdb=" O GLN I 26 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N THR I 28 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 11.744A pdb=" N VAL I 91 " --> pdb=" O TRP I 79 " (cutoff:3.500A) removed outlier: 10.443A pdb=" N TRP I 79 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N ARG I 93 " --> pdb=" O ASP I 77 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASP I 77 " --> pdb=" O ARG I 93 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE I 95 " --> pdb=" O ASP I 75 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET I 70 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET I 52 " --> pdb=" O LEU I 72 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 128 through 134 removed outlier: 3.720A pdb=" N HIS I 247 " --> pdb=" O GLU I 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 185 through 190 removed outlier: 6.491A pdb=" N ASP I 200 " --> pdb=" O GLU I 186 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER I 188 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLU I 198 " --> pdb=" O SER I 188 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N HIS I 190 " --> pdb=" O GLN I 196 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLN I 196 " --> pdb=" O HIS I 190 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 310 through 311 removed outlier: 3.741A pdb=" N GLN I 388 " --> pdb=" O ILE I 311 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 34 through 37 removed outlier: 6.253A pdb=" N GLN J 26 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL J 98 " --> pdb=" O GLN J 26 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N THR J 28 " --> pdb=" O VAL J 98 " (cutoff:3.500A) removed outlier: 11.654A pdb=" N VAL J 91 " --> pdb=" O TRP J 79 " (cutoff:3.500A) removed outlier: 10.360A pdb=" N TRP J 79 " --> pdb=" O VAL J 91 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N ARG J 93 " --> pdb=" O ASP J 77 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASP J 77 " --> pdb=" O ARG J 93 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE J 95 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N MET J 52 " --> pdb=" O LEU J 72 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 128 through 134 removed outlier: 3.806A pdb=" N HIS J 247 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL J 250 " --> pdb=" O ILE J 334 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 185 through 190 removed outlier: 6.481A pdb=" N ASP J 200 " --> pdb=" O GLU J 186 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER J 188 " --> pdb=" O GLU J 198 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLU J 198 " --> pdb=" O SER J 188 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N HIS J 190 " --> pdb=" O GLN J 196 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLN J 196 " --> pdb=" O HIS J 190 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 22 through 23 Processing sheet with id=AE7, first strand: chain 'K' and resid 34 through 36 removed outlier: 6.252A pdb=" N GLN K 26 " --> pdb=" O CYS K 96 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL K 98 " --> pdb=" O GLN K 26 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N THR K 28 " --> pdb=" O VAL K 98 " (cutoff:3.500A) removed outlier: 11.859A pdb=" N VAL K 91 " --> pdb=" O TRP K 79 " (cutoff:3.500A) removed outlier: 10.495A pdb=" N TRP K 79 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N ARG K 93 " --> pdb=" O ASP K 77 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASP K 77 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE K 95 " --> pdb=" O ASP K 75 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET K 70 " --> pdb=" O PHE K 54 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N MET K 52 " --> pdb=" O LEU K 72 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 128 through 134 removed outlier: 3.733A pdb=" N HIS K 247 " --> pdb=" O GLU K 134 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 185 through 190 removed outlier: 6.506A pdb=" N ASP K 200 " --> pdb=" O GLU K 186 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER K 188 " --> pdb=" O GLU K 198 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU K 198 " --> pdb=" O SER K 188 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N HIS K 190 " --> pdb=" O GLN K 196 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLN K 196 " --> pdb=" O HIS K 190 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 310 through 311 removed outlier: 3.806A pdb=" N GLN K 388 " --> pdb=" O ILE K 311 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 34 through 37 removed outlier: 6.253A pdb=" N GLN L 26 " --> pdb=" O CYS L 96 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL L 98 " --> pdb=" O GLN L 26 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N THR L 28 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 11.654A pdb=" N VAL L 91 " --> pdb=" O TRP L 79 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N TRP L 79 " --> pdb=" O VAL L 91 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N ARG L 93 " --> pdb=" O ASP L 77 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASP L 77 " --> pdb=" O ARG L 93 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE L 95 " --> pdb=" O ASP L 75 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET L 70 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N MET L 52 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 128 through 134 removed outlier: 3.727A pdb=" N HIS L 247 " --> pdb=" O GLU L 134 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 185 through 190 removed outlier: 6.450A pdb=" N ASP L 200 " --> pdb=" O GLU L 186 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER L 188 " --> pdb=" O GLU L 198 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLU L 198 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N HIS L 190 " --> pdb=" O GLN L 196 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLN L 196 " --> pdb=" O HIS L 190 " (cutoff:3.500A) 1708 hydrogen bonds defined for protein. 5004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.06 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13049 1.34 - 1.45: 5666 1.45 - 1.57: 21761 1.57 - 1.69: 0 1.69 - 1.80: 324 Bond restraints: 40800 Sorted by residual: bond pdb=" CG LEU C 161 " pdb=" CD2 LEU C 161 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.60e+00 bond pdb=" CG LEU I 161 " pdb=" CD2 LEU I 161 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.58e+00 bond pdb=" CB LYS L 256 " pdb=" CG LYS L 256 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.56e+00 bond pdb=" CB LYS J 256 " pdb=" CG LYS J 256 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CB ASN F 228 " pdb=" CG ASN F 228 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.07e+00 ... (remaining 40795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 54144 1.73 - 3.47: 902 3.47 - 5.20: 154 5.20 - 6.94: 18 6.94 - 8.67: 6 Bond angle restraints: 55224 Sorted by residual: angle pdb=" C LEU I 48 " pdb=" N ASP I 49 " pdb=" CA ASP I 49 " ideal model delta sigma weight residual 122.65 116.06 6.59 1.66e+00 3.63e-01 1.57e+01 angle pdb=" C LEU A 48 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta sigma weight residual 122.65 116.08 6.57 1.66e+00 3.63e-01 1.57e+01 angle pdb=" C LEU C 48 " pdb=" N ASP C 49 " pdb=" CA ASP C 49 " ideal model delta sigma weight residual 122.65 116.10 6.55 1.66e+00 3.63e-01 1.55e+01 angle pdb=" CB LYS I 256 " pdb=" CG LYS I 256 " pdb=" CD LYS I 256 " ideal model delta sigma weight residual 111.30 119.97 -8.67 2.30e+00 1.89e-01 1.42e+01 angle pdb=" C LEU G 48 " pdb=" N ASP G 49 " pdb=" CA ASP G 49 " ideal model delta sigma weight residual 122.65 116.45 6.20 1.66e+00 3.63e-01 1.40e+01 ... (remaining 55219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 20407 17.88 - 35.75: 3007 35.75 - 53.63: 847 53.63 - 71.51: 243 71.51 - 89.38: 36 Dihedral angle restraints: 24540 sinusoidal: 10116 harmonic: 14424 Sorted by residual: dihedral pdb=" CA TYR I 298 " pdb=" C TYR I 298 " pdb=" N LYS I 299 " pdb=" CA LYS I 299 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TYR C 298 " pdb=" C TYR C 298 " pdb=" N LYS C 299 " pdb=" CA LYS C 299 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TYR G 298 " pdb=" C TYR G 298 " pdb=" N LYS G 299 " pdb=" CA LYS G 299 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 24537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5041 0.058 - 0.117: 808 0.117 - 0.175: 99 0.175 - 0.234: 1 0.234 - 0.292: 3 Chirality restraints: 5952 Sorted by residual: chirality pdb=" CB ILE G 34 " pdb=" CA ILE G 34 " pdb=" CG1 ILE G 34 " pdb=" CG2 ILE G 34 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE A 34 " pdb=" CA ILE A 34 " pdb=" CG1 ILE A 34 " pdb=" CG2 ILE A 34 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE E 34 " pdb=" CA ILE E 34 " pdb=" CG1 ILE E 34 " pdb=" CG2 ILE E 34 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 5949 not shown) Planarity restraints: 7236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 49 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.74e+00 pdb=" CG ASP B 49 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASP B 49 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP B 49 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 228 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.49e+00 pdb=" C ASN C 228 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN C 228 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU C 229 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 228 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C ASN F 228 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN F 228 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU F 229 " 0.014 2.00e-02 2.50e+03 ... (remaining 7233 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 967 2.68 - 3.24: 37569 3.24 - 3.79: 65212 3.79 - 4.35: 88014 4.35 - 4.90: 153058 Nonbonded interactions: 344820 Sorted by model distance: nonbonded pdb=" O ASN L 228 " pdb=" ND2 ASN L 228 " model vdw 2.130 3.120 nonbonded pdb=" NE2 HIS C 230 " pdb=" O MET D 443 " model vdw 2.174 3.120 nonbonded pdb=" OD1 ASP H 358 " pdb=" ND2 ASN H 362 " model vdw 2.204 3.120 nonbonded pdb=" OD1 ASP L 358 " pdb=" ND2 ASN L 362 " model vdw 2.207 3.120 nonbonded pdb=" OD1 ASP B 358 " pdb=" ND2 ASN B 362 " model vdw 2.209 3.120 ... (remaining 344815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 3.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 35.890 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 : 0.004 0.053 40800 Z= 0.170 Angle : 0.583 8.672 55224 Z= 0.312 Chirality : 0.044 0.292 5952 Planarity : 0.004 0.040 7236 Dihedral : 18.683 89.382 15228 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.76 % Favored : 96.00 % Rotamer: Outliers : 2.75 % Allowed : 31.02 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.12), residues: 4872 helix: 1.15 (0.12), residues: 1992 sheet: -1.98 (0.18), residues: 744 loop : -0.86 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 93 TYR 0.016 0.001 TYR G 429 PHE 0.040 0.002 PHE E 14 TRP 0.011 0.001 TRP H 84 HIS 0.002 0.001 HIS H 247 Details of bonding type rmsd covalent geometry : bond 0.00396 (40800) covalent geometry : angle 0.58274 (55224) hydrogen bonds : bond 0.12969 ( 1706) hydrogen bonds : angle 6.97113 ( 5004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1429 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 1310 time to evaluate : 1.334 Fit side-chains REVERT: A 14 PHE cc_start: 0.7887 (m-80) cc_final: 0.7677 (m-80) REVERT: A 71 TYR cc_start: 0.8221 (m-80) cc_final: 0.7468 (m-80) REVERT: A 83 PRO cc_start: 0.7647 (Cg_endo) cc_final: 0.7435 (Cg_exo) REVERT: A 90 LYS cc_start: 0.8338 (ttmm) cc_final: 0.8130 (ttmm) REVERT: A 104 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8235 (p) REVERT: A 120 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6663 (mt-10) REVERT: A 173 ASP cc_start: 0.7605 (m-30) cc_final: 0.7379 (m-30) REVERT: A 177 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7013 (tp30) REVERT: A 198 GLU cc_start: 0.7938 (tt0) cc_final: 0.7399 (tt0) REVERT: A 256 LYS cc_start: 0.8178 (tppt) cc_final: 0.7972 (tppt) REVERT: A 257 GLU cc_start: 0.7612 (tp30) cc_final: 0.7404 (tp30) REVERT: A 335 GLU cc_start: 0.7345 (tt0) cc_final: 0.7060 (tt0) REVERT: A 436 GLU cc_start: 0.7453 (tp30) cc_final: 0.6835 (tp30) REVERT: A 438 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7022 (mt-10) REVERT: A 439 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7357 (mtm180) REVERT: A 440 ASP cc_start: 0.7457 (m-30) cc_final: 0.7212 (m-30) REVERT: B 18 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6543 (mm-30) REVERT: B 46 LYS cc_start: 0.7967 (tttt) cc_final: 0.7720 (tttp) REVERT: B 75 ASP cc_start: 0.7262 (t0) cc_final: 0.7040 (t0) REVERT: B 120 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6558 (mt-10) REVERT: B 147 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6774 (mm-30) REVERT: B 173 ASP cc_start: 0.7604 (m-30) cc_final: 0.7140 (m-30) REVERT: B 323 ARG cc_start: 0.7752 (tmt170) cc_final: 0.7519 (tmm160) REVERT: B 408 LYS cc_start: 0.7605 (tttt) cc_final: 0.7348 (mtpp) REVERT: B 436 GLU cc_start: 0.7309 (tp30) cc_final: 0.6834 (tp30) REVERT: B 438 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7065 (mt-10) REVERT: B 440 ASP cc_start: 0.7458 (m-30) cc_final: 0.7205 (m-30) REVERT: C 13 LYS cc_start: 0.7919 (ttpp) cc_final: 0.7615 (ttmm) REVERT: C 46 LYS cc_start: 0.8037 (tttt) cc_final: 0.7833 (tttm) REVERT: C 71 TYR cc_start: 0.8246 (m-80) cc_final: 0.7607 (m-80) REVERT: C 90 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7822 (tttp) REVERT: C 98 VAL cc_start: 0.8356 (t) cc_final: 0.7820 (p) REVERT: C 104 THR cc_start: 0.8527 (t) cc_final: 0.8321 (p) REVERT: C 109 ASP cc_start: 0.7622 (t0) cc_final: 0.7318 (t70) REVERT: C 147 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6949 (mm-30) REVERT: C 180 ASP cc_start: 0.6708 (m-30) cc_final: 0.6374 (m-30) REVERT: C 257 GLU cc_start: 0.7150 (tp30) cc_final: 0.6862 (tp30) REVERT: C 292 ASN cc_start: 0.8380 (m-40) cc_final: 0.8142 (m110) REVERT: C 366 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8401 (p) REVERT: C 431 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8014 (ttp-170) REVERT: C 436 GLU cc_start: 0.7368 (tp30) cc_final: 0.6510 (tp30) REVERT: C 439 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7464 (mtm110) REVERT: D 14 PHE cc_start: 0.7814 (m-80) cc_final: 0.7305 (m-80) REVERT: D 46 LYS cc_start: 0.8193 (tttt) cc_final: 0.7970 (tttm) REVERT: D 95 ILE cc_start: 0.8579 (mm) cc_final: 0.8238 (mm) REVERT: D 141 LYS cc_start: 0.8424 (mttp) cc_final: 0.8192 (mtpt) REVERT: D 147 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6750 (mm-30) REVERT: D 173 ASP cc_start: 0.7665 (m-30) cc_final: 0.7368 (m-30) REVERT: D 181 MET cc_start: 0.8094 (mtt) cc_final: 0.7648 (mtt) REVERT: D 249 ASN cc_start: 0.8051 (m-40) cc_final: 0.7816 (m-40) REVERT: D 305 TYR cc_start: 0.6064 (OUTLIER) cc_final: 0.5850 (m-10) REVERT: D 406 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7846 (p) REVERT: D 436 GLU cc_start: 0.7332 (tp30) cc_final: 0.6637 (tp30) REVERT: D 439 ARG cc_start: 0.8035 (ttp-170) cc_final: 0.7822 (ttm110) REVERT: D 440 ASP cc_start: 0.7545 (m-30) cc_final: 0.7121 (m-30) REVERT: E 13 LYS cc_start: 0.7608 (ttpp) cc_final: 0.7247 (ttmm) REVERT: E 95 ILE cc_start: 0.8553 (mm) cc_final: 0.8328 (mt) REVERT: E 104 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8394 (p) REVERT: E 120 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6787 (mt-10) REVERT: E 147 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6771 (mm-30) REVERT: E 173 ASP cc_start: 0.7650 (m-30) cc_final: 0.7424 (m-30) REVERT: E 180 ASP cc_start: 0.6718 (m-30) cc_final: 0.6343 (m-30) REVERT: E 201 PHE cc_start: 0.7508 (p90) cc_final: 0.7164 (p90) REVERT: E 203 TYR cc_start: 0.8395 (p90) cc_final: 0.7925 (p90) REVERT: E 214 GLN cc_start: 0.8206 (mm110) cc_final: 0.7959 (mm-40) REVERT: E 361 LYS cc_start: 0.7885 (mttt) cc_final: 0.7664 (mttp) REVERT: E 399 LYS cc_start: 0.8099 (mtpt) cc_final: 0.7859 (mtpp) REVERT: E 438 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7135 (mt-10) REVERT: E 439 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7639 (mtm110) REVERT: F 14 PHE cc_start: 0.7882 (m-80) cc_final: 0.7330 (m-80) REVERT: F 18 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.5926 (mp0) REVERT: F 22 TYR cc_start: 0.7793 (m-80) cc_final: 0.7546 (m-80) REVERT: F 70 MET cc_start: 0.7653 (mmt) cc_final: 0.7374 (mmt) REVERT: F 109 ASP cc_start: 0.7649 (t0) cc_final: 0.7321 (t70) REVERT: F 141 LYS cc_start: 0.8408 (mttp) cc_final: 0.8115 (mtpt) REVERT: F 198 GLU cc_start: 0.7769 (tt0) cc_final: 0.7525 (tt0) REVERT: F 366 VAL cc_start: 0.8489 (t) cc_final: 0.8176 (p) REVERT: F 409 LYS cc_start: 0.7820 (ttpt) cc_final: 0.7530 (ttpp) REVERT: F 430 TYR cc_start: 0.8510 (t80) cc_final: 0.8265 (t80) REVERT: F 440 ASP cc_start: 0.7639 (m-30) cc_final: 0.7326 (m-30) REVERT: G 13 LYS cc_start: 0.7591 (ttpp) cc_final: 0.7211 (ttmm) REVERT: G 14 PHE cc_start: 0.7851 (m-80) cc_final: 0.7523 (m-80) REVERT: G 18 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6561 (mm-30) REVERT: G 69 ASP cc_start: 0.5906 (t70) cc_final: 0.5591 (t0) REVERT: G 109 ASP cc_start: 0.7789 (t0) cc_final: 0.7584 (t0) REVERT: G 120 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6725 (mt-10) REVERT: G 147 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6688 (mm-30) REVERT: G 173 ASP cc_start: 0.7549 (m-30) cc_final: 0.7144 (m-30) REVERT: G 198 GLU cc_start: 0.7899 (tt0) cc_final: 0.7423 (tt0) REVERT: G 211 ASP cc_start: 0.8134 (m-30) cc_final: 0.7862 (m-30) REVERT: G 408 LYS cc_start: 0.8047 (tttm) cc_final: 0.7827 (ttmt) REVERT: G 430 TYR cc_start: 0.8389 (t80) cc_final: 0.8155 (t80) REVERT: G 438 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6843 (mt-10) REVERT: H 14 PHE cc_start: 0.7866 (m-80) cc_final: 0.7662 (m-80) REVERT: H 18 GLU cc_start: 0.6657 (mm-30) cc_final: 0.6443 (mm-30) REVERT: H 71 TYR cc_start: 0.8070 (m-80) cc_final: 0.7155 (m-80) REVERT: H 97 ASP cc_start: 0.7958 (m-30) cc_final: 0.7719 (m-30) REVERT: H 104 THR cc_start: 0.8630 (t) cc_final: 0.8386 (p) REVERT: H 119 LYS cc_start: 0.7818 (tptm) cc_final: 0.7608 (tttm) REVERT: H 120 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6525 (mt-10) REVERT: H 147 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6691 (mm-30) REVERT: H 151 GLU cc_start: 0.7322 (tt0) cc_final: 0.6885 (tt0) REVERT: H 168 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6985 (mt-10) REVERT: H 173 ASP cc_start: 0.7571 (m-30) cc_final: 0.7093 (m-30) REVERT: H 177 GLU cc_start: 0.7299 (tp30) cc_final: 0.6909 (tp30) REVERT: H 205 ASP cc_start: 0.7297 (t0) cc_final: 0.7048 (m-30) REVERT: H 254 LYS cc_start: 0.7886 (ttpt) cc_final: 0.7551 (ttpt) REVERT: H 323 ARG cc_start: 0.7802 (tmt170) cc_final: 0.7584 (tmm160) REVERT: H 409 LYS cc_start: 0.7887 (ttpt) cc_final: 0.7558 (ttpp) REVERT: I 13 LYS cc_start: 0.7831 (ttpp) cc_final: 0.7526 (ttmm) REVERT: I 19 ASN cc_start: 0.7792 (t0) cc_final: 0.7581 (t0) REVERT: I 45 GLU cc_start: 0.6937 (mp0) cc_final: 0.6721 (mp0) REVERT: I 53 MET cc_start: 0.7918 (mtm) cc_final: 0.7698 (ttm) REVERT: I 98 VAL cc_start: 0.8520 (t) cc_final: 0.7973 (p) REVERT: I 109 ASP cc_start: 0.7700 (t0) cc_final: 0.7398 (t70) REVERT: I 408 LYS cc_start: 0.7990 (tttm) cc_final: 0.7718 (mtpp) REVERT: I 436 GLU cc_start: 0.7485 (tp30) cc_final: 0.6703 (tp30) REVERT: I 