Starting phenix.real_space_refine on Sun Dec 29 21:48:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbj_13293/12_2024/7pbj_13293.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbj_13293/12_2024/7pbj_13293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pbj_13293/12_2024/7pbj_13293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbj_13293/12_2024/7pbj_13293.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbj_13293/12_2024/7pbj_13293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbj_13293/12_2024/7pbj_13293.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.023 sd= 0.191 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 28 5.49 5 Mg 14 5.21 5 S 294 5.16 5 C 36876 2.51 5 N 10269 2.21 5 O 12005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 266 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 59486 Number of models: 1 Model: "" Number of chains: 12 Chain: "Ad" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Ae" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Af" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 728 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "Ad" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Ae" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Ad" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Ak" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Ar" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Ay" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Bf" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Bm" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Bt" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: Ak, Ar, Ay, Bf, Bm, Bt, Al, As, Az, Bg, Bn, Bu, Am, At, Ba, Bh, Bo, Bv Time building chain proxies: 18.18, per 1000 atoms: 0.31 Number of scatterers: 59486 At special positions: 0 Unit cell: (158.301, 158.301, 218.079, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 294 16.00 P 28 15.00 Mg 14 11.99 O 12005 8.00 N 10269 7.00 C 36876 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: 11.79 Conformation dependent library (CDL) restraints added in 6.3 seconds 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14490 Finding SS restraints... Secondary structure from input PDB file: 301 helices and 105 sheets defined 55.8% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.64 Creating SS restraints... Processing helix chain 'Ad' and resid 9 through 29 removed outlier: 3.704A pdb=" N VALAd 29 " --> pdb=" O ASPAd 25 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 52 through 60 removed outlier: 3.703A pdb=" N VALAd 56 " --> pdb=" O ASPAd 52 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 64 through 85 Processing helix chain 'Ad' and resid 88 through 110 Processing helix chain 'Ad' and resid 112 through 135 Processing helix chain 'Ad' and resid 140 through 152 Processing helix chain 'Ad' and resid 155 through 169 removed outlier: 3.935A pdb=" N GLYAd 159 " --> pdb=" O ASPAd 155 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 201 through 205 Processing helix chain 'Ad' and resid 229 through 244 Proline residue: Ad 235 - end of helix Processing helix chain 'Ad' and resid 258 through 269 removed outlier: 3.880A pdb=" N VALAd 264 " --> pdb=" O ALAAd 260 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N METAd 267 " --> pdb=" O VALAd 263 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLYAd 269 " --> pdb=" O ASNAd 265 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 282 through 296 removed outlier: 3.568A pdb=" N LYSAd 286 " --> pdb=" O GLYAd 282 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 338 through 356 removed outlier: 3.712A pdb=" N GLUAd 354 " --> pdb=" O ARGAd 350 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 358 through 365 Processing helix chain 'Ad' and resid 366 through 375 Processing helix chain 'Ad' and resid 385 through 410 Processing helix chain 'Ad' and resid 416 through 426 Processing helix chain 'Ad' and resid 433 through 458 removed outlier: 3.653A pdb=" N GLUAd 448 " --> pdb=" O LEUAd 444 " (cutoff:3.500A) Proline residue: Ad 450 - end of helix Processing helix chain 'Ad' and resid 461 through 472 Processing helix chain 'Ad' and resid 488 through 492 Processing helix chain 'Ad' and resid 497 through 516 Processing helix chain 'Ae' and resid 9 through 29 removed outlier: 3.518A pdb=" N VALAe 29 " --> pdb=" O ASPAe 25 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 52 through 60 removed outlier: 3.533A pdb=" N VALAe 56 " --> pdb=" O ASPAe 52 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 64 through 85 removed outlier: 3.596A pdb=" N GLYAe 70 " --> pdb=" O PHEAe 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLUAe 76 " --> pdb=" O GLNAe 72 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VALAe 77 " --> pdb=" O METAe 73 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALAAe 78 " --> pdb=" O VALAe 74 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 88 through 109 Processing helix chain 'Ae' and resid 112 through 135 Processing helix chain 'Ae' and resid 140 through 152 Processing helix chain 'Ae' and resid 155 through 170 Processing helix chain 'Ae' and resid 201 through 205 removed outlier: 3.868A pdb=" N PHEAe 204 " --> pdb=" O SERAe 201 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 229 through 244 removed outlier: 3.977A pdb=" N METAe 233 " --> pdb=" O ASNAe 229 " (cutoff:3.500A) Proline residue: Ae 235 - end of helix Processing helix chain 'Ae' and resid 255 through 269 Processing helix chain 'Ae' and resid 281 through 297 Processing helix chain 'Ae' and resid 308 through 312 Processing helix chain 'Ae' and resid 313 through 317 removed outlier: 3.777A pdb=" N LEUAe 317 " --> pdb=" O LEUAe 314 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 338 through 354 removed outlier: 3.571A pdb=" N GLUAe 354 " --> pdb=" O ARGAe 350 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 358 through 373 removed outlier: 3.552A pdb=" N LYSAe 364 " --> pdb=" O TYRAe 360 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 385 through 410 Processing helix chain 'Ae' and resid 416 through 426 Processing helix chain 'Ae' and resid 433 through 447 Processing helix chain 'Ae' and resid 448 through 459 Processing helix chain 'Ae' and resid 461 through 472 removed outlier: 3.741A pdb=" N VALAe 465 " --> pdb=" O GLUAe 461 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 488 through 492 Processing helix chain 'Ae' and resid 497 through 516 Processing helix chain 'Af' and resid 23 through 25 No H-bonds generated for 'chain 'Af' and resid 23 through 25' Processing helix chain 'Ak' and resid 9 through 29 removed outlier: 3.704A pdb=" N VALAk 29 " --> pdb=" O ASPAk 25 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 52 through 60 removed outlier: 3.703A pdb=" N VALAk 56 " --> pdb=" O ASPAk 52 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 64 through 85 Processing helix chain 'Ak' and resid 88 through 110 Processing helix chain 'Ak' and resid 112 through 135 Processing helix chain 'Ak' and resid 140 through 152 Processing helix chain 'Ak' and resid 155 through 169 removed outlier: 3.935A pdb=" N GLYAk 159 " --> pdb=" O ASPAk 155 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 201 through 205 Processing helix chain 'Ak' and resid 229 through 244 Proline residue: Ak 235 - end of helix Processing helix chain 'Ak' and resid 258 through 269 removed outlier: 3.880A pdb=" N VALAk 264 " --> pdb=" O ALAAk 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N METAk 267 " --> pdb=" O VALAk 263 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLYAk 269 " --> pdb=" O ASNAk 265 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 282 through 296 removed outlier: 3.568A pdb=" N LYSAk 286 " --> pdb=" O GLYAk 282 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 338 through 356 removed outlier: 3.712A pdb=" N GLUAk 354 " --> pdb=" O ARGAk 350 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 358 through 365 Processing helix chain 'Ak' and resid 366 through 375 Processing helix chain 'Ak' and resid 385 through 410 Processing helix chain 'Ak' and resid 416 through 426 Processing helix chain 'Ak' and resid 433 through 458 removed outlier: 3.653A pdb=" N GLUAk 448 " --> pdb=" O LEUAk 444 " (cutoff:3.500A) Proline residue: Ak 450 - end of helix Processing helix chain 'Ak' and resid 461 through 472 Processing helix chain 'Ak' and resid 488 through 492 Processing helix chain 'Ak' and resid 497 through 516 Processing helix chain 'Al' and resid 9 through 29 removed outlier: 3.518A pdb=" N VALAl 29 " --> pdb=" O ASPAl 25 " (cutoff:3.500A) Processing helix chain 'Al' and resid 52 through 60 removed outlier: 3.533A pdb=" N VALAl 56 " --> pdb=" O ASPAl 52 " (cutoff:3.500A) Processing helix chain 'Al' and resid 64 through 85 removed outlier: 3.596A pdb=" N GLYAl 70 " --> pdb=" O PHEAl 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLUAl 76 " --> pdb=" O GLNAl 72 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VALAl 77 " --> pdb=" O METAl 73 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALAAl 78 " --> pdb=" O VALAl 74 " (cutoff:3.500A) Processing helix chain 'Al' and resid 88 through 109 Processing helix chain 'Al' and resid 112 through 135 Processing helix chain 'Al' and resid 140 through 152 Processing helix chain 'Al' and resid 155 through 170 Processing helix chain 'Al' and resid 201 through 205 removed outlier: 3.868A pdb=" N PHEAl 204 " --> pdb=" O SERAl 201 " (cutoff:3.500A) Processing helix chain 'Al' and resid 229 through 244 removed outlier: 3.977A pdb=" N METAl 233 " --> pdb=" O ASNAl 229 " (cutoff:3.500A) Proline residue: Al 235 - end of helix Processing helix chain 'Al' and resid 255 through 269 Processing helix chain 'Al' and resid 281 through 297 Processing helix chain 'Al' and resid 308 through 312 Processing helix chain 'Al' and resid 313 through 317 removed outlier: 3.776A pdb=" N LEUAl 317 " --> pdb=" O LEUAl 314 " (cutoff:3.500A) Processing helix chain 'Al' and resid 338 through 354 removed outlier: 3.571A pdb=" N GLUAl 354 " --> pdb=" O ARGAl 350 " (cutoff:3.500A) Processing helix chain 'Al' and resid 358 through 373 removed outlier: 3.551A pdb=" N LYSAl 364 " --> pdb=" O TYRAl 360 " (cutoff:3.500A) Processing helix chain 'Al' and resid 385 through 410 Processing helix chain 'Al' and resid 416 through 426 Processing helix chain 'Al' and resid 433 through 447 Processing helix chain 'Al' and resid 448 through 459 Processing helix chain 'Al' and resid 461 through 472 removed outlier: 3.741A pdb=" N VALAl 465 " --> pdb=" O GLUAl 461 " (cutoff:3.500A) Processing helix chain 'Al' and resid 488 through 492 Processing helix chain 'Al' and resid 497 through 516 Processing helix chain 'Am' and resid 23 through 25 No H-bonds generated for 'chain 'Am' and resid 23 through 25' Processing helix chain 'Ar' and resid 9 through 29 removed outlier: 3.704A pdb=" N VALAr 29 " --> pdb=" O ASPAr 25 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 52 through 60 removed outlier: 3.703A pdb=" N VALAr 56 " --> pdb=" O ASPAr 52 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 64 through 85 Processing helix chain 'Ar' and resid 88 through 110 Processing helix chain 'Ar' and resid 112 through 135 Processing helix chain 'Ar' and resid 140 through 152 Processing helix chain 'Ar' and resid 155 through 169 removed outlier: 3.935A pdb=" N GLYAr 159 " --> pdb=" O ASPAr 155 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 201 through 205 Processing helix chain 'Ar' and resid 229 through 244 Proline residue: Ar 235 - end of helix Processing helix chain 'Ar' and resid 258 through 269 removed outlier: 3.880A pdb=" N VALAr 264 " --> pdb=" O ALAAr 260 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N METAr 267 " --> pdb=" O VALAr 263 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLYAr 269 " --> pdb=" O ASNAr 265 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 282 through 296 removed outlier: 3.568A pdb=" N LYSAr 286 " --> pdb=" O GLYAr 282 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 338 through 356 removed outlier: 3.713A pdb=" N GLUAr 354 " --> pdb=" O ARGAr 350 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 358 through 365 Processing helix chain 'Ar' and resid 366 through 375 Processing helix chain 'Ar' and resid 385 through 410 Processing helix chain 'Ar' and resid 416 through 426 Processing helix chain 'Ar' and resid 433 through 458 removed outlier: 3.653A pdb=" N GLUAr 448 " --> pdb=" O LEUAr 444 " (cutoff:3.500A) Proline residue: Ar 450 - end of helix Processing helix chain 'Ar' and resid 461 through 472 Processing helix chain 'Ar' and resid 488 through 492 Processing helix chain 'Ar' and resid 497 through 516 Processing helix chain 'As' and resid 9 through 29 removed outlier: 3.518A pdb=" N VALAs 29 " --> pdb=" O ASPAs 25 " (cutoff:3.500A) Processing helix chain 'As' and resid 52 through 60 removed outlier: 3.534A pdb=" N VALAs 56 " --> pdb=" O ASPAs 52 " (cutoff:3.500A) Processing helix chain 'As' and resid 64 through 85 removed outlier: 3.596A pdb=" N GLYAs 70 " --> pdb=" O PHEAs 66 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLUAs 76 " --> pdb=" O GLNAs 72 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VALAs 77 " --> pdb=" O METAs 73 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALAAs 78 " --> pdb=" O VALAs 74 " (cutoff:3.500A) Processing helix chain 'As' and resid 88 through 109 Processing helix chain 'As' and resid 112 through 135 Processing helix chain 'As' and resid 140 through 152 Processing helix chain 'As' and resid 155 through 170 Processing helix chain 'As' and resid 201 through 205 removed outlier: 3.868A pdb=" N PHEAs 204 " --> pdb=" O SERAs 201 " (cutoff:3.500A) Processing helix chain 'As' and resid 229 through 244 removed outlier: 3.977A pdb=" N METAs 233 " --> pdb=" O ASNAs 229 " (cutoff:3.500A) Proline residue: As 235 - end of helix Processing helix chain 'As' and resid 255 through 269 Processing helix chain 'As' and resid 281 through 297 Processing helix chain 