439 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7119 (mtm110) REVERT: J 12 ARG cc_start: 0.7192 (mtt90) cc_final: 0.6952 (mtt180) REVERT: J 14 PHE cc_start: 0.7959 (m-80) cc_final: 0.7427 (m-80) REVERT: J 119 LYS cc_start: 0.8055 (tptm) cc_final: 0.7812 (tttm) REVERT: J 147 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6767 (mm-30) REVERT: J 173 ASP cc_start: 0.7599 (m-30) cc_final: 0.7315 (m-30) REVERT: J 181 MET cc_start: 0.8243 (mtt) cc_final: 0.7790 (mtt) REVERT: J 203 TYR cc_start: 0.8382 (p90) cc_final: 0.7682 (p90) REVERT: J 254 LYS cc_start: 0.7730 (ttpt) cc_final: 0.7434 (ttpt) REVERT: J 305 TYR cc_start: 0.6267 (OUTLIER) cc_final: 0.6049 (m-10) REVERT: J 395 TYR cc_start: 0.7707 (t80) cc_final: 0.7373 (t80) REVERT: J 423 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8166 (mmtt) REVERT: J 439 ARG cc_start: 0.8054 (ttp-170) cc_final: 0.7647 (ttm110) REVERT: J 440 ASP cc_start: 0.7332 (m-30) cc_final: 0.6934 (m-30) REVERT: K 19 ASN cc_start: 0.7747 (t0) cc_final: 0.7542 (t0) REVERT: K 46 LYS cc_start: 0.8144 (tttt) cc_final: 0.7802 (tttm) REVERT: K 75 ASP cc_start: 0.7228 (t0) cc_final: 0.6974 (t0) REVERT: K 97 ASP cc_start: 0.8009 (m-30) cc_final: 0.7702 (m-30) REVERT: K 121 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7700 (ttp) REVERT: K 147 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6967 (mm-30) REVERT: K 173 ASP cc_start: 0.7615 (m-30) cc_final: 0.7398 (m-30) REVERT: K 203 TYR cc_start: 0.8480 (p90) cc_final: 0.7646 (p90) REVERT: K 214 GLN cc_start: 0.8156 (mm110) cc_final: 0.7926 (mm-40) REVERT: K 256 LYS cc_start: 0.8220 (tppt) cc_final: 0.7983 (tppt) REVERT: K 292 ASN cc_start: 0.8185 (m-40) cc_final: 0.7903 (m-40) REVERT: K 361 LYS cc_start: 0.7928 (mttt) cc_final: 0.7711 (mttp) REVERT: K 436 GLU cc_start: 0.7408 (tp30) cc_final: 0.6736 (tp30) REVERT: K 438 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7186 (mt-10) REVERT: K 439 ARG cc_start: 0.8029 (mtm-85) cc_final: 0.7274 (mtm110) REVERT: L 41 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8106 (t) REVERT: L 141 LYS cc_start: 0.8421 (mttp) cc_final: 0.8171 (mtpt) REVERT: L 147 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6872 (mm-30) REVERT: L 203 TYR cc_start: 0.8349 (p90) cc_final: 0.8130 (p90) REVERT: L 254 LYS cc_start: 0.7891 (ttpt) cc_final: 0.7647 (ttpt) REVERT: L 269 LEU cc_start: 0.8587 (mt) cc_final: 0.8325 (mp) REVERT: L 409 LYS cc_start: 0.7614 (ttpt) cc_final: 0.7402 (ttpp) outliers start: 119 outliers final: 58 residues processed: 1387 average time/residue: 0.2682 time to fit residues: 582.0308 Evaluate side-chains 1278 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 1209 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 79 TRP Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 79 TRP Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 79 TRP Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 79 TRP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 79 TRP Chi-restraints excluded: chain H residue 388 GLN Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 431 ARG Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 50 ASN Chi-restraints excluded: chain J residue 79 TRP Chi-restraints excluded: chain J residue 121 MET Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 264 ASN Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 79 TRP Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 121 MET Chi-restraints excluded: chain K residue 366 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 228 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 470 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 50 ASN B 130 ASN B 249 ASN B 292 ASN B 388 GLN C 242 ASN D 130 ASN D 292 ASN E 130 ASN F 130 ASN F 214 GLN F 249 ASN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN H 388 GLN I 214 GLN I 242 ASN J 130 ASN J 292 ASN ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 ASN K 130 ASN L 130 ASN L 214 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.136364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.122457 restraints weight = 52954.634| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.82 r_work: 0.3409 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 40800 Z= 0.180 Angle : 0.549 7.395 55224 Z= 0.284 Chirality : 0.043 0.192 5952 Planarity : 0.004 0.038 7236 Dihedral : 5.449 52.239 5467 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.86 % Favored : 95.89 % Rotamer: Outliers : 4.16 % Allowed : 25.95 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.12), residues: 4872 helix: 1.35 (0.12), residues: 1992 sheet: -2.09 (0.18), residues: 672 loop : -0.58 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 285 TYR 0.022 0.002 TYR G 203 PHE 0.028 0.002 PHE D 14 TRP 0.014 0.002 TRP D 84 HIS 0.004 0.001 HIS G 190 Details of bonding type rmsd covalent geometry : bond 0.00422 (40800) covalent geometry : angle 0.54914 (55224) hydrogen bonds : bond 0.04260 ( 1706) hydrogen bonds : angle 5.48415 ( 5004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1448 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 1268 time to evaluate : 1.597 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8380 (ttpp) cc_final: 0.7909 (ttmm) REVERT: A 36 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8316 (p0) REVERT: A 69 ASP cc_start: 0.6417 (t70) cc_final: 0.6184 (t0) REVERT: A 75 ASP cc_start: 0.7500 (t0) cc_final: 0.7215 (t0) REVERT: A 83 PRO cc_start: 0.7979 (Cg_endo) cc_final: 0.7744 (Cg_exo) REVERT: A 104 THR cc_start: 0.8636 (t) cc_final: 0.8361 (p) REVERT: A 120 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6960 (mt-10) REVERT: A 136 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7445 (mt-10) REVERT: A 173 ASP cc_start: 0.7803 (m-30) cc_final: 0.7450 (m-30) REVERT: A 177 GLU cc_start: 0.7410 (tp30) cc_final: 0.7147 (tp30) REVERT: A 256 LYS cc_start: 0.8311 (tppt) cc_final: 0.8045 (tppt) REVERT: A 292 ASN cc_start: 0.8226 (m-40) cc_final: 0.7872 (m110) REVERT: A 426 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7722 (mt-10) REVERT: A 436 GLU cc_start: 0.8082 (tp30) cc_final: 0.7666 (tp30) REVERT: A 439 ARG cc_start: 0.8624 (mtm-85) cc_final: 0.8226 (mtm180) REVERT: A 440 ASP cc_start: 0.7600 (m-30) cc_final: 0.7283 (m-30) REVERT: B 35 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7442 (mmtt) REVERT: B 75 ASP cc_start: 0.7574 (t0) cc_final: 0.7313 (m-30) REVERT: B 77 ASP cc_start: 0.7642 (m-30) cc_final: 0.7429 (m-30) REVERT: B 120 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6833 (mt-10) REVERT: B 147 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6970 (mm-30) REVERT: B 173 ASP cc_start: 0.7696 (m-30) cc_final: 0.7364 (m-30) REVERT: B 181 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8182 (mtt) REVERT: B 191 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7999 (mm-30) REVERT: B 292 ASN cc_start: 0.8328 (m110) cc_final: 0.7995 (m-40) REVERT: B 409 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7860 (ttpp) REVERT: C 13 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7862 (ttmm) REVERT: C 90 LYS cc_start: 0.8367 (ttmm) cc_final: 0.8001 (ttmm) REVERT: C 104 THR cc_start: 0.8731 (t) cc_final: 0.8450 (p) REVERT: C 109 ASP cc_start: 0.7569 (t0) cc_final: 0.7203 (t70) REVERT: C 147 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7339 (mm-30) REVERT: C 161 LEU cc_start: 0.7725 (mt) cc_final: 0.7280 (mt) REVERT: C 164 THR cc_start: 0.8037 (m) cc_final: 0.7823 (p) REVERT: C 173 ASP cc_start: 0.7575 (m-30) cc_final: 0.7369 (m-30) REVERT: C 177 GLU cc_start: 0.7649 (tp30) cc_final: 0.7267 (tp30) REVERT: C 180 ASP cc_start: 0.7186 (m-30) cc_final: 0.6813 (m-30) REVERT: C 191 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7839 (tp30) REVERT: C 250 VAL cc_start: 0.8463 (t) cc_final: 0.8100 (m) REVERT: C 256 LYS cc_start: 0.8224 (tppt) cc_final: 0.8001 (tppt) REVERT: C 366 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8511 (p) REVERT: C 439 ARG cc_start: 0.8730 (mtm-85) cc_final: 0.8452 (mtm180) REVERT: D 22 TYR cc_start: 0.7678 (m-80) cc_final: 0.7369 (m-80) REVERT: D 35 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7535 (mttm) REVERT: D 70 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7148 (mmt) REVERT: D 71 TYR cc_start: 0.7913 (m-80) cc_final: 0.7598 (m-80) REVERT: D 75 ASP cc_start: 0.7826 (t70) cc_final: 0.7369 (t0) REVERT: D 95 ILE cc_start: 0.8319 (mm) cc_final: 0.8083 (mt) REVERT: D 116 ARG cc_start: 0.8399 (ttt-90) cc_final: 0.8164 (ttp80) REVERT: D 141 LYS cc_start: 0.8470 (mttp) cc_final: 0.8262 (mtpt) REVERT: D 147 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7075 (mm-30) REVERT: D 173 ASP cc_start: 0.7730 (m-30) cc_final: 0.7337 (m-30) REVERT: D 177 GLU cc_start: 0.7781 (tp30) cc_final: 0.7418 (tp30) REVERT: D 181 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7784 (mtt) REVERT: D 440 ASP cc_start: 0.7853 (m-30) cc_final: 0.7432 (m-30) REVERT: E 13 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7928 (ttmm) REVERT: E 35 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7259 (mttm) REVERT: E 49 ASP cc_start: 0.7881 (m-30) cc_final: 0.7607 (m-30) REVERT: E 75 ASP cc_start: 0.7755 (t70) cc_final: 0.7452 (t70) REVERT: E 104 THR cc_start: 0.8803 (t) cc_final: 0.8532 (p) REVERT: E 116 ARG cc_start: 0.8461 (ttp-110) cc_final: 0.8021 (ttp80) REVERT: E 120 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7092 (mt-10) REVERT: E 147 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7000 (mm-30) REVERT: E 168 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7189 (mt-10) REVERT: E 173 ASP cc_start: 0.7828 (m-30) cc_final: 0.7475 (m-30) REVERT: E 180 ASP cc_start: 0.7150 (m-30) cc_final: 0.6764 (m-30) REVERT: E 181 MET cc_start: 0.8393 (mtp) cc_final: 0.8139 (mtt) REVERT: E 203 TYR cc_start: 0.8493 (p90) cc_final: 0.8213 (p90) REVERT: E 214 GLN cc_start: 0.8360 (mm110) cc_final: 0.8104 (mm-40) REVERT: E 436 GLU cc_start: 0.7942 (tp30) cc_final: 0.7477 (tp30) REVERT: E 439 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.8157 (ttm110) REVERT: F 14 PHE cc_start: 0.7864 (m-80) cc_final: 0.7236 (m-80) REVERT: F 18 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6265 (mp0) REVERT: F 75 ASP cc_start: 0.7589 (t0) cc_final: 0.7356 (t0) REVERT: F 80 VAL cc_start: 0.7988 (t) cc_final: 0.7762 (p) REVERT: F 106 PHE cc_start: 0.8567 (t80) cc_final: 0.8296 (t80) REVERT: F 109 ASP cc_start: 0.7614 (t0) cc_final: 0.7179 (t70) REVERT: F 147 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7169 (mm-30) REVERT: F 151 GLU cc_start: 0.7614 (tt0) cc_final: 0.7316 (tm-30) REVERT: F 177 GLU cc_start: 0.7577 (tp30) cc_final: 0.7048 (tp30) REVERT: F 181 MET cc_start: 0.8367 (mtt) cc_final: 0.7924 (mtt) REVERT: F 191 GLU cc_start: 0.7931 (tp30) cc_final: 0.7625 (mm-30) REVERT: F 198 GLU cc_start: 0.7956 (tt0) cc_final: 0.7569 (tt0) REVERT: F 323 ARG cc_start: 0.7887 (ttt180) cc_final: 0.7677 (ttt-90) REVERT: F 430 TYR cc_start: 0.8569 (t80) cc_final: 0.8295 (t80) REVERT: F 431 ARG cc_start: 0.8613 (ttp-170) cc_final: 0.8400 (ttt-90) REVERT: F 438 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7571 (mt-10) REVERT: F 440 ASP cc_start: 0.7882 (m-30) cc_final: 0.7591 (m-30) REVERT: G 13 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7781 (ttmm) REVERT: G 18 GLU cc_start: 0.7256 (mm-30) cc_final: 0.7004 (mm-30) REVERT: G 69 ASP cc_start: 0.6512 (t70) cc_final: 0.6273 (t0) REVERT: G 75 ASP cc_start: 0.7393 (t0) cc_final: 0.7135 (t0) REVERT: G 120 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7063 (mt-10) REVERT: G 147 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6789 (mm-30) REVERT: G 173 ASP cc_start: 0.7736 (m-30) cc_final: 0.7339 (m-30) REVERT: G 292 ASN cc_start: 0.8286 (m-40) cc_final: 0.7969 (m-40) REVERT: G 335 GLU cc_start: 0.7789 (tt0) cc_final: 0.7496 (tt0) REVERT: G 408 LYS cc_start: 0.8105 (tttm) cc_final: 0.7892 (mtpp) REVERT: H 14 PHE cc_start: 0.7989 (m-80) cc_final: 0.7779 (m-80) REVERT: H 18 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6753 (mm-30) REVERT: H 104 THR cc_start: 0.8669 (t) cc_final: 0.8445 (p) REVERT: H 120 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6717 (mt-10) REVERT: H 124 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7906 (mp) REVERT: H 147 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7124 (mm-30) REVERT: H 151 GLU cc_start: 0.7689 (tt0) cc_final: 0.7241 (tt0) REVERT: H 173 ASP cc_start: 0.7669 (m-30) cc_final: 0.7205 (m-30) REVERT: H 177 GLU cc_start: 0.7546 (tp30) cc_final: 0.7161 (tp30) REVERT: H 181 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7966 (mtt) REVERT: H 184 ASP cc_start: 0.7618 (t0) cc_final: 0.7301 (t0) REVERT: H 186 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7872 (mt-10) REVERT: H 191 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7921 (mm-30) REVERT: H 202 LYS cc_start: 0.8263 (tttp) cc_final: 0.7967 (tttp) REVERT: H 256 LYS cc_start: 0.8273 (tppt) cc_final: 0.8061 (tppt) REVERT: H 409 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7854 (ttpp) REVERT: H 440 ASP cc_start: 0.7588 (m-30) cc_final: 0.7359 (m-30) REVERT: H 443 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7416 (ttt) REVERT: I 13 LYS cc_start: 0.8125 (ttpp) cc_final: 0.7807 (ttmm) REVERT: I 46 LYS cc_start: 0.8188 (tttm) cc_final: 0.7971 (tttm) REVERT: I 53 MET cc_start: 0.8241 (mtm) cc_final: 0.8028 (ttm) REVERT: I 106 PHE cc_start: 0.8492 (t80) cc_final: 0.8173 (t80) REVERT: I 109 ASP cc_start: 0.7634 (t0) cc_final: 0.7244 (t70) REVERT: I 250 VAL cc_start: 0.8510 (t) cc_final: 0.8216 (m) REVERT: I 292 ASN cc_start: 0.8254 (m110) cc_final: 0.7947 (m-40) REVERT: I 323 ARG cc_start: 0.7996 (ttt-90) cc_final: 0.7741 (ttt-90) REVERT: I 408 LYS cc_start: 0.8273 (tttm) cc_final: 0.7922 (mtpp) REVERT: J 35 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7656 (mttt) REVERT: J 70 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7261 (mmt) REVERT: J 71 TYR cc_start: 0.7951 (m-80) cc_final: 0.7624 (m-80) REVERT: J 75 ASP cc_start: 0.7809 (t0) cc_final: 0.7543 (t0) REVERT: J 119 LYS cc_start: 0.8269 (tptm) cc_final: 0.8028 (tttm) REVERT: J 120 GLU cc_start: 0.7623 (tt0) cc_final: 0.7282 (tt0) REVERT: J 147 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7050 (mm-30) REVERT: J 172 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7880 (ttm110) REVERT: J 181 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8020 (mtt) REVERT: J 203 TYR cc_start: 0.8500 (p90) cc_final: 0.7903 (p90) REVERT: J 211 ASP cc_start: 0.8201 (m-30) cc_final: 0.7936 (m-30) REVERT: J 254 LYS cc_start: 0.7826 (ttpt) cc_final: 0.7536 (tppt) REVERT: J 305 TYR cc_start: 0.6151 (OUTLIER) cc_final: 0.5945 (m-10) REVERT: J 354 GLU cc_start: 0.8220 (tp30) cc_final: 0.7947 (tp30) REVERT: J 395 TYR cc_start: 0.7823 (t80) cc_final: 0.7560 (t80) REVERT: J 409 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7776 (ttpp) REVERT: J 411 LEU cc_start: 0.8806 (mt) cc_final: 0.8598 (mt) REVERT: J 428 ASP cc_start: 0.8091 (m-30) cc_final: 0.7878 (m-30) REVERT: J 439 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8038 (mtm110) REVERT: J 440 ASP cc_start: 0.7665 (m-30) cc_final: 0.7339 (m-30) REVERT: K 13 LYS cc_start: 0.8106 (ttpp) cc_final: 0.7804 (ttmm) REVERT: K 34 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.8034 (tp) REVERT: K 35 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7429 (mttt) REVERT: K 46 LYS cc_start: 0.8455 (tttt) cc_final: 0.8194 (tttm) REVERT: K 71 TYR cc_start: 0.8063 (m-80) cc_final: 0.7792 (m-80) REVERT: K 75 ASP cc_start: 0.7631 (t0) cc_final: 0.7380 (m-30) REVERT: K 147 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6942 (mm-30) REVERT: K 173 ASP cc_start: 0.7812 (m-30) cc_final: 0.7425 (m-30) REVERT: K 203 TYR cc_start: 0.8526 (p90) cc_final: 0.7930 (p90) REVERT: K 340 ASP cc_start: 0.7911 (p0) cc_final: 0.7707 (p0) REVERT: K 436 GLU cc_start: 0.8033 (tp30) cc_final: 0.7715 (tp30) REVERT: K 438 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7828 (mt-10) REVERT: K 439 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8235 (mtm-85) REVERT: L 75 ASP cc_start: 0.7644 (t0) cc_final: 0.7400 (t0) REVERT: L 147 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7347 (mm-30) REVERT: L 151 GLU cc_start: 0.7490 (tt0) cc_final: 0.7175 (tm-30) REVERT: L 173 ASP cc_start: 0.7517 (m-30) cc_final: 0.7309 (m-30) REVERT: L 323 ARG cc_start: 0.8029 (ttt180) cc_final: 0.7760 (ttt-90) REVERT: L 392 SER cc_start: 0.7893 (p) cc_final: 0.7422 (t) REVERT: L 409 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7810 (ttpp) outliers start: 180 outliers final: 66 residues processed: 1352 average time/residue: 0.2640 time to fit residues: 560.2286 Evaluate side-chains 1329 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 1242 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 443 MET Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 443 MET Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 443 MET Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 181 MET Chi-restraints excluded: chain J residue 201 PHE Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 409 LYS Chi-restraints excluded: chain J residue 439 ARG Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 201 PHE Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 358 ASP Chi-restraints excluded: chain K residue 443 MET Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 288 THR Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain L residue 409 LYS Chi-restraints excluded: chain L residue 439 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 393 optimal weight: 2.9990 chunk 294 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 394 optimal weight: 0.9980 chunk 286 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 292 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 242 ASN B 249 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN D 292 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 ASN E 130 ASN E 242 ASN F 214 GLN F 249 ASN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN I 130 ASN J 113 ASN J 214 GLN J 249 ASN J 292 ASN K 113 ASN L 214 GLN L 249 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.137407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123544 restraints weight = 52487.506| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.82 r_work: 0.3420 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 40800 Z= 0.153 Angle : 0.523 7.315 55224 Z= 0.269 Chirality : 0.042 0.179 5952 Planarity : 0.004 0.057 7236 Dihedral : 4.643 50.113 5371 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.41 % Favored : 96.35 % Rotamer: Outliers : 4.16 % Allowed : 25.16 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.12), residues: 4872 helix: 1.47 (0.12), residues: 1992 sheet: -1.47 (0.17), residues: 744 loop : -0.56 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.017 0.001 TYR F 298 PHE 0.016 0.001 PHE H 14 TRP 0.015 0.001 TRP I 84 HIS 0.003 0.001 HIS K 230 Details of bonding type rmsd covalent geometry : bond 0.00360 (40800) covalent geometry : angle 0.52301 (55224) hydrogen bonds : bond 0.03956 ( 1706) hydrogen bonds : angle 5.26354 ( 5004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1432 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 1252 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8378 (ttpp) cc_final: 0.7912 (ttmm) REVERT: A 18 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7012 (mm-30) REVERT: A 35 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7536 (mmtp) REVERT: A 69 ASP cc_start: 0.6462 (t70) cc_final: 0.6250 (t0) REVERT: A 75 ASP cc_start: 0.7454 (t0) cc_final: 0.7177 (t0) REVERT: A 82 PHE cc_start: 0.8024 (m-10) cc_final: 0.7727 (m-10) REVERT: A 83 PRO cc_start: 0.7999 (Cg_endo) cc_final: 0.7790 (Cg_exo) REVERT: A 104 THR cc_start: 0.8619 (t) cc_final: 0.8401 (p) REVERT: A 120 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6883 (mt-10) REVERT: A 124 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7791 (mp) REVERT: A 152 LEU cc_start: 0.8029 (mp) cc_final: 0.7709 (mt) REVERT: A 173 ASP cc_start: 0.7824 (m-30) cc_final: 0.7460 (m-30) REVERT: A 177 GLU cc_start: 0.7434 (tp30) cc_final: 0.7139 (tp30) REVERT: A 186 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7862 (mt-10) REVERT: A 198 GLU cc_start: 0.7848 (tt0) cc_final: 0.7622 (tt0) REVERT: A 256 LYS cc_start: 0.8304 (tppt) cc_final: 0.8041 (tppt) REVERT: A 292 ASN cc_start: 0.8254 (m-40) cc_final: 0.7909 (m-40) REVERT: A 323 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7258 (ttt-90) REVERT: A 426 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7736 (mt-10) REVERT: A 436 GLU cc_start: 0.8099 (tp30) cc_final: 0.7661 (tp30) REVERT: A 439 ARG cc_start: 0.8615 (mtm-85) cc_final: 0.8240 (mtm180) REVERT: A 440 ASP cc_start: 0.7646 (m-30) cc_final: 0.7302 (m-30) REVERT: B 35 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7596 (mmtt) REVERT: B 46 LYS cc_start: 0.8014 (tttm) cc_final: 0.7802 (tttm) REVERT: B 75 ASP cc_start: 0.7557 (t0) cc_final: 0.7293 (m-30) REVERT: B 77 ASP cc_start: 0.7625 (m-30) cc_final: 0.7376 (m-30) REVERT: B 120 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6722 (mt-10) REVERT: B 124 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7863 (mp) REVERT: B 147 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7052 (mm-30) REVERT: B 173 ASP cc_start: 0.7717 (m-30) cc_final: 0.7363 (m-30) REVERT: B 181 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8221 (mtt) REVERT: B 408 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7737 (mttp) REVERT: B 409 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7931 (ttpp) REVERT: C 13 LYS cc_start: 0.8178 (ttpp) cc_final: 0.7865 (ttmm) REVERT: C 35 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7561 (mmtt) REVERT: C 71 TYR cc_start: 0.8104 (m-80) cc_final: 0.7565 (m-80) REVERT: C 90 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8140 (ttmm) REVERT: C 104 THR cc_start: 0.8771 (t) cc_final: 0.8504 (p) REVERT: C 109 ASP cc_start: 0.7527 (t0) cc_final: 0.7155 (t70) REVERT: C 147 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7337 (mm-30) REVERT: C 160 ASP cc_start: 0.8004 (m-30) cc_final: 0.7758 (m-30) REVERT: C 173 ASP cc_start: 0.7614 (m-30) cc_final: 0.7301 (m-30) REVERT: C 177 GLU cc_start: 0.7626 (tp30) cc_final: 0.7263 (tp30) REVERT: C 180 ASP cc_start: 0.7237 (m-30) cc_final: 0.6915 (m-30) REVERT: C 250 VAL cc_start: 0.8489 (t) cc_final: 0.8160 (m) REVERT: C 253 PHE cc_start: 0.8208 (m-80) cc_final: 0.7606 (m-80) REVERT: C 366 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8512 (p) REVERT: C 421 ASN cc_start: 0.8029 (m-40) cc_final: 0.7781 (m110) REVERT: C 439 ARG cc_start: 0.8738 (mtm-85) cc_final: 0.8527 (mtm-85) REVERT: D 70 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7082 (mmt) REVERT: D 71 TYR cc_start: 0.7914 (m-80) cc_final: 0.7498 (m-80) REVERT: D 75 ASP cc_start: 0.7794 (t70) cc_final: 0.7345 (t0) REVERT: D 95 ILE cc_start: 0.8275 (mm) cc_final: 0.8059 (mt) REVERT: D 147 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7074 (mm-30) REVERT: D 173 ASP cc_start: 0.7677 (m-30) cc_final: 0.7256 (m-30) REVERT: D 177 GLU cc_start: 0.7734 (tp30) cc_final: 0.7440 (tp30) REVERT: D 181 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8014 (mtt) REVERT: D 298 TYR cc_start: 0.8580 (m-80) cc_final: 0.8286 (m-80) REVERT: D 436 GLU cc_start: 0.8045 (tp30) cc_final: 0.7525 (tp30) REVERT: D 439 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7857 (mtm180) REVERT: D 440 ASP cc_start: 0.7826 (m-30) cc_final: 0.7414 (m-30) REVERT: E 13 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7946 (ttmm) REVERT: E 75 ASP cc_start: 0.7655 (t70) cc_final: 0.7341 (t70) REVERT: E 104 THR cc_start: 0.8833 (t) cc_final: 0.8542 (p) REVERT: E 116 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8147 (ttp80) REVERT: E 120 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7081 (mt-10) REVERT: E 147 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6977 (mm-30) REVERT: E 172 ARG cc_start: 0.8273 (ttp-170) cc_final: 0.7669 (ttm-80) REVERT: E 173 ASP cc_start: 0.7824 (m-30) cc_final: 0.7441 (m-30) REVERT: E 180 ASP cc_start: 0.7230 (m-30) cc_final: 0.6805 (m-30) REVERT: E 181 MET cc_start: 0.8359 (mtp) cc_final: 0.8147 (mtt) REVERT: E 198 GLU cc_start: 0.8153 (tt0) cc_final: 0.7729 (tt0) REVERT: E 203 TYR cc_start: 0.8463 (p90) cc_final: 0.8261 (p90) REVERT: E 335 GLU cc_start: 0.7832 (tt0) cc_final: 0.7555 (tt0) REVERT: E 436 GLU cc_start: 0.7974 (tp30) cc_final: 0.7604 (tp30) REVERT: E 439 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.8153 (ttm110) REVERT: F 14 PHE cc_start: 0.7798 (m-80) cc_final: 0.7242 (m-80) REVERT: F 18 GLU cc_start: 0.6829 (mp0) cc_final: 0.6247 (mp0) REVERT: F 71 TYR cc_start: 0.7940 (m-80) cc_final: 0.7722 (m-10) REVERT: F 80 VAL cc_start: 0.8027 (t) cc_final: 0.7804 (p) REVERT: F 109 ASP cc_start: 0.7588 (t0) cc_final: 0.7201 (t70) REVERT: F 116 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8173 (ttp-110) REVERT: F 168 GLU cc_start: 0.7623 (tt0) cc_final: 0.7423 (tt0) REVERT: F 173 ASP cc_start: 0.7549 (m-30) cc_final: 0.7302 (m-30) REVERT: F 177 GLU cc_start: 0.7547 (tp30) cc_final: 0.7067 (tp30) REVERT: F 181 MET cc_start: 0.8320 (mtt) cc_final: 0.8004 (mtt) REVERT: F 198 GLU cc_start: 0.7949 (tt0) cc_final: 0.7586 (tt0) REVERT: F 323 ARG cc_start: 0.7927 (ttt180) cc_final: 0.7701 (ttt-90) REVERT: F 392 SER cc_start: 0.8035 (OUTLIER) cc_final: 0.7504 (t) REVERT: F 429 TYR cc_start: 0.7861 (m-80) cc_final: 0.7615 (t80) REVERT: F 430 TYR cc_start: 0.8566 (t80) cc_final: 0.8290 (t80) REVERT: F 431 ARG cc_start: 0.8608 (ttp-170) cc_final: 0.8361 (ttt-90) REVERT: F 440 ASP cc_start: 0.7835 (m-30) cc_final: 0.7587 (m-30) REVERT: G 13 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7764 (ttmm) REVERT: G 18 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6957 (mm-30) REVERT: G 35 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7219 (mttm) REVERT: G 69 ASP cc_start: 0.6590 (t70) cc_final: 0.6333 (t0) REVERT: G 75 ASP cc_start: 0.7340 (t0) cc_final: 0.7123 (t0) REVERT: G 120 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7011 (mt-10) REVERT: G 124 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8231 (mp) REVERT: G 147 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6866 (mm-30) REVERT: G 173 ASP cc_start: 0.7697 (m-30) cc_final: 0.7364 (m-30) REVERT: G 191 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7859 (mm-30) REVERT: G 225 ARG cc_start: 0.8210 (tpp80) cc_final: 0.7792 (mmm-85) REVERT: G 292 ASN cc_start: 0.8287 (m-40) cc_final: 0.7999 (m-40) REVERT: G 335 GLU cc_start: 0.7761 (tt0) cc_final: 0.7489 (tt0) REVERT: H 17 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7059 (pt0) REVERT: H 18 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6760 (mm-30) REVERT: H 35 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7508 (mmtt) REVERT: H 75 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: H 80 VAL cc_start: 0.8041 (t) cc_final: 0.7774 (p) REVERT: H 104 THR cc_start: 0.8659 (t) cc_final: 0.8396 (p) REVERT: H 120 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6720 (mt-10) REVERT: H 147 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6967 (mm-30) REVERT: H 151 GLU cc_start: 0.7665 (tt0) cc_final: 0.7242 (tt0) REVERT: H 173 ASP cc_start: 0.7667 (m-30) cc_final: 0.7296 (m-30) REVERT: H 177 GLU cc_start: 0.7507 (tp30) cc_final: 0.7154 (tp30) REVERT: H 179 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6532 (mp0) REVERT: H 181 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8041 (mtt) REVERT: H 184 ASP cc_start: 0.7617 (t0) cc_final: 0.7322 (t0) REVERT: H 191 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7918 (mm-30) REVERT: H 256 LYS cc_start: 0.8282 (tppt) cc_final: 0.8036 (tppt) REVERT: H 257 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7520 (pt0) REVERT: H 409 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7901 (ttpp) REVERT: H 440 ASP cc_start: 0.7600 (m-30) cc_final: 0.7366 (m-30) REVERT: I 13 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7870 (ttmm) REVERT: I 53 MET cc_start: 0.8271 (mtm) cc_final: 0.8023 (ttm) REVERT: I 109 ASP cc_start: 0.7604 (t0) cc_final: 0.7221 (t70) REVERT: I 152 LEU cc_start: 0.8421 (mp) cc_final: 0.8091 (mt) REVERT: I 184 ASP cc_start: 0.7598 (t0) cc_final: 0.7379 (t0) REVERT: I 198 GLU cc_start: 0.8118 (tt0) cc_final: 0.7911 (tt0) REVERT: I 250 VAL cc_start: 0.8523 (t) cc_final: 0.8304 (m) REVERT: I 323 ARG cc_start: 0.7938 (ttt-90) cc_final: 0.7694 (ttt-90) REVERT: I 408 LYS cc_start: 0.8288 (tttm) cc_final: 0.8043 (mtpp) REVERT: J 22 TYR cc_start: 0.7635 (m-80) cc_final: 0.7274 (m-80) REVERT: J 35 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7651 (mttt) REVERT: J 71 TYR cc_start: 0.7884 (m-80) cc_final: 0.7655 (m-80) REVERT: J 75 ASP cc_start: 0.7729 (t0) cc_final: 0.7466 (t0) REVERT: J 124 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7814 (mp) REVERT: J 147 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7071 (mm-30) REVERT: J 173 ASP cc_start: 0.7624 (m-30) cc_final: 0.7177 (m-30) REVERT: J 177 GLU cc_start: 0.7649 (tp30) cc_final: 0.7360 (tp30) REVERT: J 181 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7872 (mtt) REVERT: J 198 GLU cc_start: 0.7999 (tt0) cc_final: 0.7794 (tt0) REVERT: J 203 TYR cc_start: 0.8485 (p90) cc_final: 0.7698 (p90) REVERT: J 211 ASP cc_start: 0.8205 (m-30) cc_final: 0.7974 (m-30) REVERT: J 254 LYS cc_start: 0.7843 (ttpt) cc_final: 0.7531 (tppt) REVERT: J 298 TYR cc_start: 0.8491 (m-80) cc_final: 0.8176 (m-80) REVERT: J 305 TYR cc_start: 0.6174 (OUTLIER) cc_final: 0.5947 (m-10) REVERT: J 395 TYR cc_start: 0.7786 (t80) cc_final: 0.7535 (t80) REVERT: J 409 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7900 (ttpp) REVERT: J 428 ASP cc_start: 0.8117 (m-30) cc_final: 0.7898 (m-30) REVERT: J 439 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8033 (mtm110) REVERT: J 440 ASP cc_start: 0.7652 (m-30) cc_final: 0.7323 (m-30) REVERT: K 13 LYS cc_start: 0.8121 (ttpp) cc_final: 0.7908 (ttmm) REVERT: K 35 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7524 (mmtt) REVERT: K 51 GLU cc_start: 0.7799 (tt0) cc_final: 0.7582 (tt0) REVERT: K 147 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7164 (mm-30) REVERT: K 173 ASP cc_start: 0.7791 (m-30) cc_final: 0.7365 (m-30) REVERT: K 253 PHE cc_start: 0.8190 (m-80) cc_final: 0.7493 (m-80) REVERT: K 438 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7728 (mt-10) REVERT: L 41 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8132 (t) REVERT: L 49 ASP cc_start: 0.7927 (m-30) cc_final: 0.7700 (p0) REVERT: L 75 ASP cc_start: 0.7607 (t0) cc_final: 0.7338 (t0) REVERT: L 80 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7887 (p) REVERT: L 147 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7368 (mm-30) REVERT: L 151 GLU cc_start: 0.7484 (tt0) cc_final: 0.7197 (tm-30) REVERT: L 173 ASP cc_start: 0.7513 (m-30) cc_final: 0.7268 (m-30) REVERT: L 323 ARG cc_start: 0.8043 (ttt180) cc_final: 0.7754 (ttt-90) REVERT: L 392 SER cc_start: 0.7880 (p) cc_final: 0.7446 (t) REVERT: L 399 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8010 (ttpp) REVERT: L 409 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7854 (ttpp) outliers start: 180 outliers final: 87 residues processed: 1325 average time/residue: 0.2615 time to fit residues: 543.6320 Evaluate side-chains 1340 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 1221 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 443 MET Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 90 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 392 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 443 MET Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 121 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 179 GLU Chi-restraints excluded: chain J residue 181 MET Chi-restraints excluded: chain J residue 201 PHE Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain J residue 409 LYS Chi-restraints excluded: chain J residue 439 ARG Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 179 GLU Chi-restraints excluded: chain K residue 201 PHE Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 358 ASP Chi-restraints excluded: chain K residue 443 MET Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 288 THR Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain L residue 409 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 264 optimal weight: 3.9990 chunk 432 optimal weight: 3.9990 chunk 482 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 400 optimal weight: 4.9990 chunk 463 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 245 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 478 optimal weight: 0.9990 chunk 374 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 292 ASN D 249 ASN E 130 ASN F 214 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 GLN G 292 ASN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 ASN J 214 GLN J 249 ASN J 388 GLN K 292 ASN L 214 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.137316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123451 restraints weight = 52267.857| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.82 r_work: 0.3425 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 40800 Z= 0.166 Angle : 0.528 7.289 55224 Z= 0.271 Chirality : 0.043 0.171 5952 Planarity : 0.004 0.060 7236 Dihedral : 4.419 46.702 5361 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.37 % Favored : 96.39 % Rotamer: Outliers : 4.78 % Allowed : 24.95 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.12), residues: 4872 helix: 1.45 (0.12), residues: 1992 sheet: -1.82 (0.18), residues: 672 loop : -0.37 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 439 TYR 0.019 0.001 TYR F 298 PHE 0.013 0.002 PHE E 54 TRP 0.010 0.001 TRP B 79 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00394 (40800) covalent geometry : angle 0.52807 (55224) hydrogen bonds : bond 0.03981 ( 1706) hydrogen bonds : angle 5.17575 ( 5004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1475 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 1268 time to evaluate : 1.459 Fit side-chains REVERT: A 13 LYS cc_start: 0.8400 (ttpp) cc_final: 0.7908 (ttmm) REVERT: A 18 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7020 (mm-30) REVERT: A 35 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7348 (mttp) REVERT: A 69 ASP cc_start: 0.6497 (t70) cc_final: 0.6262 (t0) REVERT: A 75 ASP cc_start: 0.7458 (t0) cc_final: 0.7181 (t0) REVERT: A 82 PHE cc_start: 0.7956 (m-10) cc_final: 0.7684 (m-10) REVERT: A 83 PRO cc_start: 0.8036 (Cg_endo) cc_final: 0.7804 (Cg_exo) REVERT: A 104 THR cc_start: 0.8694 (t) cc_final: 0.8436 (p) REVERT: A 120 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6921 (mt-10) REVERT: A 173 ASP cc_start: 0.7816 (m-30) cc_final: 0.7456 (m-30) REVERT: A 177 GLU cc_start: 0.7394 (tp30) cc_final: 0.7106 (tp30) REVERT: A 198 GLU cc_start: 0.7765 (tt0) cc_final: 0.7516 (tt0) REVERT: A 256 LYS cc_start: 0.8276 (tppt) cc_final: 0.8015 (tppt) REVERT: A 292 ASN cc_start: 0.8270 (m110) cc_final: 0.7935 (m-40) REVERT: A 436 GLU cc_start: 0.8101 (tp30) cc_final: 0.7502 (tp30) REVERT: A 439 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.8137 (mtm180) REVERT: A 440 ASP cc_start: 0.7620 (m-30) cc_final: 0.7258 (m-30) REVERT: B 35 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7392 (mmtt) REVERT: B 46 LYS cc_start: 0.7990 (tttm) cc_final: 0.7784 (tttm) REVERT: B 75 ASP cc_start: 0.7596 (t0) cc_final: 0.7308 (m-30) REVERT: B 77 ASP cc_start: 0.7651 (m-30) cc_final: 0.7397 (m-30) REVERT: B 116 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7676 (ttp-110) REVERT: B 120 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6721 (mt-10) REVERT: B 147 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6949 (mm-30) REVERT: B 173 ASP cc_start: 0.7708 (m-30) cc_final: 0.7356 (m-30) REVERT: B 181 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8207 (mtt) REVERT: B 191 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7869 (mm-30) REVERT: B 198 GLU cc_start: 0.7751 (tt0) cc_final: 0.7421 (tt0) REVERT: B 408 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7698 (mttp) REVERT: B 409 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7995 (ttpp) REVERT: B 444 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8239 (mttp) REVERT: C 13 LYS cc_start: 0.8181 (ttpp) cc_final: 0.7863 (ttmm) REVERT: C 35 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7508 (mttt) REVERT: C 71 TYR cc_start: 0.8101 (m-80) cc_final: 0.7638 (m-80) REVERT: C 104 THR cc_start: 0.8761 (t) cc_final: 0.8443 (p) REVERT: C 109 ASP cc_start: 0.7498 (t0) cc_final: 0.7132 (t70) REVERT: C 121 MET cc_start: 0.8521 (ttm) cc_final: 0.8260 (ttp) REVERT: C 147 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7277 (mm-30) REVERT: C 173 ASP cc_start: 0.7605 (m-30) cc_final: 0.7282 (m-30) REVERT: C 177 GLU cc_start: 0.7664 (tp30) cc_final: 0.7275 (tp30) REVERT: C 180 ASP cc_start: 0.7234 (m-30) cc_final: 0.6867 (m-30) REVERT: C 250 VAL cc_start: 0.8496 (t) cc_final: 0.8169 (m) REVERT: C 366 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8537 (p) REVERT: C 421 ASN cc_start: 0.8020 (m-40) cc_final: 0.7773 (m110) REVERT: C 438 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7744 (mt-10) REVERT: C 439 ARG cc_start: 0.8735 (mtm-85) cc_final: 0.8482 (mtt90) REVERT: D 35 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7571 (mttt) REVERT: D 75 ASP cc_start: 0.7770 (t70) cc_final: 0.7318 (t0) REVERT: D 124 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7810 (mp) REVERT: D 147 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7023 (mm-30) REVERT: D 173 ASP cc_start: 0.7723 (m-30) cc_final: 0.7298 (m-30) REVERT: D 177 GLU cc_start: 0.7721 (tp30) cc_final: 0.7415 (tp30) REVERT: D 181 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7957 (mtt) REVERT: D 184 ASP cc_start: 0.7371 (t0) cc_final: 0.7149 (t0) REVERT: D 436 GLU cc_start: 0.8114 (tp30) cc_final: 0.7623 (tp30) REVERT: D 439 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7816 (mtm180) REVERT: D 440 ASP cc_start: 0.7832 (m-30) cc_final: 0.7431 (m-30) REVERT: E 13 LYS cc_start: 0.8203 (ttpp) cc_final: 0.7976 (ttmm) REVERT: E 33 THR cc_start: 0.8132 (m) cc_final: 0.7848 (p) REVERT: E 35 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7241 (mmmt) REVERT: E 49 ASP cc_start: 0.7971 (m-30) cc_final: 0.7707 (m-30) REVERT: E 75 ASP cc_start: 0.7580 (t70) cc_final: 0.7274 (t70) REVERT: E 104 THR cc_start: 0.8842 (t) cc_final: 0.8534 (p) REVERT: E 147 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6978 (mm-30) REVERT: E 160 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.8025 (m-30) REVERT: E 171 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7752 (mtp-110) REVERT: E 172 ARG cc_start: 0.8267 (ttp-170) cc_final: 0.7640 (ttm-80) REVERT: E 173 ASP cc_start: 0.7813 (m-30) cc_final: 