'As' and resid 308 through 312 Processing helix chain 'As' and resid 313 through 317 removed outlier: 3.776A pdb=" N LEUAs 317 " --> pdb=" O LEUAs 314 " (cutoff:3.500A) Processing helix chain 'As' and resid 338 through 354 removed outlier: 3.571A pdb=" N GLUAs 354 " --> pdb=" O ARGAs 350 " (cutoff:3.500A) Processing helix chain 'As' and resid 358 through 373 removed outlier: 3.552A pdb=" N LYSAs 364 " --> pdb=" O TYRAs 360 " (cutoff:3.500A) Processing helix chain 'As' and resid 385 through 410 Processing helix chain 'As' and resid 416 through 426 Processing helix chain 'As' and resid 433 through 447 Processing helix chain 'As' and resid 448 through 459 Processing helix chain 'As' and resid 461 through 472 removed outlier: 3.741A pdb=" N VALAs 465 " --> pdb=" O GLUAs 461 " (cutoff:3.500A) Processing helix chain 'As' and resid 488 through 492 Processing helix chain 'As' and resid 497 through 516 Processing helix chain 'At' and resid 23 through 25 No H-bonds generated for 'chain 'At' and resid 23 through 25' Processing helix chain 'Ay' and resid 9 through 29 removed outlier: 3.704A pdb=" N VALAy 29 " --> pdb=" O ASPAy 25 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 52 through 60 removed outlier: 3.703A pdb=" N VALAy 56 " --> pdb=" O ASPAy 52 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 64 through 85 Processing helix chain 'Ay' and resid 88 through 110 Processing helix chain 'Ay' and resid 112 through 135 Processing helix chain 'Ay' and resid 140 through 152 Processing helix chain 'Ay' and resid 155 through 169 removed outlier: 3.936A pdb=" N GLYAy 159 " --> pdb=" O ASPAy 155 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 201 through 205 Processing helix chain 'Ay' and resid 229 through 244 Proline residue: Ay 235 - end of helix Processing helix chain 'Ay' and resid 258 through 269 removed outlier: 3.880A pdb=" N VALAy 264 " --> pdb=" O ALAAy 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N METAy 267 " --> pdb=" O VALAy 263 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLYAy 269 " --> pdb=" O ASNAy 265 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 282 through 296 removed outlier: 3.568A pdb=" N LYSAy 286 " --> pdb=" O GLYAy 282 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 338 through 356 removed outlier: 3.713A pdb=" N GLUAy 354 " --> pdb=" O ARGAy 350 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 358 through 365 Processing helix chain 'Ay' and resid 366 through 375 Processing helix chain 'Ay' and resid 385 through 410 Processing helix chain 'Ay' and resid 416 through 426 Processing helix chain 'Ay' and resid 433 through 458 removed outlier: 3.654A pdb=" N GLUAy 448 " --> pdb=" O LEUAy 444 " (cutoff:3.500A) Proline residue: Ay 450 - end of helix Processing helix chain 'Ay' and resid 461 through 472 Processing helix chain 'Ay' and resid 488 through 492 Processing helix chain 'Ay' and resid 497 through 516 Processing helix chain 'Az' and resid 9 through 29 removed outlier: 3.518A pdb=" N VALAz 29 " --> pdb=" O ASPAz 25 " (cutoff:3.500A) Processing helix chain 'Az' and resid 52 through 60 removed outlier: 3.534A pdb=" N VALAz 56 " --> pdb=" O ASPAz 52 " (cutoff:3.500A) Processing helix chain 'Az' and resid 64 through 85 removed outlier: 3.597A pdb=" N GLYAz 70 " --> pdb=" O PHEAz 66 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLUAz 76 " --> pdb=" O GLNAz 72 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VALAz 77 " --> pdb=" O METAz 73 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALAAz 78 " --> pdb=" O VALAz 74 " (cutoff:3.500A) Processing helix chain 'Az' and resid 88 through 109 Processing helix chain 'Az' and resid 112 through 135 Processing helix chain 'Az' and resid 140 through 152 Processing helix chain 'Az' and resid 155 through 170 Processing helix chain 'Az' and resid 201 through 205 removed outlier: 3.868A pdb=" N PHEAz 204 " --> pdb=" O SERAz 201 " (cutoff:3.500A) Processing helix chain 'Az' and resid 229 through 244 removed outlier: 3.977A pdb=" N METAz 233 " --> pdb=" O ASNAz 229 " (cutoff:3.500A) Proline residue: Az 235 - end of helix Processing helix chain 'Az' and resid 255 through 269 Processing helix chain 'Az' and resid 281 through 297 Processing helix chain 'Az' and resid 308 through 312 Processing helix chain 'Az' and resid 313 through 317 removed outlier: 3.777A pdb=" N LEUAz 317 " --> pdb=" O LEUAz 314 " (cutoff:3.500A) Processing helix chain 'Az' and resid 338 through 354 removed outlier: 3.572A pdb=" N GLUAz 354 " --> pdb=" O ARGAz 350 " (cutoff:3.500A) Processing helix chain 'Az' and resid 358 through 373 removed outlier: 3.552A pdb=" N LYSAz 364 " --> pdb=" O TYRAz 360 " (cutoff:3.500A) Processing helix chain 'Az' and resid 385 through 410 Processing helix chain 'Az' and resid 416 through 426 Processing helix chain 'Az' and resid 433 through 447 Processing helix chain 'Az' and resid 448 through 459 Processing helix chain 'Az' and resid 461 through 472 removed outlier: 3.741A pdb=" N VALAz 465 " --> pdb=" O GLUAz 461 " (cutoff:3.500A) Processing helix chain 'Az' and resid 488 through 492 Processing helix chain 'Az' and resid 497 through 516 Processing helix chain 'Ba' and resid 23 through 25 No H-bonds generated for 'chain 'Ba' and resid 23 through 25' Processing helix chain 'Bf' and resid 9 through 29 removed outlier: 3.703A pdb=" N VALBf 29 " --> pdb=" O ASPBf 25 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 52 through 60 removed outlier: 3.704A pdb=" N VALBf 56 " --> pdb=" O ASPBf 52 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 64 through 85 Processing helix chain 'Bf' and resid 88 through 110 Processing helix chain 'Bf' and resid 112 through 135 Processing helix chain 'Bf' and resid 140 through 152 Processing helix chain 'Bf' and resid 155 through 169 removed outlier: 3.936A pdb=" N GLYBf 159 " --> pdb=" O ASPBf 155 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 201 through 205 Processing helix chain 'Bf' and resid 229 through 244 Proline residue: Bf 235 - end of helix Processing helix chain 'Bf' and resid 258 through 269 removed outlier: 3.879A pdb=" N VALBf 264 " --> pdb=" O ALABf 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N METBf 267 " --> pdb=" O VALBf 263 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLYBf 269 " --> pdb=" O ASNBf 265 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 282 through 296 removed outlier: 3.568A pdb=" N LYSBf 286 " --> pdb=" O GLYBf 282 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 338 through 356 removed outlier: 3.712A pdb=" N GLUBf 354 " --> pdb=" O ARGBf 350 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 358 through 365 Processing helix chain 'Bf' and resid 366 through 375 Processing helix chain 'Bf' and resid 385 through 410 Processing helix chain 'Bf' and resid 416 through 426 Processing helix chain 'Bf' and resid 433 through 458 removed outlier: 3.654A pdb=" N GLUBf 448 " --> pdb=" O LEUBf 444 " (cutoff:3.500A) Proline residue: Bf 450 - end of helix Processing helix chain 