0.7414 (m-30) REVERT: E 180 ASP cc_start: 0.7304 (m-30) cc_final: 0.6995 (m-30) REVERT: E 181 MET cc_start: 0.8379 (mtp) cc_final: 0.8164 (mtt) REVERT: E 198 GLU cc_start: 0.8100 (tt0) cc_final: 0.7642 (tt0) REVERT: E 202 LYS cc_start: 0.8341 (ttmm) cc_final: 0.8140 (tttp) REVERT: E 203 TYR cc_start: 0.8403 (p90) cc_final: 0.8120 (p90) REVERT: E 335 GLU cc_start: 0.7826 (tt0) cc_final: 0.7560 (tt0) REVERT: E 436 GLU cc_start: 0.8007 (tp30) cc_final: 0.7552 (tp30) REVERT: E 439 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.8164 (ttm110) REVERT: E 440 ASP cc_start: 0.7743 (m-30) cc_final: 0.7531 (m-30) REVERT: F 14 PHE cc_start: 0.7722 (m-80) cc_final: 0.7129 (m-80) REVERT: F 18 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: F 53 MET cc_start: 0.8358 (ttm) cc_final: 0.8110 (mmm) REVERT: F 80 VAL cc_start: 0.8052 (t) cc_final: 0.7815 (p) REVERT: F 109 ASP cc_start: 0.7579 (t0) cc_final: 0.7159 (t70) REVERT: F 124 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7640 (mp) REVERT: F 151 GLU cc_start: 0.7638 (tt0) cc_final: 0.7297 (tt0) REVERT: F 173 ASP cc_start: 0.7614 (m-30) cc_final: 0.7329 (m-30) REVERT: F 177 GLU cc_start: 0.7539 (tp30) cc_final: 0.7078 (tp30) REVERT: F 181 MET cc_start: 0.8335 (mtt) cc_final: 0.7941 (mtt) REVERT: F 323 ARG cc_start: 0.7992 (ttt180) cc_final: 0.7748 (ttt-90) REVERT: F 392 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7835 (m) REVERT: F 426 GLU cc_start: 0.7917 (tt0) cc_final: 0.7602 (mt-10) REVERT: F 430 TYR cc_start: 0.8553 (t80) cc_final: 0.8283 (t80) REVERT: F 431 ARG cc_start: 0.8578 (ttp-170) cc_final: 0.8321 (ttt-90) REVERT: F 440 ASP cc_start: 0.7829 (m-30) cc_final: 0.7612 (m-30) REVERT: G 13 LYS cc_start: 0.8189 (ttpp) cc_final: 0.7781 (ttmm) REVERT: G 18 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7005 (mm-30) REVERT: G 35 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7516 (mmtt) REVERT: G 69 ASP cc_start: 0.6695 (t70) cc_final: 0.6445 (t0) REVERT: G 75 ASP cc_start: 0.7368 (t0) cc_final: 0.7106 (t0) REVERT: G 120 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6957 (mt-10) REVERT: G 147 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6873 (mm-30) REVERT: G 173 ASP cc_start: 0.7693 (m-30) cc_final: 0.7370 (m-30) REVERT: G 191 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7712 (mm-30) REVERT: G 198 GLU cc_start: 0.7785 (tt0) cc_final: 0.7549 (tt0) REVERT: G 225 ARG cc_start: 0.8202 (tpp80) cc_final: 0.7802 (mmm-85) REVERT: G 257 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7240 (tp30) REVERT: G 292 ASN cc_start: 0.8253 (m110) cc_final: 0.7988 (m-40) REVERT: G 335 GLU cc_start: 0.7761 (tt0) cc_final: 0.7505 (tt0) REVERT: H 17 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7102 (pt0) REVERT: H 18 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6755 (mm-30) REVERT: H 35 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7660 (mmtt) REVERT: H 75 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: H 80 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7833 (p) REVERT: H 104 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8391 (p) REVERT: H 120 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6761 (mt-10) REVERT: H 147 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6980 (mm-30) REVERT: H 151 GLU cc_start: 0.7653 (tt0) cc_final: 0.7259 (tt0) REVERT: H 173 ASP cc_start: 0.7716 (m-30) cc_final: 0.7312 (m-30) REVERT: H 177 GLU cc_start: 0.7548 (tp30) cc_final: 0.7185 (tp30) REVERT: H 179 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: H 181 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8077 (mtt) REVERT: H 184 ASP cc_start: 0.7581 (t0) cc_final: 0.7367 (t0) REVERT: H 186 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7876 (mt-10) REVERT: H 256 LYS cc_start: 0.8297 (tppt) cc_final: 0.8045 (tppt) REVERT: H 409 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7899 (ttpp) REVERT: H 440 ASP cc_start: 0.7574 (m-30) cc_final: 0.7360 (m-30) REVERT: I 13 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7906 (ttmm) REVERT: I 109 ASP cc_start: 0.7568 (t0) cc_final: 0.7197 (t70) REVERT: I 124 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7894 (mp) REVERT: I 152 LEU cc_start: 0.8432 (mp) cc_final: 0.8130 (mt) REVERT: I 161 LEU cc_start: 0.7561 (mt) cc_final: 0.7282 (mt) REVERT: I 184 ASP cc_start: 0.7637 (t0) cc_final: 0.7428 (t0) REVERT: I 198 GLU cc_start: 0.8119 (tt0) cc_final: 0.7857 (tt0) REVERT: I 408 LYS cc_start: 0.8242 (tttm) cc_final: 0.8016 (mtpp) REVERT: I 438 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7661 (mt-10) REVERT: I 439 ARG cc_start: 0.8484 (ttm110) cc_final: 0.7730 (mtm110) REVERT: J 22 TYR cc_start: 0.7639 (m-80) cc_final: 0.7269 (m-80) REVERT: J 35 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7659 (mttt) REVERT: J 70 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7123 (mmt) REVERT: J 71 TYR cc_start: 0.7937 (m-80) cc_final: 0.7640 (m-80) REVERT: J 75 ASP cc_start: 0.7674 (t0) cc_final: 0.7399 (t0) REVERT: J 80 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7802 (p) REVERT: J 124 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7834 (mp) REVERT: J 147 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7036 (mm-30) REVERT: J 168 GLU cc_start: 0.7480 (tt0) cc_final: 0.7250 (tt0) REVERT: J 173 ASP cc_start: 0.7658 (m-30) cc_final: 0.7195 (m-30) REVERT: J 177 GLU cc_start: 0.7620 (tp30) cc_final: 0.7356 (tp30) REVERT: J 181 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7887 (mtt) REVERT: J 203 TYR cc_start: 0.8398 (p90) cc_final: 0.7675 (p90) REVERT: J 305 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.5934 (m-10) REVERT: J 366 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8226 (p) REVERT: J 395 TYR cc_start: 0.7749 (t80) cc_final: 0.7533 (t80) REVERT: J 403 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7770 (mt-10) REVERT: J 409 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8072 (ttpp) REVERT: J 439 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8154 (mtm-85) REVERT: J 440 ASP cc_start: 0.7644 (m-30) cc_final: 0.7306 (m-30) REVERT: K 13 LYS cc_start: 0.8148 (ttpp) cc_final: 0.7919 (ttmm) REVERT: K 35 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7428 (mttt) REVERT: K 51 GLU cc_start: 0.7831 (tt0) cc_final: 0.7558 (tt0) REVERT: K 147 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7142 (mm-30) REVERT: K 171 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7915 (mtp-110) REVERT: K 173 ASP cc_start: 0.7766 (m-30) cc_final: 0.7328 (m-30) REVERT: K 253 PHE cc_start: 0.8197 (m-80) cc_final: 0.7492 (m-80) REVERT: K 438 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7736 (mt-10) REVERT: L 18 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6993 (mm-30) REVERT: L 22 TYR cc_start: 0.7559 (m-80) cc_final: 0.7210 (m-10) REVERT: L 24 ARG cc_start: 0.8112 (ttm170) cc_final: 0.7903 (ttm-80) REVERT: L 49 ASP cc_start: 0.7944 (m-30) cc_final: 0.7691 (m-30) REVERT: L 51 GLU cc_start: 0.8129 (tp30) cc_final: 0.7846 (tp30) REVERT: L 71 TYR cc_start: 0.7928 (m-80) cc_final: 0.7637 (m-80) REVERT: L 80 VAL cc_start: 0.8121 (OUTLIER) cc_final: 0.7905 (p) REVERT: L 147 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7372 (mm-30) REVERT: L 173 ASP cc_start: 0.7548 (m-30) cc_final: 0.7262 (m-30) REVERT: L 323 ARG cc_start: 0.8115 (ttt180) cc_final: 0.7826 (ttt-90) REVERT: L 392 SER cc_start: 0.7893 (p) cc_final: 0.7466 (t) REVERT: L 399 LYS cc_start: 0.8450 (ttmt) cc_final: 0.7995 (ttpp) outliers start: 207 outliers final: 103 residues processed: 1359 average time/residue: 0.2624 time to fit residues: 560.2219 Evaluate side-chains 1387 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 1243 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 90 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 392 SER Chi-restraints excluded: chain H residue 409 LYS Chi-restraints excluded: chain H residue 444 LYS Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 443 MET Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 121 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 179 GLU Chi-restraints excluded: chain J residue 181 MET Chi-restraints excluded: chain J residue 201 PHE Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain J residue 409 LYS Chi-restraints excluded: chain J residue 439 ARG Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain K residue 121 MET Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 171 ARG Chi-restraints excluded: chain K residue 179 GLU Chi-restraints excluded: chain K residue 201 PHE Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 358 ASP Chi-restraints excluded: chain K residue 443 MET Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 288 THR Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain L residue 388 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 309 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 454 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 483 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN E 130 ASN E 214 GLN F 214 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 ASN J 214 GLN J 249 ASN K 214 GLN L 214 GLN L 249 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.136880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123555 restraints weight = 52883.740| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.78 r_work: 0.3443 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 40800 Z= 0.150 Angle : 0.517 7.097 55224 Z= 0.265 Chirality : 0.042 0.184 5952 Planarity : 0.004 0.058 7236 Dihedral : 4.367 49.758 5361 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.28 % Favored : 96.47 % Rotamer: Outliers : 4.62 % Allowed : 25.14 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.12), residues: 4872 helix: 1.50 (0.12), residues: 1992 sheet: -1.79 (0.18), residues: 672 loop : -0.28 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 439 TYR 0.020 0.001 TYR F 298 PHE 0.018 0.001 PHE J 14 TRP 0.009 0.001 TRP E 79 HIS 0.002 0.001 HIS I 190 Details of bonding type rmsd covalent geometry : bond 0.00354 (40800) covalent geometry : angle 0.51668 (55224) hydrogen bonds : bond 0.03856 ( 1706) hydrogen bonds : angle 5.09474 ( 5004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1445 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 1245 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8387 (ttpp) cc_final: 0.7902 (ttmm) REVERT: A 18 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6987 (mm-30) REVERT: A 35 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7537 (mmtt) REVERT: A 69 ASP cc_start: 0.6478 (t70) cc_final: 0.6272 (t0) REVERT: A 75 ASP cc_start: 0.7367 (t0) cc_final: 0.7144 (t0) REVERT: A 82 PHE cc_start: 0.7915 (m-10) cc_final: 0.7695 (m-10) REVERT: A 104 THR cc_start: 0.8705 (t) cc_final: 0.8444 (p) REVERT: A 120 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6993 (mt-10) REVERT: A 173 ASP cc_start: 0.7707 (m-30) cc_final: 0.7357 (m-30) REVERT: A 177 GLU cc_start: 0.7396 (tp30) cc_final: 0.7109 (tp30) REVERT: A 198 GLU cc_start: 0.7715 (tt0) cc_final: 0.7416 (tt0) REVERT: A 256 LYS cc_start: 0.8298 (tppt) cc_final: 0.8047 (tppt) REVERT: A 292 ASN cc_start: 0.8300 (m110) cc_final: 0.7982 (m-40) REVERT: A 436 GLU cc_start: 0.8077 (tp30) cc_final: 0.7475 (tp30) REVERT: A 439 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.8109 (mtm180) REVERT: A 440 ASP cc_start: 0.7644 (m-30) cc_final: 0.7297 (m-30) REVERT: B 7 THR cc_start: 0.7348 (OUTLIER) cc_final: 0.7033 (p) REVERT: B 35 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7608 (mmtt) REVERT: B 46 LYS cc_start: 0.8007 (tttm) cc_final: 0.7775 (tttm) REVERT: B 75 ASP cc_start: 0.7483 (t0) cc_final: 0.7230 (m-30) REVERT: B 116 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7696 (ttp-110) REVERT: B 120 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6781 (mt-10) REVERT: B 147 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6978 (mm-30) REVERT: B 173 ASP cc_start: 0.7657 (m-30) cc_final: 0.7300 (m-30) REVERT: B 181 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8266 (mtt) REVERT: B 184 ASP cc_start: 0.7645 (t0) cc_final: 0.7389 (t0) REVERT: B 186 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7850 (mt-10) REVERT: B 198 GLU cc_start: 0.7668 (tt0) cc_final: 0.7413 (tt0) REVERT: B 408 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7600 (mttp) REVERT: B 409 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8090 (ttpp) REVERT: C 13 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7879 (ttmm) REVERT: C 35 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7672 (mttt) REVERT: C 71 TYR cc_start: 0.8084 (m-80) cc_final: 0.7592 (m-80) REVERT: C 104 THR cc_start: 0.8727 (t) cc_final: 0.8475 (p) REVERT: C 109 ASP cc_start: 0.7455 (t0) cc_final: 0.7089 (t70) REVERT: C 147 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7276 (mm-30) REVERT: C 152 LEU cc_start: 0.8239 (mp) cc_final: 0.7925 (mt) REVERT: C 173 ASP cc_start: 0.7498 (m-30) cc_final: 0.7199 (m-30) REVERT: C 177 GLU cc_start: 0.7622 (tp30) cc_final: 0.7336 (tp30) REVERT: C 180 ASP cc_start: 0.7170 (m-30) cc_final: 0.6826 (m-30) REVERT: C 191 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7838 (mm-30) REVERT: C 198 GLU cc_start: 0.8098 (tt0) cc_final: 0.7868 (tt0) REVERT: C 250 VAL cc_start: 0.8532 (t) cc_final: 0.8222 (m) REVERT: C 314 SER cc_start: 0.8152 (m) cc_final: 0.7902 (p) REVERT: C 366 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8566 (p) REVERT: C 392 SER cc_start: 0.7567 (OUTLIER) cc_final: 0.7007 (t) REVERT: C 421 ASN cc_start: 0.7993 (m-40) cc_final: 0.7758 (m110) REVERT: D 70 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7192 (mmt) REVERT: D 75 ASP cc_start: 0.7708 (t70) cc_final: 0.7312 (t0) REVERT: D 124 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7834 (mp) REVERT: D 147 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6906 (mm-30) REVERT: D 173 ASP cc_start: 0.7619 (m-30) cc_final: 0.7186 (m-30) REVERT: D 177 GLU cc_start: 0.7671 (tp30) cc_final: 0.7401 (tp30) REVERT: D 181 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8038 (mtt) REVERT: D 184 ASP cc_start: 0.7423 (t0) cc_final: 0.7214 (t0) REVERT: D 202 LYS cc_start: 0.8208 (tttp) cc_final: 0.8002 (tttp) REVERT: D 436 GLU cc_start: 0.8140 (tp30) cc_final: 0.7690 (tp30) REVERT: D 439 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7778 (mtm180) REVERT: D 440 ASP cc_start: 0.7823 (m-30) cc_final: 0.7444 (m-30) REVERT: E 13 LYS cc_start: 0.8244 (ttpp) cc_final: 0.8015 (ttmm) REVERT: E 29 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7544 (p0) REVERT: E 35 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7660 (mttt) REVERT: E 75 ASP cc_start: 0.7452 (t70) cc_final: 0.7205 (t70) REVERT: E 104 THR cc_start: 0.8802 (t) cc_final: 0.8521 (p) REVERT: E 147 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6971 (mm-30) REVERT: E 173 ASP cc_start: 0.7688 (m-30) cc_final: 0.7305 (m-30) REVERT: E 180 ASP cc_start: 0.7205 (m-30) cc_final: 0.6854 (m-30) REVERT: E 181 MET cc_start: 0.8429 (mtp) cc_final: 0.8222 (mtt) REVERT: E 198 GLU cc_start: 0.8012 (tt0) cc_final: 0.7569 (tt0) REVERT: E 203 TYR cc_start: 0.8373 (p90) cc_final: 0.8119 (p90) REVERT: E 253 PHE cc_start: 0.8202 (m-80) cc_final: 0.7497 (m-80) REVERT: E 335 GLU cc_start: 0.7878 (tt0) cc_final: 0.7572 (tt0) REVERT: E 436 GLU cc_start: 0.7948 (tp30) cc_final: 0.7453 (tp30) REVERT: E 439 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.8160 (ttm110) REVERT: E 440 ASP cc_start: 0.7643 (m-30) cc_final: 0.7367 (m-30) REVERT: F 14 PHE cc_start: 0.7723 (m-80) cc_final: 0.7137 (m-80) REVERT: F 18 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: F 80 VAL cc_start: 0.8030 (t) cc_final: 0.7792 (p) REVERT: F 109 ASP cc_start: 0.7498 (t0) cc_final: 0.7103 (t70) REVERT: F 151 GLU cc_start: 0.7555 (tt0) cc_final: 0.7228 (tt0) REVERT: F 173 ASP cc_start: 0.7523 (m-30) cc_final: 0.7202 (m-30) REVERT: F 191 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7694 (mm-30) REVERT: F 323 ARG cc_start: 0.7939 (ttt180) cc_final: 0.7707 (ttt-90) REVERT: F 392 SER cc_start: 0.8012 (OUTLIER) cc_final: 0.7809 (m) REVERT: F 426 GLU cc_start: 0.7943 (tt0) cc_final: 0.7652 (mt-10) REVERT: F 430 TYR cc_start: 0.8552 (t80) cc_final: 0.8302 (t80) REVERT: F 431 ARG cc_start: 0.8539 (ttp-170) cc_final: 0.8287 (ttt-90) REVERT: F 440 ASP cc_start: 0.7804 (m-30) cc_final: 0.7551 (m-30) REVERT: G 13 LYS cc_start: 0.8236 (ttpp) cc_final: 0.7809 (ttmm) REVERT: G 18 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7015 (mm-30) REVERT: G 35 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7546 (mmtt) REVERT: G 38 GLU cc_start: 0.7938 (tt0) cc_final: 0.7691 (tt0) REVERT: G 69 ASP cc_start: 0.6659 (t70) cc_final: 0.6420 (t0) REVERT: G 120 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7005 (mt-10) REVERT: G 147 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6834 (mm-30) REVERT: G 173 ASP cc_start: 0.7573 (m-30) cc_final: 0.7286 (m-30) REVERT: G 198 GLU cc_start: 0.7781 (tt0) cc_final: 0.7530 (tt0) REVERT: G 225 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7746 (mmm-85) REVERT: G 257 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7163 (tp30) REVERT: G 292 ASN cc_start: 0.8280 (m110) cc_final: 0.8055 (m-40) REVERT: G 335 GLU cc_start: 0.7739 (tt0) cc_final: 0.7469 (tt0) REVERT: H 18 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6714 (mm-30) REVERT: H 46 LYS cc_start: 0.8099 (tttm) cc_final: 0.7898 (tttm) REVERT: H 75 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7286 (m-30) REVERT: H 80 VAL cc_start: 0.8014 (t) cc_final: 0.7772 (p) REVERT: H 104 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8434 (p) REVERT: H 120 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6765 (mt-10) REVERT: H 147 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6954 (mm-30) REVERT: H 151 GLU cc_start: 0.7642 (tt0) cc_final: 0.7294 (tt0) REVERT: H 173 ASP cc_start: 0.7590 (m-30) cc_final: 0.7180 (m-30) REVERT: H 177 GLU cc_start: 0.7519 (tp30) cc_final: 0.7171 (tp30) REVERT: H 179 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6517 (mp0) REVERT: H 181 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8188 (mtt) REVERT: H 184 ASP cc_start: 0.7608 (t0) cc_final: 0.7404 (t0) REVERT: H 186 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7883 (mt-10) REVERT: H 256 LYS cc_start: 0.8313 (tppt) cc_final: 0.8060 (tppt) REVERT: H 257 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7501 (pt0) REVERT: H 409 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7958 (ttpp) REVERT: H 440 ASP cc_start: 0.7516 (m-30) cc_final: 0.7292 (m-30) REVERT: I 13 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7889 (ttmm) REVERT: I 35 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7610 (mmtt) REVERT: I 41 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8202 (t) REVERT: I 71 TYR cc_start: 0.8139 (m-80) cc_final: 0.7648 (m-80) REVERT: I 198 GLU cc_start: 0.8022 (tt0) cc_final: 0.7749 (tt0) REVERT: J 22 TYR cc_start: 0.7561 (m-80) cc_final: 0.7262 (m-80) REVERT: J 70 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.6955 (mmt) REVERT: J 71 TYR cc_start: 0.7978 (m-80) cc_final: 0.7547 (m-80) REVERT: J 80 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7849 (p) REVERT: J 124 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7872 (mp) REVERT: J 147 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7008 (mm-30) REVERT: J 168 GLU cc_start: 0.7411 (tt0) cc_final: 