'Bf' and resid 461 through 472 Processing helix chain 'Bf' and resid 488 through 492 Processing helix chain 'Bf' and resid 497 through 516 Processing helix chain 'Bg' and resid 9 through 29 removed outlier: 3.518A pdb=" N VALBg 29 " --> pdb=" O ASPBg 25 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 52 through 60 removed outlier: 3.533A pdb=" N VALBg 56 " --> pdb=" O ASPBg 52 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 64 through 85 removed outlier: 3.596A pdb=" N GLYBg 70 " --> pdb=" O PHEBg 66 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLUBg 76 " --> pdb=" O GLNBg 72 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VALBg 77 " --> pdb=" O METBg 73 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALABg 78 " --> pdb=" O VALBg 74 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 88 through 109 Processing helix chain 'Bg' and resid 112 through 135 Processing helix chain 'Bg' and resid 140 through 152 Processing helix chain 'Bg' and resid 155 through 170 Processing helix chain 'Bg' and resid 201 through 205 removed outlier: 3.869A pdb=" N PHEBg 204 " --> pdb=" O SERBg 201 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 229 through 244 removed outlier: 3.977A pdb=" N METBg 233 " --> pdb=" O ASNBg 229 " (cutoff:3.500A) Proline residue: Bg 235 - end of helix Processing helix chain 'Bg' and resid 255 through 269 Processing helix chain 'Bg' and resid 281 through 297 Processing helix chain 'Bg' and resid 308 through 312 Processing helix chain 'Bg' and resid 313 through 317 removed outlier: 3.776A pdb=" N LEUBg 317 " --> pdb=" O LEUBg 314 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 338 through 354 removed outlier: 3.571A pdb=" N GLUBg 354 " --> pdb=" O ARGBg 350 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 358 through 373 removed outlier: 3.552A pdb=" N LYSBg 364 " --> pdb=" O TYRBg 360 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 385 through 410 Processing helix chain 'Bg' and resid 416 through 426 Processing helix chain 'Bg' and resid 433 through 447 Processing helix chain 'Bg' and resid 448 through 459 Processing helix chain 'Bg' and resid 461 through 472 removed outlier: 3.741A pdb=" N VALBg 465 " --> pdb=" O GLUBg 461 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 488 through 492 Processing helix chain 'Bg' and resid 497 through 516 Processing helix chain 'Bh' and resid 23 through 25 No H-bonds generated for 'chain 'Bh' and resid 23 through 25' Processing helix chain 'Bm' and resid 9 through 29 removed outlier: 3.705A pdb=" N VALBm 29 " --> pdb=" O ASPBm 25 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 52 through 60 removed outlier: 3.703A pdb=" N VALBm 56 " --> pdb=" O ASPBm 52 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 64 through 85 Processing helix chain 'Bm' and resid 88 through 110 Processing helix chain 'Bm' and resid 112 through 135 Processing helix chain 'Bm' and resid 140 through 152 Processing helix chain 'Bm' and resid 155 through 169 removed outlier: 3.935A pdb=" N GLYBm 159 " --> pdb=" O ASPBm 155 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 201 through 205 Processing helix chain 'Bm' and resid 229 through 244 Proline residue: Bm 235 - end of helix Processing helix chain 'Bm' and resid 258 through 269 removed outlier: 3.880A pdb=" N VALBm 264 " --> pdb=" O ALABm 260 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N METBm 267 " --> pdb=" O VALBm 263 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLYBm 269 " --> pdb=" O ASNBm 265 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 282 through 296 removed outlier: 3.568A pdb=" N LYSBm 286 " --> pdb=" O GLYBm 282 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 338 through 356 removed outlier: 3.712A pdb=" N GLUBm 354 " --> pdb=" O ARGBm 350 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 358 through 365 Processing helix chain 'Bm' and resid 366 through 375 Processing helix chain 'Bm' and resid 385 through 410 Processing helix chain 'Bm' and resid 416 through 426 Processing helix chain 'Bm' and resid 433 through 458 removed outlier: 3.653A pdb=" N GLUBm 448 " --> pdb=" O LEUBm 444 " (cutoff:3.500A) Proline residue: Bm 450 - end of helix Processing helix chain 'Bm' and resid 461 through 472 Processing helix chain 'Bm' and resid 488 through 492 Processing helix chain 'Bm' and resid 497 through 516 Processing helix chain 'Bn' and resid 9 through 29 removed outlier: 3.518A pdb=" N VALBn 29 " --> pdb=" O ASPBn 25 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 52 through 60 removed outlier: 3.533A pdb=" N VALBn 56 " --> pdb=" O ASPBn 52 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 64 through 85 removed outlier: 3.596A pdb=" N GLYBn 70 " --> pdb=" O PHEBn 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLUBn 76 " --> pdb=" O GLNBn 72 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VALBn 77 " --> pdb=" O METBn 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALABn 78 " --> pdb=" O VALBn 74 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 88 through 109 Processing helix chain 'Bn' and resid 112 through 135 Processing helix chain 'Bn' and resid 140 through 152 Processing helix chain 'Bn' and resid 155 through 170 Processing helix chain 'Bn' and resid 201 through 205 removed outlier: 3.868A pdb=" N PHEBn 204 " --> pdb=" O SERBn 201 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 229 through 244 removed outlier: 3.976A pdb=" N METBn 233 " --> pdb=" O ASNBn 229 " (cutoff:3.500A) Proline residue: Bn 235 - end of helix Processing helix chain 'Bn' and resid 255 through 269 Processing helix chain 'Bn' and resid 281 through 297 Processing helix chain 'Bn' and resid 308 through 312 Processing helix chain 'Bn' and resid 313 through 317 removed outlier: 3.776A pdb=" N LEUBn 317 " --> pdb=" O LEUBn 314 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 338 through 354 removed outlier: 3.572A pdb=" N GLUBn 354 " --> pdb=" O ARGBn 350 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 358 through 373 removed outlier: 3.552A pdb=" N LYSBn 364 " --> pdb=" O TYRBn 360 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 385 through 410 Processing helix chain 'Bn' and resid 416 through 426 Processing helix chain 'Bn' and resid 433 through 447 Processing helix chain 'Bn' and resid 448 through 459 Processing helix chain 'Bn' and resid 461 through 472 removed outlier: 3.742A pdb=" N VALBn 465 " --> pdb=" O GLUBn 461 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 488 through 492 Processing helix chain 'Bn' and resid 497 through 516 Processing helix chain 'Bo' and resid 23 through 25 No H-bonds generated for 'chain 'Bo' and resid 23 through 25' Processing helix chain 'Bt' and resid 9 through 29 removed outlier: 3.705A pdb=" N VALBt 29 " --> pdb=" O ASPBt 25 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 52 through 60 removed outlier: 3.703A pdb=" N VALBt 56 " --> pdb=" O ASPBt 52 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 64 through 85 Processing helix chain 'Bt' and resid 88 through 110 Processing helix chain 'Bt' and resid 112 through 135 Processing helix chain 'Bt' and resid 140 through 152 Processing helix chain 'Bt' and resid 155 through 169 removed outlier: 3.936A pdb=" N GLYBt 159 " --> pdb=" O ASPBt 155 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 201 through 205 Processing helix chain 'Bt' and resid 229 through 244 Proline residue: Bt 235 - end of helix Processing helix chain 'Bt' and resid 258 through 269 removed outlier: 3.880A pdb=" N VALBt 264 " --> pdb=" O ALABt 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N METBt 267 " --> pdb=" O VALBt 263 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLYBt 269 " --> pdb=" O ASNBt 265 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 282 through 296 removed outlier: 3.568A pdb=" N LYSBt 286 " --> pdb=" O GLYBt 282 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 338 through 356 removed outlier: 3.712A pdb=" N GLUBt 354 " --> pdb=" O ARGBt 350 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 358 through 365 Processing helix chain 'Bt' and resid 366 through 375 Processing helix chain 'Bt' and resid 385 through 410 Processing helix chain 'Bt' and resid 416 through 426 Processing helix chain 'Bt' and resid 433 through 458 removed outlier: 3.654A pdb=" N GLUBt 448 " --> pdb=" O LEUBt 444 " (cutoff:3.500A) Proline residue: Bt 450 - end of helix Processing helix chain 'Bt' and resid 461 through 472 Processing helix chain 'Bt' and resid 488 through 492 Processing helix chain 'Bt' and resid 497 through 516 Processing helix chain 'Bu' and resid 9 through 29 removed outlier: 3.518A pdb=" N VALBu 29 " --> pdb=" O ASPBu 25 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 52 through 60 removed outlier: 3.533A pdb=" N VALBu 56 " --> pdb=" O ASPBu 52 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 64 through 85 removed outlier: 3.596A pdb=" N GLYBu 70 " --> pdb=" O PHEBu 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLUBu 76 " --> pdb=" O GLNBu 72 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VALBu 77 " --> pdb=" O METBu 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALABu 78 " --> pdb=" O VALBu 74 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 88 through 109 Processing helix chain 'Bu' and resid 112 through 135 Processing helix chain 'Bu' and resid 140 through 152 Processing helix chain 'Bu' and resid 155 through 170 Processing helix chain 'Bu' and resid 201 through 205 removed outlier: 3.869A pdb=" N PHEBu 204 " --> pdb=" O SERBu 201 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 229 through 244 removed outlier: 3.976A pdb=" N METBu 233 " --> pdb=" O ASNBu 229 " (cutoff:3.500A) Proline residue: Bu 235 - end of helix Processing helix chain 'Bu' and resid 255 through 269 Processing helix chain 'Bu' and resid 281 through 297 Processing helix chain 'Bu' and resid 308 through 312 Processing helix chain 'Bu' and resid 313 through 317 removed outlier: 3.776A pdb=" N LEUBu 317 " --> pdb=" O LEUBu 314 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 338 through 354 removed outlier: 3.571A pdb=" N GLUBu 354 " --> pdb=" O ARGBu 350 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 358 through 373 removed outlier: 3.552A pdb=" N LYSBu 364 " --> pdb=" O TYRBu 360 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 385 through 410 Processing helix chain 'Bu' and resid 416 through 426 Processing helix chain 'Bu' and resid 433 through 447 Processing helix chain 'Bu' and resid 448 through 459 Processing helix chain 'Bu' and resid 461 through 472 removed outlier: 3.741A pdb=" N VALBu 465 " --> pdb=" O GLUBu 461 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 488 through 492 Processing helix chain 'Bu' and resid 497 through 516 Processing helix chain 'Bv' and resid 23 through 25 No H-bonds generated for 'chain 'Bv' and resid 23 through 25' Processing sheet with id=AA1, first strand: chain 'Ad' and resid 4 through 8 removed outlier: 6.235A pdb=" N ASNAr 37 " --> pdb=" O THRAd 517 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N CYSAd 519 " --> pdb=" O ASNAr 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Ad' and resid 48 through 50 removed outlier: 6.846A pdb=" N ASNAd 37 " --> pdb=" O CYSAk 519 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N VALAk 521 " --> pdb=" O ASNAd 37 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VALAd 39 " --> pdb=" O VALAk 521 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ASPAk 523 " --> pdb=" O VALAd 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Ad' and resid 175 through 180 removed outlier: 6.221A pdb=" N THRAd 176 " --> pdb=" O ILEAd 379 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VALAd 381 " --> pdb=" O THRAd 176 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLUAd 178 " --> pdb=" O VALAd 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Ad' and resid 194 through 195 Processing sheet with id=AA5, first strand: chain 'Ad' and resid 274 through 277 removed outlier: 6.244A pdb=" N LEUAd 247 " --> pdb=" O ALAAd 274 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VALAd 276 " --> pdb=" O LEUAd 247 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILEAd 249 " --> pdb=" O VALAd 276 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHEAd 219 " --> pdb=" O LEUAd 248 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILEAd 250 " --> pdb=" O PHEAd 219 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEUAd 221 " --> pdb=" O ILEAd 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Ad' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'Ad' and resid 476 through 479 Processing sheet with id=AA8, first strand: chain 'Ae' and resid 4 through 8 removed outlier: 7.256A pdb=" N VALAl 39 " --> pdb=" O GLUAe 518 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N METAe 520 " --> pdb=" O VALAl 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Ae' and resid 48 through 50 removed outlier: 7.442A pdb=" N ASNAe 37 " --> pdb=" O GLUAs 518 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N METAs 520 " --> pdb=" O ASNAe 37 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VALAe 39 " --> pdb=" O METAs 520 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N THRAs 522 " --> pdb=" O VALAe 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Ae' and resid 174 through 179 removed outlier: 6.365A pdb=" N VALAe 174 " --> pdb=" O ALAAe 377 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILEAe 379 " --> pdb=" O VALAe 174 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THRAe 176 " --> pdb=" O ILEAe 379 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VALAe 381 " --> pdb=" O THRAe 176 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLUAe 178 " --> pdb=" O VALAe 381 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Ae' and resid 193 through 195 removed outlier: 6.619A pdb=" N GLYAe 335 " --> pdb=" O ALAAe 320 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALAAe 320 " --> pdb=" O GLYAe 335 