0.7153 (tt0) REVERT: J 173 ASP cc_start: 0.7591 (m-30) cc_final: 0.7145 (m-30) REVERT: J 177 GLU cc_start: 0.7619 (tp30) cc_final: 0.7354 (tp30) REVERT: J 181 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7994 (mtt) REVERT: J 191 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7924 (mm-30) REVERT: J 203 TYR cc_start: 0.8367 (p90) cc_final: 0.7699 (p90) REVERT: J 305 TYR cc_start: 0.6266 (OUTLIER) cc_final: 0.5963 (m-10) REVERT: J 353 LEU cc_start: 0.8602 (tp) cc_final: 0.8343 (tt) REVERT: J 366 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8271 (p) REVERT: J 403 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7761 (mt-10) REVERT: J 409 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8143 (ttpp) REVERT: J 421 ASN cc_start: 0.7903 (m-40) cc_final: 0.7599 (m110) REVERT: J 439 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8195 (ttm110) REVERT: J 440 ASP cc_start: 0.7602 (m-30) cc_final: 0.7281 (m-30) REVERT: K 13 LYS cc_start: 0.8175 (ttpp) cc_final: 0.7954 (ttmm) REVERT: K 35 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7450 (mttt) REVERT: K 51 GLU cc_start: 0.7804 (tt0) cc_final: 0.7489 (tt0) REVERT: K 147 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7110 (mm-30) REVERT: K 171 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7887 (mtp-110) REVERT: K 173 ASP cc_start: 0.7648 (m-30) cc_final: 0.7207 (m-30) REVERT: K 353 LEU cc_start: 0.8539 (tp) cc_final: 0.8256 (tt) REVERT: K 438 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7631 (mt-10) REVERT: L 18 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6975 (mm-30) REVERT: L 22 TYR cc_start: 0.7524 (m-80) cc_final: 0.7187 (m-10) REVERT: L 51 GLU cc_start: 0.8080 (tp30) cc_final: 0.7791 (tp30) REVERT: L 71 TYR cc_start: 0.7875 (m-80) cc_final: 0.7568 (m-80) REVERT: L 75 ASP cc_start: 0.7406 (t0) cc_final: 0.7131 (t0) REVERT: L 80 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7867 (p) REVERT: L 147 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7270 (mm-30) REVERT: L 151 GLU cc_start: 0.7538 (tt0) cc_final: 0.7161 (tm-30) REVERT: L 173 ASP cc_start: 0.7396 (m-30) cc_final: 0.7123 (m-30) REVERT: L 323 ARG cc_start: 0.8092 (ttt180) cc_final: 0.7780 (ttt-90) REVERT: L 392 SER cc_start: 0.7863 (OUTLIER) cc_final: 0.7478 (t) REVERT: L 399 LYS cc_start: 0.8457 (ttmt) cc_final: 0.8051 (ttpp) outliers start: 200 outliers final: 111 residues processed: 1327 average time/residue: 0.2559 time to fit residues: 534.1029 Evaluate side-chains 1367 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 1217 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 388 GLN Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 392 SER Chi-restraints excluded: chain H residue 409 LYS Chi-restraints excluded: chain H residue 444 LYS Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 443 MET Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 121 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 179 GLU Chi-restraints excluded: chain J residue 181 MET Chi-restraints excluded: chain J residue 201 PHE Chi-restraints excluded: chain J residue 226 LYS Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 409 LYS Chi-restraints excluded: chain J residue 439 ARG Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain K residue 121 MET Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 171 ARG Chi-restraints excluded: chain K residue 179 GLU Chi-restraints excluded: chain K residue 201 PHE Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 358 ASP Chi-restraints excluded: chain K residue 392 SER Chi-restraints excluded: chain K residue 443 MET Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 288 THR Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain L residue 388 GLN Chi-restraints excluded: chain L residue 392 SER Chi-restraints excluded: chain L residue 409 LYS Chi-restraints excluded: chain L residue 420 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 38 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 345 optimal weight: 0.0970 chunk 449 optimal weight: 0.9980 chunk 296 optimal weight: 0.9990 chunk 432 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 chunk 343 optimal weight: 2.9990 chunk 431 optimal weight: 0.3980 chunk 321 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN B 214 GLN B 249 ASN E 130 ASN E 214 GLN F 214 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 214 GLN J 249 ASN K 113 ASN K 214 GLN K 292 ASN L 214 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.137788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.124445 restraints weight = 52960.990| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.79 r_work: 0.3456 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 40800 Z= 0.129 Angle : 0.504 6.878 55224 Z= 0.258 Chirality : 0.041 0.170 5952 Planarity : 0.004 0.062 7236 Dihedral : 4.277 52.066 5361 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.20 % Favored : 96.55 % Rotamer: Outliers : 4.48 % Allowed : 25.42 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.12), residues: 4872 helix: 1.62 (0.12), residues: 1980 sheet: -1.74 (0.18), residues: 672 loop : -0.16 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 439 TYR 0.020 0.001 TYR F 298 PHE 0.019 0.001 PHE J 14 TRP 0.009 0.001 TRP E 79 HIS 0.002 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00302 (40800) covalent geometry : angle 0.50391 (55224) hydrogen bonds : bond 0.03686 ( 1706) hydrogen bonds : angle 5.01434 ( 5004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1454 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 1260 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8353 (ttpp) cc_final: 0.7858 (ttmm) REVERT: A 18 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7003 (mm-30) REVERT: A 35 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7502 (mmtt) REVERT: A 69 ASP cc_start: 0.6477 (t70) cc_final: 0.6265 (t0) REVERT: A 75 ASP cc_start: 0.7311 (t0) cc_final: 0.7103 (t0) REVERT: A 82 PHE cc_start: 0.7924 (m-10) cc_final: 0.7706 (m-10) REVERT: A 83 PRO cc_start: 0.8016 (Cg_endo) cc_final: 0.7645 (Cg_exo) REVERT: A 104 THR cc_start: 0.8696 (t) cc_final: 0.8430 (p) REVERT: A 120 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6965 (mt-10) REVERT: A 173 ASP cc_start: 0.7716 (m-30) cc_final: 0.7361 (m-30) REVERT: A 177 GLU cc_start: 0.7399 (tp30) cc_final: 0.7188 (tp30) REVERT: A 198 GLU cc_start: 0.7748 (tt0) cc_final: 0.7381 (tt0) REVERT: A 253 PHE cc_start: 0.8241 (m-80) cc_final: 0.7446 (m-80) REVERT: A 256 LYS cc_start: 0.8292 (tppt) cc_final: 0.8053 (tppt) REVERT: A 436 GLU cc_start: 0.8092 (tp30) cc_final: 0.7663 (tp30) REVERT: A 440 ASP cc_start: 0.7649 (m-30) cc_final: 0.7304 (m-30) REVERT: B 7 THR cc_start: 0.7396 (OUTLIER) cc_final: 0.7067 (p) REVERT: B 35 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7545 (mmtt) REVERT: B 46 LYS cc_start: 0.8037 (tttm) cc_final: 0.7819 (tttm) REVERT: B 71 TYR cc_start: 0.7767 (m-80) cc_final: 0.7143 (m-80) REVERT: B 75 ASP cc_start: 0.7495 (t0) cc_final: 0.7238 (m-30) REVERT: B 116 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7668 (ttp-110) REVERT: B 120 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6745 (mt-10) REVERT: B 147 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7056 (mm-30) REVERT: B 173 ASP cc_start: 0.7590 (m-30) cc_final: 0.7221 (m-30) REVERT: B 181 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8246 (mtt) REVERT: B 184 ASP cc_start: 0.7616 (t0) cc_final: 0.7379 (t0) REVERT: B 198 GLU cc_start: 0.7696 (tt0) cc_final: 0.7458 (tt0) REVERT: B 202 LYS cc_start: 0.8248 (tttp) cc_final: 0.7715 (tttm) REVERT: B 292 ASN cc_start: 0.8291 (m110) cc_final: 0.8035 (m-40) REVERT: B 409 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8123 (ttpp) REVERT: B 444 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8203 (mttp) REVERT: C 13 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7839 (ttmm) REVERT: C 35 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7610 (mttt) REVERT: C 41 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8123 (t) REVERT: C 71 TYR cc_start: 0.8098 (m-80) cc_final: 0.7617 (m-80) REVERT: C 104 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8521 (p) REVERT: C 109 ASP cc_start: 0.7416 (t0) cc_final: 0.7063 (t70) REVERT: C 121 MET cc_start: 0.8489 (ttm) cc_final: 0.8215 (ttp) REVERT: C 147 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7252 (mm-30) REVERT: C 152 LEU cc_start: 0.8211 (mp) cc_final: 0.7894 (mt) REVERT: C 173 ASP cc_start: 0.7486 (m-30) cc_final: 0.7145 (m-30) REVERT: C 177 GLU cc_start: 0.7569 (tp30) cc_final: 0.7272 (tp30) REVERT: C 180 ASP cc_start: 0.7208 (m-30) cc_final: 0.6840 (m-30) REVERT: C 198 GLU cc_start: 0.8084 (tt0) cc_final: 0.7809 (tt0) REVERT: C 250 VAL cc_start: 0.8532 (t) cc_final: 0.8240 (m) REVERT: C 253 PHE cc_start: 0.8101 (m-80) cc_final: 0.7492 (m-80) REVERT: C 314 SER cc_start: 0.8117 (m) cc_final: 0.7876 (p) REVERT: C 366 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8557 (p) REVERT: C 392 SER cc_start: 0.7547 (OUTLIER) cc_final: 0.6983 (t) REVERT: D 70 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7148 (mmt) REVERT: D 75 ASP cc_start: 0.7678 (t70) cc_final: 0.7305 (t70) REVERT: D 124 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7832 (mp) REVERT: D 147 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6904 (mm-30) REVERT: D 173 ASP cc_start: 0.7645 (m-30) cc_final: 0.7209 (m-30) REVERT: D 177 GLU cc_start: 0.7666 (tp30) cc_final: 0.7381 (tp30) REVERT: D 181 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8069 (mtt) REVERT: D 184 ASP cc_start: 0.7400 (t0) cc_final: 0.7183 (t0) REVERT: D 202 LYS cc_start: 0.8185 (tttp) cc_final: 0.7948 (tttp) REVERT: D 436 GLU cc_start: 0.8122 (tp30) cc_final: 0.7751 (tp30) REVERT: D 439 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7755 (mtm180) REVERT: D 440 ASP cc_start: 0.7830 (m-30) cc_final: 0.7454 (m-30) REVERT: E 13 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7845 (ttmm) REVERT: E 35 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7863 (mmtt) REVERT: E 49 ASP cc_start: 0.7774 (m-30) cc_final: 0.7472 (m-30) REVERT: E 75 ASP cc_start: 0.7416 (t70) cc_final: 0.7168 (t70) REVERT: E 104 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8524 (p) REVERT: E 147 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6942 (mm-30) REVERT: E 160 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: E 164 THR cc_start: 0.7936 (m) cc_final: 0.7699 (p) REVERT: E 171 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7829 (mtp-110) REVERT: E 173 ASP cc_start: 0.7651 (m-30) cc_final: 0.7265 (m-30) REVERT: E 180 ASP cc_start: 0.7236 (m-30) cc_final: 0.6868 (m-30) REVERT: E 181 MET cc_start: 0.8430 (mtp) cc_final: 0.8213 (mtt) REVERT: E 198 GLU cc_start: 0.7992 (tt0) cc_final: 0.7369 (tt0) REVERT: E 253 PHE cc_start: 0.8163 (m-80) cc_final: 0.7469 (m-80) REVERT: E 335 GLU cc_start: 0.7838 (tt0) cc_final: 0.7547 (tt0) REVERT: E 436 GLU cc_start: 0.7938 (tp30) cc_final: 0.7330 (tp30) REVERT: E 439 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8158 (ttm110) REVERT: E 440 ASP cc_start: 0.7674 (m-30) cc_final: 0.7305 (m-30) REVERT: F 80 VAL cc_start: 0.8058 (t) cc_final: 0.7809 (p) REVERT: F 109 ASP cc_start: 0.7486 (t0) cc_final: 0.7112 (t70) REVERT: F 151 GLU cc_start: 0.7569 (tt0) cc_final: 0.7224 (tt0) REVERT: F 173 ASP cc_start: 0.7502 (m-30) cc_final: 0.7184 (m-30) REVERT: F 323 ARG cc_start: 0.7943 (ttt180) cc_final: 0.7710 (ttt-90) REVERT: F 426 GLU cc_start: 0.7933 (tt0) cc_final: 0.7652 (mt-10) REVERT: F 430 TYR cc_start: 0.8543 (t80) cc_final: 0.8298 (t80) REVERT: F 431 ARG cc_start: 0.8520 (ttp-170) cc_final: 0.8258 (ttt-90) REVERT: F 440 ASP cc_start: 0.7818 (m-30) cc_final: 0.7557 (m-30) REVERT: G 13 LYS cc_start: 0.8234 (ttpp) cc_final: 0.7814 (ttmm) REVERT: G 18 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7055 (mm-30) REVERT: G 69 ASP cc_start: 0.6666 (t70) cc_final: 0.6423 (t0) REVERT: G 120 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7040 (mt-10) REVERT: G 147 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6813 (mm-30) REVERT: G 173 ASP cc_start: 0.7576 (m-30) cc_final: 0.7276 (m-30) REVERT: G 191 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7757 (mm-30) REVERT: G 198 GLU cc_start: 0.7823 (tt0) cc_final: 0.7612 (tt0) REVERT: G 225 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7762 (mmm-85) REVERT: G 257 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7099 (tp30) REVERT: G 335 GLU cc_start: 0.7721 (tt0) cc_final: 0.7392 (tt0) REVERT: G 403 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7822 (mt-10) REVERT: H 18 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6718 (mm-30) REVERT: H 75 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: H 80 VAL cc_start: 0.8001 (t) cc_final: 0.7765 (p) REVERT: H 104 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8442 (p) REVERT: H 120 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6762 (mt-10) REVERT: H 147 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6913 (mm-30) REVERT: H 151 GLU cc_start: 0.7688 (tt0) cc_final: 0.7350 (tt0) REVERT: H 173 ASP cc_start: 0.7565 (m-30) cc_final: 0.7159 (m-30) REVERT: H 177 GLU cc_start: 0.7526 (tp30) cc_final: 0.7175 (tp30) REVERT: H 179 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: H 181 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8170 (mtt) REVERT: H 186 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7866 (mt-10) REVERT: H 256 LYS cc_start: 0.8303 (tppt) cc_final: 0.8052 (tppt) REVERT: H 257 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7473 (pt0) REVERT: H 409 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7973 (ttpp) REVERT: H 440 ASP cc_start: 0.7501 (m-30) cc_final: 0.7285 (m-30) REVERT: H 444 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8029 (mtmt) REVERT: I 13 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7875 (ttmm) REVERT: I 41 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8194 (t) REVERT: I 71 TYR cc_start: 0.8142 (m-80) cc_final: 0.7681 (m-80) REVERT: I 109 ASP cc_start: 0.7510 (t0) cc_final: 0.7132 (t70) REVERT: I 152 LEU cc_start: 0.8316 (mp) cc_final: 0.8046 (mt) REVERT: I 177 GLU cc_start: 0.7549 (tp30) cc_final: 0.7342 (tp30) REVERT: I 198 GLU cc_start: 0.8034 (tt0) cc_final: 0.7753 (tt0) REVERT: J 22 TYR cc_start: 0.7528 (m-80) cc_final: 0.7285 (m-80) REVERT: J 35 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7715 (mttt) REVERT: J 70 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.6980 (mmt) REVERT: J 71 TYR cc_start: 0.8000 (m-80) cc_final: 0.7552 (m-80) REVERT: J 124 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7861 (mp) REVERT: J 147 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7002 (mm-30) REVERT: J 173 ASP cc_start: 0.7584 (m-30) cc_final: 0.7134 (m-30) REVERT: J 177 GLU cc_start: 0.7638 (tp30) cc_final: 0.7364 (tp30) REVERT: J 181 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8018 (mtt) REVERT: J 191 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7925 (mm-30) REVERT: J 203 TYR cc_start: 0.8361 (p90) cc_final: 0.7646 (p90) REVERT: J 298 TYR cc_start: 0.8396 (m-80) cc_final: 0.8080 (m-80) REVERT: J 305 TYR cc_start: 0.6293 (OUTLIER) cc_final: 0.6049 (m-10) REVERT: J 353 LEU cc_start: 0.8612 (tp) cc_final: 0.8342 (tt) REVERT: J 366 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8249 (p) REVERT: J 403 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7769 (mt-10) REVERT: J 409 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8146 (ttpp) REVERT: J 421 ASN cc_start: 0.7888 (m-40) cc_final: 0.7578 (m110) REVERT: J 439 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8204 (ttm110) REVERT: J 440 ASP cc_start: 0.7590 (m-30) cc_final: 0.7274 (m-30) REVERT: K 13 LYS cc_start: 0.8170 (ttpp) cc_final: 0.7858 (ttmm) REVERT: K 35 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7474 (mttt) REVERT: K 51 GLU cc_start: 0.7873 (tt0) cc_final: 0.7541 (tt0) REVERT: K 75 ASP cc_start: 0.7287 (t70) cc_final: 0.6960 (t70) REVERT: K 147 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7016 (mm-30) REVERT: K 173 ASP cc_start: 0.7618 (m-30) cc_final: 0.7181 (m-30) REVERT: K 203 TYR cc_start: 0.8415 (p90) cc_final: 0.7732 (p90) REVERT: K 253 PHE cc_start: 0.8183 (m-80) cc_final: 0.7528 (m-80) REVERT: K 353 LEU cc_start: 0.8517 (tp) cc_final: 0.8232 (tt) REVERT: K 438 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7645 (mt-10) REVERT: L 18 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6932 (mm-30) REVERT: L 22 TYR cc_start: 0.7500 (m-80) cc_final: 0.7172 (m-10) REVERT: L 51 GLU cc_start: 0.8105 (tp30) cc_final: 0.7787 (tp30) REVERT: L 71 TYR cc_start: 0.7886 (m-80) cc_final: 0.7538 (m-80) REVERT: L 75 ASP cc_start: 0.7377 (t0) cc_final: 0.7097 (t0) REVERT: L 80 VAL cc_start: 0.8074 (OUTLIER) cc_final: 0.7848 (p) REVERT: L 147 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7266 (mm-30) REVERT: L 151 GLU cc_start: 0.7546 (tt0) cc_final: 0.7175 (tm-30) REVERT: L 173 ASP cc_start: 0.7361 (m-30) cc_final: 0.7073 (m-30) REVERT: L 323 ARG cc_start: 0.8058 (ttt180) cc_final: 0.7806 (ttt-90) REVERT: L 399 LYS cc_start: 0.8450 (ttmt) cc_final: 0.8042 (ttpp) outliers start: 194 outliers final: 118 residues processed: 1338 average time/residue: 0.2510 time to fit residues: 529.1474 Evaluate side-chains 1382 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 1225 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 409 LYS Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 408 LYS Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 388 GLN Chi-restraints excluded: chain F residue 409 LYS Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 90 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 392 SER Chi-restraints excluded: chain H residue 409 LYS Chi-restraints excluded: chain H residue 444 LYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 121 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 181 MET Chi-restraints excluded: chain J residue 201 PHE Chi-restraints excluded: chain J residue 226 LYS Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain J residue 409 LYS Chi-restraints excluded: chain J residue 439 ARG Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 121 MET Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 151 GLU Chi-restraints excluded: chain K residue 179 GLU Chi-restraints excluded: chain K residue 201 PHE Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 392 SER Chi-restraints excluded: chain K residue 443 MET Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 288 THR Chi-restraints excluded: chain L residue 297 SER Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 330 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain L residue 388 GLN Chi-restraints excluded: chain L residue 392 SER Chi-restraints excluded: chain L residue 409 LYS Chi-restraints excluded: chain L residue 420 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 93 optimal weight: 0.7980 chunk 294 optimal weight: 4.9990 chunk 461 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 392 optimal weight: 2.9990 chunk 250 optimal weight: 0.4980 chunk 29 optimal weight: 0.0770 chunk 47 optimal weight: 0.7980 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 GLN A 214 GLN D 249 ASN E 113 ASN E 130 ASN E 214 GLN F 214 GLN G 292 ASN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 ASN J 214 GLN J 249 ASN K 214 GLN L 214 GLN L 249 