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLYAe 318 " --> pdb=" O ILEAe 220 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALAAe 251 " --> pdb=" O VALAe 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Ae' and resid 213 through 216 removed outlier: 3.536A pdb=" N GLYAe 318 " --> pdb=" O ILEAe 220 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ILEAe 301 " --> pdb=" O ILEAe 220 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEUAe 222 " --> pdb=" O ILEAe 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Ae' and resid 226 through 227 Processing sheet with id=AB5, first strand: chain 'Ae' and resid 411 through 413 Processing sheet with id=AB6, first strand: chain 'Ae' and resid 476 through 479 Processing sheet with id=AB7, first strand: chain 'Af' and resid 4 through 5 removed outlier: 6.530A pdb=" N ILEAt 66 " --> pdb=" O LEUAt 92 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILEAt 94 " --> pdb=" O ILEAt 64 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILEAt 64 " --> pdb=" O ILEAt 94 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILEAt 11 " --> pdb=" O LEUAt 41 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VALAt 43 " --> pdb=" O ARGAt 9 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ARGAt 9 " --> pdb=" O VALAt 43 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ARGAt 14 " --> pdb=" O GLUAt 82 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N GLUAt 82 " --> pdb=" O ARGAt 14 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Af' and resid 74 through 78 removed outlier: 8.720A pdb=" N GLUAf 82 " --> pdb=" O ARGAf 14 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ARGAf 14 " --> pdb=" O GLUAf 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ARGAf 9 " --> pdb=" O VALAf 43 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VALAf 43 " --> pdb=" O ARGAf 9 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILEAf 11 " --> pdb=" O LEUAf 41 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILEAf 64 " --> pdb=" O ILEAf 94 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILEAf 94 " --> pdb=" O ILEAf 64 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILEAf 66 " --> pdb=" O LEUAf 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Af' and resid 21 through 22 Processing sheet with id=AC1, first strand: chain 'Ak' and resid 48 through 50 removed outlier: 6.881A pdb=" N ASNAk 37 " --> pdb=" O CYSAy 519 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N VALAy 521 " --> pdb=" O ASNAk 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VALAk 39 " --> pdb=" O VALAy 521 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASPAy 523 " --> pdb=" O VALAk 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Ak' and resid 175 through 180 removed outlier: 6.221A pdb=" N THRAk 176 " --> pdb=" O ILEAk 379 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VALAk 381 " --> pdb=" O THRAk 176 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLUAk 178 " --> pdb=" O VALAk 381 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Ak' and resid 194 through 195 Processing sheet with id=AC4, first strand: chain 'Ak' and resid 274 through 277 removed outlier: 6.244A pdb=" N LEUAk 247 " --> pdb=" O ALAAk 274 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VALAk 276 " --> pdb=" O LEUAk 247 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILEAk 249 " --> pdb=" O VALAk 276 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHEAk 219 " --> pdb=" O LEUAk 248 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILEAk 250 " --> pdb=" O PHEAk 219 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEUAk 221 " --> pdb=" O ILEAk 250 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Ak' and resid 411 through 413 Processing sheet with id=AC6, first strand: chain 'Ak' and resid 476 through 479 Processing sheet with id=AC7, first strand: chain 'Al' and resid 4 through 8 removed outlier: 7.289A pdb=" N VALAz 39 " --> pdb=" O GLUAl 518 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N METAl 520 " --> pdb=" O VALAz 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Al' and resid 174 through 179 removed outlier: 6.365A pdb=" N VALAl 174 " --> pdb=" O ALAAl 377 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILEAl 379 " --> pdb=" O VALAl 174 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THRAl 176 " --> pdb=" O ILEAl 379 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VALAl 381 " --> pdb=" O THRAl 176 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLUAl 178 " --> pdb=" O VALAl 381 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Al' and resid 193 through 195 removed outlier: 6.619A pdb=" N GLYAl 335 " --> pdb=" O ALAAl 320 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALAAl 320 " --> pdb=" O GLYAl 335 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLYAl 318 " --> pdb=" O ILEAl 220 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALAAl 251 " --> pdb=" O VALAl 276 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Al' and resid 213 through 216 removed outlier: 3.536A pdb=" N GLYAl 318 " --> pdb=" O ILEAl 220 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ILEAl 301 " --> pdb=" O ILEAl 220 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEUAl 222 " --> pdb=" O ILEAl 301 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Al' and resid 226 through 227 Processing sheet with id=AD3, first strand: chain 'Al' and resid 411 through 413 Processing sheet with id=AD4, first strand: chain 'Al' and resid 476 through 479 Processing sheet with id=AD5, first strand: chain 'Am' and resid 74 through 78 removed outlier: 8.720A pdb=" N GLUAm 82 " --> pdb=" O ARGAm 14 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ARGAm 14 " --> pdb=" O GLUAm 82 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ARGAm 9 " --> pdb=" O VALAm 43 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VALAm 43 " --> pdb=" O ARGAm 9 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILEAm 11 " --> pdb=" O LEUAm 41 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILEAm 64 " --> pdb=" O ILEAm 94 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILEAm 94 " --> pdb=" O ILEAm 64 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILEAm 66 " --> pdb=" O LEUAm 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Am' and resid 21 through 22 Processing sheet with id=AD7, first strand: chain 'Ar' and resid 4 through 8 removed outlier: 6.232A pdb=" N ASNBm 37 " --> pdb=" O THRAr 517 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYSAr 519 " --> pdb=" O ASNBm 37 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Ar' and resid 175 through 180 removed outlier: 6.221A pdb=" N THRAr 176 " --> pdb=" O ILEAr 379 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VALAr 381 " --> pdb=" O THRAr 176 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLUAr 178 " --> pdb=" O VALAr 381 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Ar' and resid 194 through 195 Processing sheet with id=AE1, first strand: chain 'Ar' and resid 274 through 277 removed outlier: 6.244A pdb=" N LEUAr 247 " --> pdb=" O ALAAr 274 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VALAr 276 " --> pdb=" O LEUAr 247 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILEAr 249 " --> pdb=" O VALAr 276 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHEAr 219 " --> pdb=" O LEUAr 248 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILEAr 250 " --> pdb=" O PHEAr 219 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEUAr 221 " --> pdb=" O ILEAr 250 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Ar' and resid 411 through 413 Processing sheet with id=AE3, first strand: chain 'Ar' and resid 476 through 479 Processing sheet with id=AE4, first strand: chain 'As' and resid 48 through 50 removed outlier: 7.436A pdb=" N ASNAs 37 " --> pdb=" O GLUBn 518 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N METBn 520 " --> pdb=" O ASNAs 37 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VALAs 39 " --> pdb=" O METBn 520 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N THRBn 522 " --> pdb=" O VALAs 39 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'As' and resid 174 through 179 removed outlier: 6.365A pdb=" N VALAs 174 " --> pdb=" O ALAAs 377 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILEAs 379 " --> pdb=" O VALAs 174 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THRAs 176 " --> pdb=" O ILEAs 379 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VALAs 381 " --> pdb=" O THRAs 176 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLUAs 178 " --> pdb=" O VALAs 381 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'As' and resid 193 through 195 removed outlier: 6.618A pdb=" N GLYAs 335 " --> pdb=" O ALAAs 320 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALAAs 320 " --> pdb=" O GLYAs 335 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLYAs 318 " --> pdb=" O ILEAs 220 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALAAs 251 " --> pdb=" O VALAs 276 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'As' and resid 213 through 216 removed outlier: 3.535A pdb=" N GLYAs 318 " --> pdb=" O ILEAs 220 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ILEAs 301 " --> pdb=" O ILEAs 220 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEUAs 222 " --> pdb=" O ILEAs 301 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'As' and resid 226 through 227 Processing sheet with id=AE9, first strand: chain 'As' and resid 411 through 413 Processing sheet with id=AF1, first strand: chain 'As' and resid 476 through 479 Processing sheet with id=AF2, first strand: chain 'At' and resid 21 through 22 Processing sheet with id=AF3, first strand: chain 'Ay' and resid 48 through 50 removed outlier: 6.898A pdb=" N ASNAy 37 " --> pdb=" O CYSBt 519 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N VALBt 521 " --> pdb=" O ASNAy 37 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VALAy 39 " --> pdb=" O VALBt 521 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ASPBt 523 " --> pdb=" O VALAy 39 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Ay' and resid 175 through 180 removed outlier: 6.221A pdb=" N THRAy 176 " --> pdb=" O ILEAy 379 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VALAy 381 " --> pdb=" O THRAy 176 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLUAy 178 " --> pdb=" O VALAy 381 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Ay' and resid 194 through 195 Processing sheet with id=AF6, first strand: chain 'Ay' and resid 274 through 277 removed outlier: 6.245A pdb=" N LEUAy 247 " --> pdb=" O ALAAy 274 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VALAy 276 " --> pdb=" O LEUAy 247 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILEAy 249 " --> pdb=" O VALAy 276 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHEAy 219 " --> pdb=" O LEUAy 248 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILEAy 250 " --> pdb=" O PHEAy 219 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEUAy 221 " --> pdb=" O ILEAy 250 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Ay' and resid 411 through 413 Processing sheet with id=AF8, first strand: chain 'Ay' and resid 476 through 479 Processing sheet with id=AF9, first strand: chain 'Az' and resid 4 through 8 removed outlier: 7.308A pdb=" N VALBu 39 " --> pdb=" O GLUAz 518 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N METAz 520 " --> pdb=" O VALBu 39 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Az' and resid 174 through 179 removed outlier: 6.365A pdb=" N VALAz 174 " --> pdb=" O ALAAz 377 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILEAz 379 " --> pdb=" O VALAz 174 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THRAz 176 " --> pdb=" O ILEAz 379 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VALAz 381 " --> pdb=" O THRAz 176 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLUAz 178 " --> pdb=" O VALAz 381 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Az' and resid 193 through 195 removed outlier: 6.618A pdb=" N GLYAz 335 " --> pdb=" O ALAAz 320 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALAAz 320 " --> pdb=" O GLYAz 335 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLYAz 318 " --> pdb=" O ILEAz 220 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALAAz 251 " --> pdb=" O VALAz 276 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Az' and resid 213 through 216 removed outlier: 3.536A pdb=" N GLYAz 318 " --> pdb=" O ILEAz 220 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ILEAz 301 " --> pdb=" O ILEAz 220 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEUAz 222 " --> pdb=" O ILEAz 301 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Az' and resid 226 through 227 Processing sheet with id=AG5, first strand: chain 'Az' and resid 411 through 413 Processing sheet with id=AG6, first strand: chain 'Az' and resid 476 through 479 Processing sheet with id=AG7, first strand: chain 'Ba' and resid 74 through 78 removed outlier: 8.720A pdb=" N GLUBa 82 " --> pdb=" O ARGBa 14 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ARGBa 14 " --> pdb=" O GLUBa 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ARGBa 9 " --> pdb=" O VALBa 43 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VALBa 43 " --> pdb=" O ARGBa 9 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILEBa 11 " --> pdb=" O LEUBa 41 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILEBa 64 " --> pdb=" O ILEBa 94 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILEBa 94 " --> pdb=" O ILEBa 64 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILEBa 66 " --> pdb=" O LEUBa 92 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Ba' and resid 21 through 22 Processing sheet with id=AG9, first strand: chain 'Bf' and resid 4 through 8 removed outlier: 6.228A pdb=" N ASNBt 37 " --> pdb=" O THRBf 517 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYSBf 519 " --> pdb=" O ASNBt 37 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Bf' and resid 48 