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.137879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124587 restraints weight = 52910.182| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.81 r_work: 0.3449 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 40800 Z= 0.145 Angle : 0.519 6.842 55224 Z= 0.266 Chirality : 0.042 0.151 5952 Planarity : 0.004 0.061 7236 Dihedral : 4.316 53.741 5361 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.43 % Favored : 96.33 % Rotamer: Outliers : 4.78 % Allowed : 25.21 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.12), residues: 4872 helix: 1.60 (0.12), residues: 1980 sheet: -1.71 (0.18), residues: 672 loop : -0.13 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 439 TYR 0.021 0.001 TYR I 298 PHE 0.020 0.001 PHE J 14 TRP 0.009 0.001 TRP E 79 HIS 0.003 0.001 HIS H 73 Details of bonding type rmsd covalent geometry : bond 0.00343 (40800) covalent geometry : angle 0.51861 (55224) hydrogen bonds : bond 0.03781 ( 1706) hydrogen bonds : angle 4.98853 ( 5004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1450 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 1243 time to evaluate : 1.424 Fit side-chains REVERT: A 13 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7815 (ttmm) REVERT: A 18 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7049 (mm-30) REVERT: A 35 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7592 (mmtt) REVERT: A 69 ASP cc_start: 0.6457 (t70) cc_final: 0.6253 (t0) REVERT: A 82 PHE cc_start: 0.7951 (m-10) cc_final: 0.7712 (m-10) REVERT: A 83 PRO cc_start: 0.8073 (Cg_endo) cc_final: 0.7745 (Cg_exo) REVERT: A 104 THR cc_start: 0.8719 (t) cc_final: 0.8447 (p) REVERT: A 120 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6939 (mt-10) REVERT: A 173 ASP cc_start: 0.7805 (m-30) cc_final: 0.7464 (m-30) REVERT: A 177 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7125 (tp30) REVERT: A 180 ASP cc_start: 0.7262 (m-30) cc_final: 0.6855 (m-30) REVERT: A 191 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7850 (mm-30) REVERT: A 198 GLU cc_start: 0.7843 (tt0) cc_final: 0.7609 (tt0) REVERT: A 253 PHE cc_start: 0.8256 (m-80) cc_final: 0.7480 (m-80) REVERT: A 256 LYS cc_start: 0.8231 (tppt) cc_final: 0.8005 (tppt) REVERT: A 436 GLU cc_start: 0.8132 (tp30) cc_final: 0.7819 (tp30) REVERT: A 439 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.8217 (mtm180) REVERT: A 440 ASP cc_start: 0.7696 (m-30) cc_final: 0.7483 (m-30) REVERT: B 7 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.7158 (p) REVERT: B 35 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7436 (mmtt) REVERT: B 46 LYS cc_start: 0.8043 (tttm) cc_final: 0.7832 (tttm) REVERT: B 71 TYR cc_start: 0.7764 (m-80) cc_final: 0.7209 (m-80) REVERT: B 75 ASP cc_start: 0.7468 (t0) cc_final: 0.7214 (m-30) REVERT: B 116 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7679 (ttp-110) REVERT: B 120 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6749 (mt-10) REVERT: B 147 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7001 (mm-30) REVERT: B 173 ASP cc_start: 0.7665 (m-30) cc_final: 0.7311 (m-30) REVERT: B 181 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8203 (mtt) REVERT: B 184 ASP cc_start: 0.7641 (t0) cc_final: 0.7132 (t0) REVERT: B 186 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7651 (mp0) REVERT: B 191 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7927 (mm-30) REVERT: B 198 GLU cc_start: 0.7690 (tt0) cc_final: 0.7343 (tt0) REVERT: B 202 LYS cc_start: 0.7952 (tttp) cc_final: 0.7626 (tttm) REVERT: B 292 ASN cc_start: 0.8301 (m110) cc_final: 0.8046 (m-40) REVERT: B 409 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8150 (ttpp) REVERT: C 13 LYS cc_start: 0.8140 (ttpp) cc_final: 0.7806 (ttmm) REVERT: C 35 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7774 (mttt) REVERT: C 41 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8142 (t) REVERT: C 71 TYR cc_start: 0.8091 (m-80) cc_final: 0.7619 (m-80) REVERT: C 82 PHE cc_start: 0.7897 (m-10) cc_final: 0.7690 (m-80) REVERT: C 104 THR cc_start: 0.8759 (t) cc_final: 0.8492 (p) REVERT: C 109 ASP cc_start: 0.7450 (t0) cc_final: 0.7089 (t70) REVERT: C 115 LYS cc_start: 0.8360 (mttt) cc_final: 0.8096 (mttt) REVERT: C 121 MET cc_start: 0.8533 (ttm) cc_final: 0.8236 (ttp) REVERT: C 152 LEU cc_start: 0.8232 (mp) cc_final: 0.7960 (mt) REVERT: C 173 ASP cc_start: 0.7554 (m-30) cc_final: 0.7204 (m-30) REVERT: C 180 ASP cc_start: 0.7264 (m-30) cc_final: 0.6911 (m-30) REVERT: C 198 GLU cc_start: 0.8109 (tt0) cc_final: 0.7841 (tt0) REVERT: C 250 VAL cc_start: 0.8531 (t) cc_final: 0.8255 (m) REVERT: C 253 PHE cc_start: 0.8145 (m-80) cc_final: 0.7490 (m-80) REVERT: C 314 SER cc_start: 0.8152 (m) cc_final: 0.7893 (p) REVERT: C 366 VAL cc_start: 0.8863 (OUTLIER) cc_final: 0.8554 (p) REVERT: C 392 SER cc_start: 0.7592 (OUTLIER) cc_final: 0.7026 (t) REVERT: C 421 ASN cc_start: 0.8018 (m-40) cc_final: 0.7792 (m110) REVERT: C 436 GLU cc_start: 0.8064 (tp30) cc_final: 0.7427 (tp30) REVERT: C 439 ARG cc_start: 0.8648 (mtt90) cc_final: 0.8148 (mtm110) REVERT: D 70 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7130 (mmt) REVERT: D 75 ASP cc_start: 0.7641 (t70) cc_final: 0.7235 (t0) REVERT: D 124 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7854 (mp) REVERT: D 147 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6989 (mm-30) REVERT: D 173 ASP cc_start: 0.7691 (m-30) cc_final: 0.7271 (m-30) REVERT: D 177 GLU cc_start: 0.7703 (tp30) cc_final: 0.7425 (tp30) REVERT: D 181 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8211 (mtt) REVERT: D 436 GLU cc_start: 0.8163 (tp30) cc_final: 0.7805 (tp30) REVERT: D 439 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7801 (mtm180) REVERT: D 440 ASP cc_start: 0.7880 (m-30) cc_final: 0.7504 (m-30) REVERT: E 13 LYS cc_start: 0.8182 (ttpp) cc_final: 0.7820 (ttmm) REVERT: E 35 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7715 (mttt) REVERT: E 75 ASP cc_start: 0.7438 (t70) cc_final: 0.7199 (t70) REVERT: E 104 THR cc_start: 0.8827 (t) cc_final: 0.8550 (p) REVERT: E 147 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6919 (mm-30) REVERT: E 160 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8062 (m-30) REVERT: E 171 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7876 (mtp-110) REVERT: E 173 ASP cc_start: 0.7777 (m-30) cc_final: 0.7409 (m-30) REVERT: E 180 ASP cc_start: 0.7218 (m-30) cc_final: 0.6868 (m-30) REVERT: E 181 MET cc_start: 0.8434 (mtp) cc_final: 0.8227 (mtt) REVERT: E 198 GLU cc_start: 0.8019 (tt0) cc_final: 0.7415 (tt0) REVERT: E 253 PHE cc_start: 0.8179 (m-80) cc_final: 0.7509 (m-80) REVERT: E 335 GLU cc_start: 0.7869 (tt0) cc_final: 0.7558 (tt0) REVERT: E 436 GLU cc_start: 0.8017 (tp30) cc_final: 0.7393 (tp30) REVERT: E 439 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.8173 (ttm110) REVERT: E 440 ASP cc_start: 0.7764 (m-30) cc_final: 0.7383 (m-30) REVERT: F 18 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: F 80 VAL cc_start: 0.8075 (t) cc_final: 0.7846 (p) REVERT: F 109 ASP cc_start: 0.7518 (t0) cc_final: 0.7165 (t70) REVERT: F 151 GLU cc_start: 0.7615 (tt0) cc_final: 0.7276 (tt0) REVERT: F 173 ASP cc_start: 0.7563 (m-30) cc_final: 0.7249 (m-30) REVERT: F 191 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7851 (mm-30) REVERT: F 323 ARG cc_start: 0.7996 (ttt180) cc_final: 0.7764 (ttt-90) REVERT: F 426 GLU cc_start: 0.7987 (tt0) cc_final: 0.7699 (mt-10) REVERT: F 430 TYR cc_start: 0.8536 (t80) cc_final: 0.8307 (t80) REVERT: G 13 LYS cc_start: 0.8217 (ttpp) cc_final: 0.7799 (ttmm) REVERT: G 18 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7076 (mm-30) REVERT: G 35 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7479 (mttt) REVERT: G 38 GLU cc_start: 0.7926 (tt0) cc_final: 0.7720 (tt0) REVERT: G 69 ASP cc_start: 0.6681 (t70) cc_final: 0.6438 (t0) REVERT: G 120 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7014 (mt-10) REVERT: G 147 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6814 (mm-30) REVERT: G 173 ASP cc_start: 0.7651 (m-30) cc_final: 0.7336 (m-30) REVERT: G 198 GLU cc_start: 0.7871 (tt0) cc_final: 0.7533 (tt0) REVERT: G 225 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7777 (mmm-85) REVERT: G 257 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7114 (tp30) REVERT: G 335 GLU cc_start: 0.7744 (tt0) cc_final: 0.7459 (tt0) REVERT: H 18 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6745 (mm-30) REVERT: H 75 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7238 (m-30) REVERT: H 80 VAL cc_start: 0.8012 (t) cc_final: 0.7786 (p) REVERT: H 104 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8443 (p) REVERT: H 116 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7637 (ttp-110) REVERT: H 120 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6719 (mt-10) REVERT: H 147 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6992 (mm-30) REVERT: H 151 GLU cc_start: 0.7703 (tt0) cc_final: 0.7394 (tt0) REVERT: H 173 ASP cc_start: 0.7626 (m-30) cc_final: 0.7219 (m-30) REVERT: H 177 GLU cc_start: 0.7541 (tp30) cc_final: 0.7199 (tp30) REVERT: H 179 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: H 181 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8184 (mtt) REVERT: H 256 LYS cc_start: 0.8210 (tppt) cc_final: 0.7975 (tppt) REVERT: H 257 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7455 (pt0) REVERT: H 409 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8067 (ttpp) REVERT: H 440 ASP cc_start: 0.7581 (m-30) cc_final: 0.7349 (m-30) REVERT: I 13 LYS cc_start: 0.8151 (ttpp) cc_final: 0.7832 (ttmm) REVERT: I 41 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8168 (t) REVERT: I 71 TYR cc_start: 0.8139 (m-80) cc_final: 0.7663 (m-80) REVERT: I 152 LEU cc_start: 0.8302 (mp) cc_final: 0.8040 (mt) REVERT: I 177 GLU cc_start: 0.7542 (tp30) cc_final: 0.7326 (tp30) REVERT: I 198 GLU cc_start: 0.8119 (tt0) cc_final: 0.7838 (tt0) REVERT: J 22 TYR cc_start: 0.7552 (m-80) cc_final: 0.7328 (m-80) REVERT: J 35 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7752 (mttt) REVERT: J 70 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.6988 (mmt) REVERT: J 71 TYR cc_start: 0.8032 (m-80) cc_final: 0.7821 (m-80) REVERT: J 80 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7893 (p) REVERT: J 124 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7880 (mp) REVERT: J 147 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7155 (mm-30) REVERT: J 173 ASP cc_start: 0.7630 (m-30) cc_final: 0.7202 (m-30) REVERT: J 177 GLU cc_start: 0.7677 (tp30) cc_final: 0.7433 (tp30) REVERT: J 181 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8040 (mtt) REVERT: J 203 TYR cc_start: 0.8382 (p90) cc_final: 0.7701 (p90) REVERT: J 298 TYR cc_start: 0.8424 (m-80) cc_final: 0.8126 (m-80) REVERT: J 353 LEU cc_start: 0.8574 (tp) cc_final: 0.8308 (tt) REVERT: J 366 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8246 (p) REVERT: J 403 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7608 (mt-10) REVERT: J 421 ASN cc_start: 0.7933 (m-40) cc_final: 0.7623 (m110) REVERT: J 439 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8198 (ttm110) REVERT: J 440 ASP cc_start: 0.7585 (m-30) cc_final: 0.7247 (m-30) REVERT: K 13 LYS cc_start: 0.8138 (ttpp) cc_final: 0.7822 (ttmm) REVERT: K 35 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7549 (mmtt) REVERT: K 51 GLU cc_start: 0.7812 (tt0) cc_final: 0.7493 (tt0) REVERT: K 147 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6987 (mm-30) REVERT: K 171 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7923 (mtp-110) REVERT: K 173 ASP cc_start: 0.7706 (m-30) cc_final: 0.7290 (m-30) REVERT: K 203 TYR cc_start: 0.8447 (p90) cc_final: 0.7796 (p90) REVERT: K 253 PHE cc_start: 0.8230 (m-80) cc_final: 0.7553 (m-80) REVERT: K 353 LEU cc_start: 0.8508 (tp) cc_final: 0.8218 (tt) REVERT: K 438 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7615 (mt-10) REVERT: L 18 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6909 (mm-30) REVERT: L 22 TYR cc_start: 0.7505 (m-80) cc_final: 0.7135 (m-10) REVERT: L 49 ASP cc_start: 0.7942 (m-30) cc_final: 0.7585 (m-30) REVERT: L 51 GLU cc_start: 0.8071 (tp30) cc_final: 0.7754 (tp30) REVERT: L 71 TYR cc_start: 0.7862 (m-80) cc_final: 0.7468 (m-80) REVERT: L 75 ASP cc_start: 0.7384 (t0) cc_final: 0.7120 (t0) REVERT: L 80 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7880 (p) REVERT: L 147 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7266 (mm-30) REVERT: L 151 GLU cc_start: 0.7608 (tt0) cc_final: 0.7222 (tm-30) REVERT: L 173 ASP cc_start: 0.7463 (m-30) cc_final: 0.7188 (m-30) REVERT: L 323 ARG cc_start: 0.8185 (ttt180) cc_final: 0.7932 (ttt-90) REVERT: L 399 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8042 (ttpp) outliers start: 207 outliers final: 124 residues processed: 1328 average time/residue: 0.2499 time to fit residues: 524.0528 Evaluate side-chains 1392 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1229 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 409 LYS Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 388 GLN Chi-restraints excluded: chain F residue 409 LYS Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 392 SER Chi-restraints excluded: chain H residue 409 LYS Chi-restraints excluded: chain H residue 444 LYS Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 121 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 179 GLU Chi-restraints excluded: chain J residue 181 MET Chi-restraints excluded: chain J residue 201 PHE Chi-restraints excluded: chain J residue 226 LYS Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain J residue 439 ARG Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain K residue 121 MET Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 151 GLU Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 171 ARG Chi-restraints excluded: chain K residue 179 GLU Chi-restraints excluded: chain K residue 201 PHE Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 358 ASP Chi-restraints excluded: chain K residue 366 VAL Chi-restraints excluded: chain K residue 392 SER Chi-restraints excluded: chain K residue 443 MET Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 288 THR Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain L residue 388 GLN Chi-restraints excluded: chain L residue 409 LYS Chi-restraints excluded: chain L residue 420 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 164 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 263 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 327 optimal weight: 2.9990 chunk 476 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN B 249 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN F 214 GLN F 388 GLN G 283 ASN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 214 GLN K 214 GLN K 230 HIS L 214 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122716 restraints weight = 52727.333| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.79 r_work: 0.3431 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 40800 Z= 0.202 Angle : 0.553 7.228 55224 Z= 0.285 Chirality : 0.044 0.174 5952 Planarity : 0.004 0.056 7236 Dihedral : 4.483 55.214 5359 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.59 % Favored : 96.16 % Rotamer: Outliers : 4.48 % Allowed : 25.42 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.12), residues: 4872 helix: 1.19 (0.11), residues: 2064 sheet: -1.75 (0.18), residues: 672 loop : -0.15 (0.15), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 439 TYR 0.024 0.001 TYR I 298 PHE 0.021 0.002 PHE J 14 TRP 0.011 0.001 TRP E 79 HIS 0.004 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00479 (40800) covalent geometry : angle 0.55299 (55224) hydrogen bonds : bond 0.04157 ( 1706) hydrogen bonds : angle 5.07672 ( 5004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1454 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 1260 time to evaluate : 1.488 Fit side-chains REVERT: A 13 LYS cc_start: 0.8392 (ttpp) cc_final: 0.7912 (ttmm) REVERT: A 18 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6998 (mm-30) REVERT: A 35 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7560 (mmtt) REVERT: A 104 THR cc_start: 0.8709 (t) cc_final: 0.8459 (p) REVERT: A 119 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7862 (mmmt) REVERT: A 120 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7024 (mt-10) REVERT: A 173 ASP cc_start: 0.7737 (m-30) cc_final: 0.7377 (m-30) REVERT: A 177 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7118 (tp30) REVERT: A 191 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7946 (mm-30) REVERT: A 198 GLU cc_start: 0.7834 (tt0) cc_final: 0.7303 (tt0) REVERT: A 256 LYS cc_start: 0.8286 (tppt) cc_final: 0.8033 (tppt) REVERT: A 436 GLU cc_start: 0.8102 (tp30) cc_final: 0.7782 (tp30) REVERT: A 439 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8170 (mtm180) REVERT: A 440 ASP cc_start: 0.7627 (m-30) cc_final: 0.7423 (m-30) REVERT: B 7 THR cc_start: 0.7376 (OUTLIER) cc_final: 0.7148 (p) REVERT: B 35 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7908 (mmtt) REVERT: B 71 TYR cc_start: 0.7818 (m-80) cc_final: 0.7167 (m-80) REVERT: B 75 ASP cc_start: 0.7533 (t0) cc_final: 0.7261 (m-30) REVERT: B 116 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7747 (ttp-110) REVERT: B 120 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6814 (mt-10) REVERT: B 147 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7014 (mm-30) REVERT: B 173 ASP cc_start: 0.7630 (m-30) cc_final: 0.7265 (m-30) REVERT: B 181 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8177 (mtt) REVERT: B 184 ASP cc_start: 0.7641 (t0) cc_final: 0.7088 (t0) REVERT: B 186 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7573 (mp0) REVERT: B 198 GLU cc_start: 0.7744 (tt0) cc_final: 0.7407 (tt0) REVERT: B 202 LYS cc_start: 0.8035 (tttp) cc_final: 0.7676 (tttm) REVERT: B 292 ASN cc_start: 0.8313 (m110) cc_final: 0.7986 (m-40) REVERT: B 401 MET cc_start: 0.8357 (ttt) cc_final: 0.7967 (ttp) REVERT: B 423 LYS cc_start: 0.8610 (mmtt) cc_final: 0.8355 (mmtt) REVERT: C 13 LYS cc_start: 0.8187 (ttpp) cc_final: 0.7863 (ttmm) REVERT: C 35 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7776 (mttt) REVERT: C 71 TYR cc_start: 0.8111 (m-80) cc_final: 0.7668 (m-80) REVERT: C 80 VAL cc_start: 0.8181 (t) cc_final: 0.7939 (p) REVERT: C 104 THR cc_start: 0.8799 (t) cc_final: 0.8508 (p) REVERT: C 109 ASP cc_start: 0.7468 (t0) cc_final: 0.7118 (t70) REVERT: C 121 MET cc_start: 0.8548 (ttm) cc_final: 0.8245 (ttp) REVERT: C 152 LEU cc_start: 0.8289 (mp) cc_final: 0.8039 (mt) REVERT: C 173 ASP cc_start: 0.7534 (m-30) cc_final: 0.7203 (m-30) REVERT: C 180 ASP cc_start: 0.7200 (m-30) cc_final: 0.6850 (m-30) REVERT: C 250 VAL cc_start: 0.8529 (t) cc_final: 0.8206 (m) REVERT: C 314 SER cc_start: 0.8176 (m) cc_final: 0.7897 (p) REVERT: C 366 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8573 (p) REVERT: C 436 GLU cc_start: 0.8058 (tp30) cc_final: 0.7845 (tp30) REVERT: D 70 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7242 (mmt) REVERT: D 75 ASP cc_start: 0.7719 (t70) cc_final: 0.7318 (t0) REVERT: D 124 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7895 (mp) REVERT: D 147 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6935 (mm-30) REVERT: D 173 ASP cc_start: 0.7665 (m-30) cc_final: 0.7235 (m-30) REVERT: D 177 GLU cc_start: 0.7655 (tp30) cc_final: 0.7348 (tp30) REVERT: D 181 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8169 (mtt) REVERT: D 331 SER cc_start: 0.8592 (p) cc_final: 0.8346 (p) REVERT: D 436 GLU cc_start: 0.8130 (tp30) cc_final: 0.7760 (tp30) REVERT: D 439 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7797 (mtm180) REVERT: D 440 ASP cc_start: 0.7850 (m-30) cc_final: 0.7465 (m-30) REVERT: E 13 LYS cc_start: 0.8192 (ttpp) cc_final: 0.7965 (ttmm) REVERT: E 35 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7866 (mmtt) REVERT: E 53 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7984 (mmm) REVERT: E 71 TYR cc_start: 0.7871 (m-10) cc_final: 0.7657 (m-10) REVERT: E 75 ASP cc_start: 0.7462 (t70) cc_final: 0.7235 (t70) REVERT: E 104 THR cc_start: 0.8793 (t) cc_final: 0.8481 (p) REVERT: E 147 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6787 (mm-30) REVERT: E 160 ASP cc_start: 0.8280 (m-30) cc_final: 0.8076 (m-30) REVERT: E 171 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7809 (mtp-110) REVERT: E 173 ASP cc_start: 0.7660 (m-30) cc_final: 0.7276 (m-30) REVERT: E 180 ASP cc_start: 0.7245 (m-30) cc_final: 0.6938 (m-30) REVERT: E 198 GLU cc_start: 0.8000 (tt0) cc_final: 0.7600 (tt0) REVERT: E 335 GLU cc_start: 0.7886 (tt0) cc_final: 0.7672 (tt0) REVERT: E 399 LYS cc_start: 0.8384 (mtpt) cc_final: 0.8175 (mtpp) REVERT: E 440 ASP cc_start: 0.7660 (m-30) cc_final: 0.7261 (m-30) REVERT: F 18 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6197 (mp0) REVERT: F 80 VAL cc_start: 0.8109 (t) cc_final: 0.7859 (p) REVERT: F 109 ASP cc_start: 0.7525 (t0) cc_final: 0.7110 (t70) REVERT: F 151 GLU cc_start: 0.7532 (tt0) cc_final: 0.7199 (tt0) REVERT: F 173 ASP cc_start: 0.7568 (m-30) cc_final: 0.7263 (m-30) REVERT: F 323 ARG cc_start: 0.8034 (ttt180) cc_final: 0.7784 (ttt-90) REVERT: F 426 GLU cc_start: 0.7944 (tt0) cc_final: 0.7663 (mt-10) REVERT: G 13 LYS cc_start: 0.8279 (ttpp) cc_final: 0.7856 (ttmm) REVERT: G 18 GLU cc_start: 0.7269 (mm-30) cc_final: 0.7001 (mm-30) REVERT: G 35 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7490 (mttt) REVERT: G 69 ASP cc_start: 0.6820 (t70) cc_final: 0.6545 (t0) REVERT: G 120 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7069 (mt-10) REVERT: G 147 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6789 (mm-30) REVERT: G 173 ASP cc_start: 0.7589 (m-30) cc_final: 0.7277 (m-30) REVERT: G 198 GLU cc_start: 0.7795 (tt0) cc_final: 0.7398 (tt0) REVERT: G 225 ARG cc_start: 0.8149 (tpp80) cc_final: 0.7762 (mmm-85) REVERT: G 257 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7182 (tp30) REVERT: G 335 GLU cc_start: 0.7709 (tt0) cc_final: 0.7394 (tt0) REVERT: H 18 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6704 (mm-30) REVERT: H 75 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: H 80 VAL cc_start: 0.8058 (t) cc_final: 0.7827 (p) REVERT: H 104 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8442 (p) REVERT: H 120 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6855 (mt-10) REVERT: H 147 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6950 (mm-30) REVERT: H 151 GLU cc_start: 0.7672 (tt0) cc_final: 0.7389 (tt0) REVERT: H 173 ASP cc_start: 0.7592 (m-30) cc_final: 0.7183 (m-30) REVERT: H 177 GLU cc_start: 0.7545 (tp30) cc_final: 0.7185 (tp30) REVERT: H 179 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: H 181 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8177 (mtt) REVERT: H 256 LYS cc_start: 0.8287 (tppt) cc_final: 0.8036 (tppt) REVERT: H 257 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7550 (pt0) REVERT: H 409 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8005 (ttpp) REVERT: H 440 ASP cc_start: 0.7514 (m-30) cc_final: 0.7310 (m-30) REVERT: I 13 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7933 (ttmm) REVERT: I 71 TYR cc_start: 0.8145 (m-80) cc_final: 0.7686 (m-80) REVERT: I 152 LEU cc_start: 0.8360 (mp) cc_final: 0.8096 (mt) REVERT: J 22 TYR cc_start: 0.7518 (m-80) cc_final: 0.7291 (m-80) REVERT: J 70 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7104 (mmt) REVERT: J 80 VAL cc_start: 0.8171 (OUTLIER) cc_final: 0.7927 (p) REVERT: J 124 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7940 (mp) REVERT: J 147 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7128 (mm-30) REVERT: J 173 ASP cc_start: 0.7578 (m-30) cc_final: 0.7130 (m-30) REVERT: J 177 GLU cc_start: 0.7683 (tp30) cc_final: 0.7413 (tp30) REVERT: J 181 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8047 (mtt) REVERT: J 191 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7813 (tp30) REVERT: J 298 TYR cc_start: 0.8437 (m-80) cc_final: 0.8108 (m-80) REVERT: J 305 TYR cc_start: 0.6347 (OUTLIER) cc_final: 0.6083 (m-10) REVERT: J 353 LEU cc_start: 0.8602 (tp) cc_final: 0.8343 (tt) REVERT: J 366 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8287 (p) REVERT: J 403 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7630 (mt-10) REVERT: J 439 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8192 (ttm110) REVERT: J 440 ASP cc_start: 0.7574 (m-30) cc_final: 0.7245 (m-30) REVERT: K 13 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7956 (ttmm) REVERT: K 35 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7524 (mmtt) REVERT: K 51 GLU cc_start: 0.7842 (tt0) cc_final: 0.7510 (tt0) REVERT: K 75 ASP cc_start: 0.7325 (t70) cc_final: 0.7057 (t70) REVERT: K 147 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7105 (mm-30) REVERT: K 171 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7869 (mtp-110) REVERT: K 173 ASP cc_start: 0.7604 (m-30) cc_final: 0.7162 (m-30) REVERT: K 203 TYR cc_start: 0.8420 (p90) cc_final: 0.7688 (p90) REVERT: K 253 PHE cc_start: 0.8219 (m-80) cc_final: 0.7564 (m-80) REVERT: K 353 LEU cc_start: 0.8511 (tp) cc_final: 0.8237 (tt) REVERT: K 438 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7715 (mt-10) REVERT: L 18 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6901 (mm-30) REVERT: L 22 TYR cc_start: 0.7532 (m-80) cc_final: 0.7198 (m-10) REVERT: L 49 ASP cc_start: 0.7939 (m-30) cc_final: 0.7541 (m-30) REVERT: L 51 GLU cc_start: 0.8128 (tp30) cc_final: 0.7813 (tp30) REVERT: L 71 TYR cc_start: 0.7913 (m-80) cc_final: 0.7553 (m-80) REVERT: L 75 ASP cc_start: 0.7438 (t0) cc_final: 0.7147 (t0) REVERT: L 80 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7932 (p) REVERT: L 147 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7264 (mm-30) REVERT: L 151 GLU cc_start: 0.7549 (tt0) cc_final: 0.7166 (tm-30) REVERT: L 173 ASP cc_start: 0.7453 (m-30) cc_final: 0.7189 (m-30) REVERT: L 177 GLU cc_start: 0.7705 (tp30) cc_final: 0.7349 (tp30) REVERT: L 191 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7777 (mm-30) REVERT: L 198 GLU cc_start: 0.8000 (tt0) cc_final: 0.7610 (tt0) REVERT: L 323 ARG cc_start: 0.8170 (ttt180) cc_final: 0.7809 (ttt-90) REVERT: L 399 LYS cc_start: 0.8441 (ttmt) cc_final: 0.8096 (ttpp) outliers start: 194 outliers final: 123 residues processed: 1338 average time/residue: 0.2486 time to fit residues: 525.1635 Evaluate side-chains 1389 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1231 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 409 LYS Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 388 GLN Chi-restraints excluded: chain F residue 409 LYS Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 392 SER Chi-restraints excluded: chain H residue 409 LYS Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 121 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 179 GLU Chi-restraints excluded: chain J residue 181 MET Chi-restraints excluded: chain J residue 201 PHE Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain J residue 409 LYS Chi-restraints excluded: chain J residue 439 ARG Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 151 GLU Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 171 ARG Chi-restraints excluded: chain K residue 179 GLU Chi-restraints excluded: chain K residue 201 PHE Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 358 ASP Chi-restraints excluded: chain K residue 366 VAL Chi-restraints excluded: chain K residue 392 SER Chi-restraints excluded: chain K residue 409 LYS Chi-restraints excluded: chain K residue 443 MET Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 288 THR Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain L residue 388 GLN Chi-restraints excluded: chain L residue 392 SER Chi-restraints excluded: chain L residue 409 LYS Chi-restraints excluded: chain L residue 420 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 463 optimal weight: 0.6980 chunk 386 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 484 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 194 optimal weight: 0.1980 chunk 227 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 287 optimal weight: 3.9990 chunk 432 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN F 214 GLN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 214 GLN J 249 ASN K 214 GLN L 214 GLN L 227 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124524 restraints weight = 52690.992| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.80 r_work: 0.3458 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 40800 Z= 0.133 Angle : 0.522 7.026 55224 Z= 0.268 Chirality : 0.042 0.150 5952 Planarity : 0.004 0.053 7236 Dihedral : 4.359 57.276 5359 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.43 % Favored : 96.33 % Rotamer: Outliers : 3.76 % Allowed : 26.20 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.12), residues: 4872 helix: 1.56 (0.12), residues: 1992 sheet: -1.73 (0.18), residues: 672 loop : -0.06 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 439 TYR 0.022 0.001 TYR I 298 PHE 0.020 0.001 PHE J 14 TRP 0.014 0.001 TRP L 84 HIS 0.003 0.001 HIS I 73 Details of bonding type rmsd covalent geometry : bond 0.00313 (40800) covalent geometry : angle 0.52202 (55224) hydrogen bonds : bond 0.03740 ( 1706) hydrogen bonds : angle 4.98945 ( 5004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1409 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1246 time to evaluate : 1.442 Fit side-chains REVERT: A 13 LYS cc_start: 0.8358 (ttpp) cc_final: 0.7883 (ttmm) REVERT: A 18 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6974 (mm-30) REVERT: A 35 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7595 (mmtt) REVERT: A 69 ASP cc_start: 0.6484 (t70) cc_final: 0.6267 (t0) REVERT: A 104 THR cc_start: 0.8715 (t) cc_final: 0.8462 (p) REVERT: A 120 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7014 (mt-10) REVERT: A 147 GLU cc_start: 0.7239 (mm-30) cc_final: 0.7029 (mm-30) REVERT: A 173 ASP cc_start: 0.7741 (m-30) cc_final: 0.7378 (m-30) REVERT: A 177 GLU cc_start: 0.7418 (tp30) cc_final: 0.7104 (tp30) REVERT: A 253 PHE cc_start: 0.8261 (m-80) cc_final: 0.7463 (m-80) REVERT: A 256 LYS cc_start: 0.8246 (tppt) cc_final: 0.8016 (tppt) REVERT: A 436 GLU cc_start: 0.8116 (tp30) cc_final: 0.7817 (tp30) REVERT: A 440 ASP cc_start: 0.7607 (m-30) cc_final: 0.7390 (m-30) REVERT: B 7 THR cc_start: 0.7325 (OUTLIER) cc_final: 0.7040 (p) REVERT: B 35 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7515 (mmtt) REVERT: B 71 TYR cc_start: 0.7783 (m-80) cc_final: 0.7149 (m-80) REVERT: B 75 ASP cc_start: 0.7527 (t0) cc_final: 0.7286 (m-30) REVERT: B 116 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7656 (ttp-110) REVERT: B 120 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6807 (mt-10) REVERT: B 147 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6994 (mm-30) REVERT: B 173 ASP cc_start: 0.7604 (m-30) cc_final: 0.7234 (m-30) REVERT: B 181 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8166 (mtt) REVERT: B 184 ASP cc_start: 0.7649 (t0) cc_final: 0.7081 (t0) REVERT: B 186 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7597 (mp0) REVERT: B 198 GLU cc_start: 0.7638 (tt0) cc_final: 0.7295 (tt0) REVERT: B 202 LYS cc_start: 0.7974 (tttp) cc_final: 0.7643 (tttm) REVERT: B 401 MET cc_start: 0.8363 (ttt) cc_final: 0.7969 (ttp) REVERT: B 409 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8083 (ttpp) REVERT: C 13 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7838 (ttmm) REVERT: C 35 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7758 (mttt) REVERT: C 41 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8137 (t) REVERT: C 71 TYR cc_start: 0.8090 (m-80) cc_final: 0.7658 (m-80) REVERT: C 80 VAL cc_start: 0.8162 (t) cc_final: 0.7913 (p) REVERT: C 82 PHE cc_start: 0.7868 (m-10) cc_final: 0.7665 (m-80) REVERT: C 104 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8524 (p) REVERT: C 109 ASP cc_start: 0.7443 (t0) cc_final: 0.7096 (t70) REVERT: C 121 MET cc_start: 0.8526 (ttm) cc_final: 0.8253 (ttp) REVERT: C 147 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7331 (mm-30) REVERT: C 152 LEU cc_start: 0.8256 (mp) cc_final: 0.7988 (mt) REVERT: C 173 ASP cc_start: 0.7511 (m-30) cc_final: 0.7166 (m-30) REVERT: C 191 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7834 (tp30) REVERT: C 198 GLU cc_start: 0.8075 (tt0) cc_final: 0.7839 (tt0) REVERT: C 250 VAL cc_start: 0.8509 (t) cc_final: 0.8240 (m) REVERT: C 253 PHE cc_start: 0.8116 (m-80) cc_final: 0.7496 (m-80) REVERT: C 314 SER cc_start: 0.8154 (m) cc_final: 0.7874 (p) REVERT: C 366 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8568 (p) REVERT: C 392 SER cc_start: 0.7526 (OUTLIER) cc_final: 0.6956 (t) REVERT: C 436 GLU cc_start: 0.8053 (tp30) cc_final: 0.7835 (tp30) REVERT: D 70 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7083 (mmt) REVERT: D 75 ASP cc_start: 0.7704 (t70) cc_final: 0.7293 (t0) REVERT: D 124 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7831 (mp) REVERT: D 147 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6919 (mm-30) REVERT: D 173 ASP cc_start: 0.7624 (m-30) cc_final: 0.7196 (m-30) REVERT: D 177 GLU cc_start: 0.7654 (tp30) cc_final: 0.7338 (tp30) REVERT: D 181 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8144 (mtt) REVERT: D 270 THR cc_start: 0.8696 (t) cc_final: 0.8393 (p) REVERT: D 331 SER cc_start: 0.8571 (p) cc_final: 0.8355 (p) REVERT: D 353 LEU cc_start: 0.8507 (tp) cc_final: 0.8252 (tt) REVERT: D 436 GLU cc_start: 0.8133 (tp30) cc_final: 0.7780 (tp30) REVERT: D 439 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7712 (mtm180) REVERT: D 440 ASP cc_start: 0.7842 (m-30) cc_final: 0.7466 (m-30) REVERT: E 13 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7794 (ttmm) REVERT: E 35 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7772 (mmtt) REVERT: E 53 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7882 (mmm) REVERT: E 75 ASP cc_start: 0.7443 (t70) cc_final: 0.7215 (t70) REVERT: E 104 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8559 (p) REVERT: E 147 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7011 (mm-30) REVERT: E 160 ASP cc_start: 0.8299 (m-30) cc_final: 0.8079 (m-30) REVERT: E 171 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7852 (mtp-110) REVERT: E 173 ASP cc_start: 0.7649 (m-30) cc_final: 0.7268 (m-30) REVERT: E 180 ASP cc_start: 0.7239 (m-30) cc_final: 0.6921 (m-30) REVERT: E 198 GLU cc_start: 0.7965 (tt0) cc_final: 0.7590 (tt0) REVERT: E 253 PHE cc_start: 0.8166 (m-80) cc_final: 0.7488 (m-80) REVERT: E 331 SER cc_start: 0.8649 (p) cc_final: 0.8404 (t) REVERT: E 335 GLU cc_start: 0.7833 (tt0) cc_final: 0.7615 (tt0) REVERT: E 436 GLU cc_start: 0.7960 (tp30) cc_final: 0.7466 (tp30) REVERT: E 440 ASP cc_start: 0.7635 (m-30) cc_final: 0.7214 (m-30) REVERT: F 18 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6171 (mp0) REVERT: F 80 VAL cc_start: 0.8091 (t) cc_final: 0.7845 (p) REVERT: F 98 VAL cc_start: 0.8345 (t) cc_final: 0.7859 (p) REVERT: F 109 ASP cc_start: 0.7476 (t0) cc_final: 0.7081 (t70) REVERT: F 151 GLU cc_start: 0.7562 (tt0) cc_final: 0.7185 (tt0) REVERT: F 173 ASP cc_start: 0.7543 (m-30) cc_final: 0.7225 (m-30) REVERT: F 191 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7657 (mm-30) REVERT: F 198 GLU cc_start: 0.8028 (tt0) cc_final: 0.7689 (tt0) REVERT: F 323 ARG cc_start: 0.8001 (ttt180) cc_final: 0.7759 (ttt-90) REVERT: F 426 GLU cc_start: 0.7916 (tt0) cc_final: 0.7647 (mt-10) REVERT: G 13 LYS cc_start: 0.8189 (ttpp) cc_final: 0.7765 (ttmm) REVERT: G 18 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6989 (mm-30) REVERT: G 35 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7467 (mttt) REVERT: G 38 GLU cc_start: 0.7962 (tt0) cc_final: 0.7695 (tt0) REVERT: G 69 ASP cc_start: 0.6806 (t70) cc_final: 0.6528 (t0) REVERT: G 120 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7017 (mt-10) REVERT: G 147 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6790 (mm-30) REVERT: G 173 ASP cc_start: 0.7563 (m-30) cc_final: 0.7265 (m-30) REVERT: G 198 GLU cc_start: 0.7833 (tt0) cc_final: 0.7469 (tt0) REVERT: G 225 ARG cc_start: 0.8123 (tpp80) cc_final: 0.7741 (mmm-85) REVERT: G 257 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7105 (tp30) REVERT: G 335 GLU cc_start: 0.7666 (tt0) cc_final: 0.7339 (tt0) REVERT: G 439 ARG cc_start: 0.8597 (ttm110) cc_final: 0.8382 (ttm170) REVERT: H 18 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6709 (mm-30) REVERT: H 75 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7231 (m-30) REVERT: H 80 VAL cc_start: 0.8034 (t) cc_final: 0.7811 (p) REVERT: H 104 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8424 (p) REVERT: H 116 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7624 (ttp-110) REVERT: H 120 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6755 (mt-10) REVERT: H 147 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6943 (mm-30) REVERT: H 151 GLU cc_start: 0.7678 (tt0) cc_final: 0.7395 (tt0) REVERT: H 173 ASP cc_start: 0.7573 (m-30) cc_final: 0.7136 (m-30) REVERT: H 177 GLU cc_start: 0.7494 (tp30) cc_final: 0.7139 (tp30) REVERT: H 179 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: H 181 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8161 (mtt) REVERT: H 256 LYS cc_start: 0.8254 (tppt) cc_final: 0.8008 (tppt) REVERT: H 257 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7515 (pt0) REVERT: H 409 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7983 (ttpp) REVERT: H 440 ASP cc_start: 0.7511 (m-30) cc_final: 0.7269 (m-30) REVERT: I 13 LYS cc_start: 0.8215 (ttpp) cc_final: 0.7910 (ttmm) REVERT: I 41 VAL cc_start: 0.8470 (OUTLIER) cc_final: 0.8134 (t) REVERT: I 71 TYR cc_start: 0.8125 (m-80) cc_final: 0.7651 (m-80) REVERT: I 152 LEU cc_start: 0.8321 (mp) cc_final: 0.8070 (mt) REVERT: J 70 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7093 (mmt) REVERT: J 80 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7910 (p) REVERT: J 124 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7863 (mp) REVERT: J 147 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7112 (mm-30) REVERT: J 173 ASP cc_start: 0.7632 (m-30) cc_final: 0.7199 (m-30) REVERT: J 177 GLU cc_start: 0.7655 (tp30) cc_final: 0.7365 (tp30) REVERT: J 181 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8044 (mtt) REVERT: J 191 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7891 (mm-30) REVERT: J 203 TYR cc_start: 0.8275 (p90) cc_final: 0.7709 (p90) REVERT: J 211 ASP cc_start: 0.8159 (m-30) cc_final: 0.7917 (m-30) REVERT: J 298 TYR cc_start: 0.8379 (m-80) cc_final: 0.8058 (m-80) REVERT: J 353 LEU cc_start: 0.8589 (tp) cc_final: 0.8346 (tt) REVERT: J 366 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8276 (p) REVERT: J 403 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7756 (mt-10) REVERT: J 405 GLU cc_start: 0.7892 (tp30) cc_final: 0.7632 (tp30) REVERT: J 421 ASN cc_start: 0.7845 (m-40) cc_final: 0.7549 (m110) REVERT: J 439 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8152 (ttm110) REVERT: J 440 ASP cc_start: 0.7601 (m-30) cc_final: 0.7269 (m-30) REVERT: K 13 LYS cc_start: 0.8141 (ttpp) cc_final: 0.7910 (ttmm) REVERT: K 35 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7553 (mmtt) REVERT: K 51 GLU cc_start: 0.7771 (tt0) cc_final: 0.7450 (tt0) REVERT: K 75 ASP cc_start: 0.7265 (t70) cc_final: 0.7008 (t70) REVERT: K 147 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6928 (mm-30) REVERT: K 171 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7985 (mtp-110) REVERT: K 173 ASP cc_start: 0.7584 (m-30) cc_final: 0.7142 (m-30) REVERT: K 203 TYR cc_start: 0.8390 (p90) cc_final: 0.7738 (p90) REVERT: K 253 PHE cc_start: 0.8155 (m-80) cc_final: 0.7507 (m-80) REVERT: K 353 LEU cc_start: 0.8514 (tp) cc_final: 0.8236 (tt) REVERT: K 438 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7664 (mt-10) REVERT: K 439 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8172 (mtm180) REVERT: L 18 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6881 (mm-30) REVERT: L 22 TYR cc_start: 0.7502 (m-80) cc_final: 0.7207 (m-10) REVERT: L 49 ASP cc_start: 0.7927 (m-30) cc_final: 0.7534 (m-30) REVERT: L 51 GLU cc_start: 0.8139 (tp30) cc_final: 0.7804 (tp30) REVERT: L 71 TYR cc_start: 0.7899 (m-80) cc_final: 0.7527 (m-80) REVERT: L 75 ASP cc_start: 0.7413 (t0) cc_final: 0.7126 (t0) REVERT: L 147 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7252 (mm-30) REVERT: L 151 GLU cc_start: 0.7538 (tt0) cc_final: 0.7159 (tm-30) REVERT: L 173 ASP cc_start: 0.7398 (m-30) cc_final: 0.7123 (m-30) REVERT: L 177 GLU cc_start: 0.7632 (tp30) cc_final: 0.7431 (tp30) REVERT: L 323 ARG cc_start: 0.8113 (ttt180) cc_final: 0.7755 (ttt-90) REVERT: L 399 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8068 (ttpp) outliers start: 163 outliers final: 109 residues processed: 1315 average time/residue: 0.2498 time to fit residues: 519.3544 Evaluate side-chains 1376 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1229 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 409 LYS Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 388 GLN Chi-restraints excluded: chain F residue 409 LYS Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 392 SER Chi-restraints excluded: chain H residue 409 LYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 121 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 179 GLU Chi-restraints excluded: chain J residue 181 MET Chi-restraints excluded: chain J residue 201 PHE Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain J residue 409 LYS Chi-restraints excluded: chain J residue 439 ARG Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain K residue 121 MET Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 171 ARG Chi-restraints excluded: chain K residue 179 GLU Chi-restraints excluded: chain K residue 201 PHE Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 358 ASP Chi-restraints excluded: chain K residue 366 VAL Chi-restraints excluded: chain K residue 392 SER Chi-restraints excluded: chain K residue 443 MET Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 288 THR Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain L residue 388 GLN Chi-restraints excluded: chain L residue 392 SER Chi-restraints excluded: chain L residue 409 LYS Chi-restraints excluded: chain L residue 420 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 376 optimal weight: 4.9990 chunk 441 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 316 optimal weight: 0.9980 chunk 392 optimal weight: 0.7980 chunk 486 optimal weight: 0.6980 chunk 465 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 268 optimal weight: 0.0770 chunk 400 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN E 214 GLN F 214 GLN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 214 GLN J 249 ASN K 214 GLN L 214 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.138328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124910 restraints weight = 52383.255| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.79 r_work: 0.3464 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 40800 Z= 0.131 Angle : 0.525 7.114 55224 Z= 0.269 Chirality : 0.042 0.151 5952 Planarity : 0.004 0.054 7236 Dihedral : 4.329 57.901 5359 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.47 % Favored : 96.28 % Rotamer: Outliers : 3.51 % Allowed : 26.41 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.12), residues: 4872 helix: 1.60 (0.12), residues: 1992 sheet: -1.70 (0.18), residues: 672 loop : -0.04 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 439 TYR 0.023 0.001 TYR I 298 PHE 0.021 0.001 PHE J 14 TRP 0.028 0.001 TRP I 84 HIS 0.003 0.001 HIS I 73 Details of bonding type rmsd covalent geometry : bond 0.00308 (40800) covalent geometry : angle 0.52496 (55224) hydrogen bonds : bond 0.03673 ( 1706) hydrogen bonds : angle 4.95319 ( 5004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1392 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 1240 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8333 (ttpp) cc_final: 0.7854 (ttmm) REVERT: A 18 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6943 (mm-30) REVERT: A 35 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7560 (mmtt) REVERT: A 69 ASP cc_start: 0.6495 (t70) cc_final: 0.6257 (t0) REVERT: A 104 THR cc_start: 0.8720 (t) cc_final: 0.8464 (p) REVERT: A 120 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7004 (mt-10) REVERT: A 147 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6968 (mm-30) REVERT: A 173 ASP cc_start: 0.7698 (m-30) cc_final: 0.7367 (m-30) REVERT: A 180 ASP cc_start: 0.7237 (m-30) cc_final: 0.6828 (m-30) REVERT: A 253 PHE cc_start: 0.8221 (m-80) cc_final: 0.7372 (m-80) REVERT: A 256 LYS cc_start: 0.8224 (tppt) cc_final: 0.7998 (tppt) REVERT: A 436 GLU cc_start: 0.8106 (tp30) cc_final: 0.7832 (tp30) REVERT: A 439 ARG cc_start: 0.8552 (mtm-85) cc_final: 0.8348 (mtm-85) REVERT: A 440 ASP cc_start: 0.7591 (m-30) cc_final: 0.7379 (m-30) REVERT: B 7 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.6932 (p) REVERT: B 35 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7492 (mmtt) REVERT: B 71 TYR cc_start: 0.7775 (m-80) cc_final: 0.7137 (m-80) REVERT: B 75 ASP cc_start: 0.7510 (t0) cc_final: 0.7267 (m-30) REVERT: B 116 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7637 (ttp-110) REVERT: B 120 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6787 (mt-10) REVERT: B 147 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7013 (mm-30) REVERT: B 173 ASP cc_start: 0.7572 (m-30) cc_final: 0.7210 (m-30) REVERT: B 181 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8175 (mtt) REVERT: B 184 ASP cc_start: 0.7655 (t0) cc_final: 0.7066 (t0) REVERT: B 186 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7606 (mp0) REVERT: B 198 GLU cc_start: 0.7626 (tt0) cc_final: 0.7291 (tt0) REVERT: B 202 LYS cc_start: 0.7960 (tttp) cc_final: 0.7614 (tttm) REVERT: B 401 MET cc_start: 0.8368 (ttt) cc_final: 0.7981 (ttp) REVERT: C 13 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7831 (ttmm) REVERT: C 35 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7776 (mttt) REVERT: C 41 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8144 (t) REVERT: C 71 TYR cc_start: 0.8079 (m-80) cc_final: 0.7653 (m-80) REVERT: C 80 VAL cc_start: 0.8148 (t) cc_final: 0.7898 (p) REVERT: C 82 PHE cc_start: 0.7873 (m-10) cc_final: 0.7614 (m-80) REVERT: C 104 THR cc_start: 0.8788 (t) cc_final: 0.8522 (p) REVERT: C 109 ASP cc_start: 0.7411 (t0) cc_final: 0.7070 (t70) REVERT: C 116 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8217 (ttp80) REVERT: C 121 MET cc_start: 0.8526 (ttm) cc_final: 0.8246 (ttp) REVERT: C 147 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7306 (mm-30) REVERT: C 152 LEU cc_start: 0.8234 (mp) cc_final: 0.7953 (mt) REVERT: C 173 ASP cc_start: 0.7506 (m-30) cc_final: 0.7158 (m-30) REVERT: C 191 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7836 (tp30) REVERT: C 198 GLU cc_start: 0.8072 (tt0) cc_final: 0.7817 (tt0) REVERT: C 250 VAL cc_start: 0.8441 (t) cc_final: 0.8185 (m) REVERT: C 253 PHE cc_start: 0.8101 (m-80) cc_final: 0.7449 (m-80) REVERT: C 314 SER cc_start: 0.8148 (m) cc_final: 0.7871 (p) REVERT: C 436 GLU cc_start: 0.8077 (tp30) cc_final: 0.7858 (tp30) REVERT: D 70 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7083 (mmt) REVERT: D 75 ASP cc_start: 0.7673 (t70) cc_final: 0.7333 (t70) REVERT: D 124 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7802 (mp) REVERT: D 147 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6932 (mm-30) REVERT: D 173 ASP cc_start: 0.7620 (m-30) cc_final: 0.7202 (m-30) REVERT: D 177 GLU cc_start: 0.7636 (tp30) cc_final: 0.7320 (tp30) REVERT: D 181 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8225 (mtt) REVERT: D 203 TYR cc_start: 0.8216 (p90) cc_final: 0.7996 (p90) REVERT: D 270 THR cc_start: 0.8633 (t) cc_final: 0.8381 (p) REVERT: D 331 SER cc_start: 0.8584 (p) cc_final: 0.8370 (p) REVERT: D 335 GLU cc_start: 0.7844 (tt0) cc_final: 0.7585 (tt0) REVERT: D 353 LEU cc_start: 0.8516 (tp) cc_final: 0.8256 (tt) REVERT: D 436 GLU cc_start: 0.8148 (tp30) cc_final: 0.7787 (tp30) REVERT: D 439 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7681 (mtm180) REVERT: D 440 ASP cc_start: 0.7803 (m-30) cc_final: 0.7425 (m-30) REVERT: E 13 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7793 (ttmm) REVERT: E 35 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7767 (mmtt) REVERT: E 53 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7907 (mmm) REVERT: E 75 ASP cc_start: 0.7402 (t70) cc_final: 0.7190 (t70) REVERT: E 104 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8575 (p) REVERT: E 147 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6891 (mm-30) REVERT: E 171 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7837 (mtp-110) REVERT: E 173 ASP cc_start: 0.7657 (m-30) cc_final: 0.7256 (m-30) REVERT: E 180 ASP cc_start: 0.7250 (m-30) cc_final: 0.6931 (m-30) REVERT: E 198 GLU cc_start: 0.7968 (tt0) cc_final: 0.7597 (tt0) REVERT: E 253 PHE cc_start: 0.8128 (m-80) cc_final: 0.7474 (m-80) REVERT: E 331 SER cc_start: 0.8653 (p) cc_final: 0.8406 (t) REVERT: E 335 GLU cc_start: 0.7832 (tt0) cc_final: 0.7555 (tt0) REVERT: E 436 GLU cc_start: 0.7997 (tp30) cc_final: 0.7490 (tp30) REVERT: E 440 ASP cc_start: 0.7639 (m-30) cc_final: 0.7218 (m-30) REVERT: E 443 MET cc_start: 0.8002 (ttt) cc_final: 0.7313 (ttt) REVERT: F 18 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6199 (mp0) REVERT: F 80 VAL cc_start: 0.8085 (t) cc_final: 0.7828 (p) REVERT: F 109 ASP cc_start: 0.7460 (t0) cc_final: 0.7116 (t70) REVERT: F 120 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7197 (mt-10) REVERT: F 151 GLU cc_start: 0.7580 (tt0) cc_final: 0.7205 (tt0) REVERT: F 173 ASP cc_start: 0.7527 (m-30) cc_final: 0.7214 (m-30) REVERT: F 181 MET cc_start: 0.8363 (mtm) cc_final: 0.8148 (mtt) REVERT: F 191 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7571 (mm-30) REVERT: F 198 GLU cc_start: 0.8009 (tt0) cc_final: 0.7588 (tt0) REVERT: F 323 ARG cc_start: 0.7993 (ttt180) cc_final: 0.7752 (ttt-90) REVERT: F 426 GLU cc_start: 0.7949 (tt0) cc_final: 0.7665 (mt-10) REVERT: G 13 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7758 (ttmm) REVERT: G 18 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6972 (mm-30) REVERT: G 35 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7475 (mttt) REVERT: G 38 GLU cc_start: 0.7940 (tt0) cc_final: 0.7695 (tt0) REVERT: G 69 ASP cc_start: 0.6774 (t70) cc_final: 0.6495 (t0) REVERT: G 120 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6954 (mt-10) REVERT: G 147 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6832 (mm-30) REVERT: G 173 ASP cc_start: 0.7575 (m-30) cc_final: 0.7273 (m-30) REVERT: G 198 GLU cc_start: 0.7829 (tt0) cc_final: 0.7455 (tt0) REVERT: G 225 ARG cc_start: 0.8131 (tpp80) cc_final: 0.7753 (mmm-85) REVERT: G 253 PHE cc_start: 0.8216 (m-80) cc_final: 0.7379 (m-80) REVERT: G 257 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7135 (tp30) REVERT: G 335 GLU cc_start: 0.7657 (tt0) cc_final: 0.7325 (tt0) REVERT: G 439 ARG cc_start: 0.8584 (ttm110) cc_final: 0.8369 (ttm170) REVERT: H 18 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6687 (mm-30) REVERT: H 75 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7189 (m-30) REVERT: H 80 VAL cc_start: 0.8037 (t) cc_final: 0.7815 (p) REVERT: H 104 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8495 (p) REVERT: H 120 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6785 (mt-10) REVERT: H 147 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6960 (mm-30) REVERT: H 151 GLU cc_start: 0.7700 (tt0) cc_final: 0.7415 (tt0) REVERT: H 173 ASP cc_start: 0.7546 (m-30) cc_final: 0.7119 (m-30) REVERT: H 179 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: H 181 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8137 (mtt) REVERT: H 256 LYS cc_start: 0.8199 (tppt) cc_final: 0.7956 (tppt) REVERT: H 257 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7474 (pt0) REVERT: H 409 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7987 (ttpp) REVERT: H 440 ASP cc_start: 0.7522 (m-30) cc_final: 0.7286 (m-30) REVERT: I 13 LYS cc_start: 0.8190 (ttpp) cc_final: 0.7880 (ttmm) REVERT: I 41 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8174 (t) REVERT: I 53 MET cc_start: 0.8213 (mtm) cc_final: 0.7931 (ttm) REVERT: I 109 ASP cc_start: 0.7484 (t0) cc_final: 0.7134 (t70) REVERT: I 152 LEU cc_start: 0.8308 (mp) cc_final: 0.8058 (mt) REVERT: I 346 TYR cc_start: 0.8690 (m-80) cc_final: 0.8425 (m-80) REVERT: J 70 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.6964 (mmt) REVERT: J 124 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7840 (mp) REVERT: J 147 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7137 (mm-30) REVERT: J 173 ASP cc_start: 0.7621 (m-30) cc_final: 0.7169 (m-30) REVERT: J 177 GLU cc_start: 0.7661 (tp30) cc_final: 0.7376 (tp30) REVERT: J 181 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8022 (mtt) REVERT: J 191 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7877 (mm-30) REVERT: J 211 ASP cc_start: 0.8174 (m-30) cc_final: 0.7937 (m-30) REVERT: J 298 TYR cc_start: 0.8365 (m-80) cc_final: 0.8045 (m-80) REVERT: J 353 LEU cc_start: 0.8548 (tp) cc_final: 0.8274 (tt) REVERT: J 366 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8286 (p) REVERT: J 403 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7680 (mt-10) REVERT: J 421 ASN cc_start: 0.7829 (m-40) cc_final: 0.7506 (m110) REVERT: J 439 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8148 (ttm110) REVERT: J 440 ASP cc_start: 0.7534 (m-30) cc_final: 0.7199 (m-30) REVERT: K 13 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7876 (ttmm) REVERT: K 35 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7540 (mmtt) REVERT: K 51 GLU cc_start: 0.7736 (tt0) cc_final: 0.7416 (tt0) REVERT: K 147 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6990 (mm-30) REVERT: K 171 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7975 (mtp-110) REVERT: K 173 ASP cc_start: 0.7592 (m-30) cc_final: 0.7139 (m-30) REVERT: K 202 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7992 (tttp) REVERT: K 203 TYR cc_start: 0.8388 (p90) cc_final: 0.7712 (p90) REVERT: K 239 PHE cc_start: 0.8536 (t80) cc_final: 0.8204 (t80) REVERT: K 353 LEU cc_start: 0.8517 (tp) cc_final: 0.8242 (tt) REVERT: K 438 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7675 (mt-10) REVERT: K 439 ARG cc_start: 0.8427 (mtm-85) cc_final: 0.8136 (mtm180) REVERT: K 440 ASP cc_start: 0.7827 (m-30) cc_final: 0.7541 (m-30) REVERT: L 18 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6870 (mm-30) REVERT: L 22 TYR cc_start: 0.7505 (m-80) cc_final: 0.7156 (m-10) REVERT: L 51 GLU cc_start: 0.8120 (tp30) cc_final: 0.7780 (tp30) REVERT: L 71 TYR cc_start: 0.7832 (m-80) cc_final: 0.7435 (m-80) REVERT: L 75 ASP cc_start: 0.7407 (t0) cc_final: 0.7112 (t0) REVERT: L 147 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7236 (mm-30) REVERT: L 151 GLU cc_start: 0.7559 (tt0) cc_final: 0.7171 (tm-30) REVERT: L 173 ASP cc_start: 0.7398 (m-30) cc_final: 0.7129 (m-30) REVERT: L 177 GLU cc_start: 0.7682 (tp30) cc_final: 0.7470 (tp30) REVERT: L 323 ARG cc_start: 0.8098 (ttt180) cc_final: 0.7745 (ttt-90) REVERT: L 399 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8071 (ttpp) outliers start: 152 outliers final: 107 residues processed: 1308 average time/residue: 0.2500 time to fit residues: 515.5710 Evaluate side-chains 1363 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 1224 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 409 LYS Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 409 LYS Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 392 SER Chi-restraints excluded: chain H residue 409 LYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 121 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 179 GLU Chi-restraints excluded: chain J residue 181 MET Chi-restraints excluded: chain J residue 201 PHE Chi-restraints excluded: chain J residue 207 VAL Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain J residue 409 LYS Chi-restraints excluded: chain J residue 439 ARG Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 171 ARG Chi-restraints excluded: chain K residue 179 GLU Chi-restraints excluded: chain K residue 201 PHE Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 358 ASP Chi-restraints excluded: chain K residue 366 VAL Chi-restraints excluded: chain K residue 392 SER Chi-restraints excluded: chain K residue 443 MET Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 288 THR Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain L residue 388 GLN Chi-restraints excluded: chain L residue 392 SER Chi-restraints excluded: chain L residue 409 LYS Chi-restraints excluded: chain L residue 420 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 255 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 chunk 286 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 415 optimal weight: 0.0040 chunk 160 optimal weight: 0.7980 chunk 167 optimal weight: 0.4980 chunk 241 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN D 214 GLN E 113 ASN E 214 GLN F 214 GLN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 214 GLN K 214 GLN L 214 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.138812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125347 restraints weight = 52706.595| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.80 r_work: 0.3476 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 40800 Z= 0.123 Angle : 0.519 6.995 55224 Z= 0.266 Chirality : 0.041 0.152 5952 Planarity : 0.004 0.054 7236 Dihedral : 4.285 58.754 5359 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.55 % Favored : 96.20 % Rotamer: Outliers : 3.62 % Allowed : 26.39 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.12), residues: 4872 helix: 1.66 (0.12), residues: 1992 sheet: -1.68 (0.18), residues: 672 loop : 0.01 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 439 TYR 0.021 0.001 TYR I 298 PHE 0.018 0.001 PHE H 287 TRP 0.017 0.001 TRP I 84 HIS 0.004 0.001 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00289 (40800) covalent geometry : angle 0.51942 (55224) hydrogen bonds : bond 0.03559 ( 1706) hydrogen bonds : angle 4.89751 ( 5004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11635.45 seconds wall clock time: 199 minutes 5.23 seconds (11945.23 seconds total)