through 50 removed outlier: 6.874A pdb=" N ASNBf 37 " --> pdb=" O CYSBm 519 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N VALBm 521 " --> pdb=" O ASNBf 37 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VALBf 39 " --> pdb=" O VALBm 521 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ASPBm 523 " --> pdb=" O VALBf 39 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Bf' and resid 175 through 180 removed outlier: 6.221A pdb=" N THRBf 176 " --> pdb=" O ILEBf 379 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VALBf 381 " --> pdb=" O THRBf 176 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLUBf 178 " --> pdb=" O VALBf 381 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Bf' and resid 194 through 195 Processing sheet with id=AH4, first strand: chain 'Bf' and resid 274 through 277 removed outlier: 6.244A pdb=" N LEUBf 247 " --> pdb=" O ALABf 274 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VALBf 276 " --> pdb=" O LEUBf 247 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILEBf 249 " --> pdb=" O VALBf 276 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHEBf 219 " --> pdb=" O LEUBf 248 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILEBf 250 " --> pdb=" O PHEBf 219 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEUBf 221 " --> pdb=" O ILEBf 250 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Bf' and resid 411 through 413 Processing sheet with id=AH6, first strand: chain 'Bf' and resid 476 through 479 Processing sheet with id=AH7, first strand: chain 'Bg' and resid 4 through 8 removed outlier: 7.305A pdb=" N VALBn 39 " --> pdb=" O GLUBg 518 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N METBg 520 " --> pdb=" O VALBn 39 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Bg' and resid 48 through 50 removed outlier: 7.430A pdb=" N ASNBg 37 " --> pdb=" O GLUBu 518 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N METBu 520 " --> pdb=" O ASNBg 37 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VALBg 39 " --> pdb=" O METBu 520 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THRBu 522 " --> pdb=" O VALBg 39 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Bg' and resid 174 through 179 removed outlier: 6.365A pdb=" N VALBg 174 " --> pdb=" O ALABg 377 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILEBg 379 " --> pdb=" O VALBg 174 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THRBg 176 " --> pdb=" O ILEBg 379 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VALBg 381 " --> pdb=" O THRBg 176 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLUBg 178 " --> pdb=" O VALBg 381 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Bg' and resid 193 through 195 removed outlier: 6.619A pdb=" N GLYBg 335 " --> pdb=" O ALABg 320 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ALABg 320 " --> pdb=" O GLYBg 335 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLYBg 318 " --> pdb=" O ILEBg 220 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALABg 251 " --> pdb=" O VALBg 276 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Bg' and resid 213 through 216 removed outlier: 3.536A pdb=" N GLYBg 318 " --> pdb=" O ILEBg 220 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ILEBg 301 " --> pdb=" O ILEBg 220 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEUBg 222 " --> pdb=" O ILEBg 301 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Bg' and resid 226 through 227 Processing sheet with id=AI4, first strand: chain 'Bg' and resid 411 through 413 Processing sheet with id=AI5, first strand: chain 'Bg' and resid 476 through 479 Processing sheet with id=AI6, first strand: chain 'Bh' and resid 74 through 78 removed outlier: 8.720A pdb=" N GLUBh 82 " --> pdb=" O ARGBh 14 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ARGBh 14 " --> pdb=" O GLUBh 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ARGBh 9 " --> pdb=" O VALBh 43 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VALBh 43 " --> pdb=" O ARGBh 9 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILEBh 11 " --> pdb=" O LEUBh 41 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILEBh 64 " --> pdb=" O ILEBh 94 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILEBh 94 " --> pdb=" O ILEBh 64 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILEBh 66 " --> pdb=" O LEUBh 92 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Bh' and resid 21 through 22 Processing sheet with id=AI8, first strand: chain 'Bm' and resid 175 through 180 removed outlier: 6.221A pdb=" N THRBm 176 " --> pdb=" O ILEBm 379 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VALBm 381 " --> pdb=" O THRBm 176 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLUBm 178 " --> pdb=" O VALBm 381 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Bm' and resid 194 through 195 Processing sheet with id=AJ1, first strand: chain 'Bm' and resid 274 through 277 removed outlier: 6.245A pdb=" N LEUBm 247 " --> pdb=" O ALABm 274 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VALBm 276 " --> pdb=" O LEUBm 247 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILEBm 249 " --> pdb=" O VALBm 276 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHEBm 219 " --> pdb=" O LEUBm 248 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILEBm 250 " --> pdb=" O PHEBm 219 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEUBm 221 " --> pdb=" O ILEBm 250 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'Bm' and resid 411 through 413 Processing sheet with id=AJ3, first strand: chain 'Bm' and resid 476 through 479 Processing sheet with id=AJ4, first strand: chain 'Bn' and resid 174 through 179 removed outlier: 6.364A pdb=" N VALBn 174 " --> pdb=" O ALABn 377 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILEBn 379 " --> pdb=" O VALBn 174 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THRBn 176 " --> pdb=" O ILEBn 379 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VALBn 381 " --> pdb=" O THRBn 176 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLUBn 178 " --> pdb=" O VALBn 381 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Bn' and resid 193 through 195 removed outlier: 6.618A pdb=" N GLYBn 335 " --> pdb=" O ALABn 320 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ALABn 320 " --> pdb=" O GLYBn 335 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLYBn 318 " --> pdb=" O ILEBn 220 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALABn 251 " --> pdb=" O VALBn 276 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Bn' and resid 213 through 216 removed outlier: 3.536A pdb=" N GLYBn 318 " --> pdb=" O ILEBn 220 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ILEBn 301 " --> pdb=" O ILEBn 220 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEUBn 222 " --> pdb=" O ILEBn 301 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Bn' and resid 226 through 227 Processing sheet with id=AJ8, first strand: chain 'Bn' and resid 411 through 413 Processing sheet with id=AJ9, first strand: chain 'Bn' and resid 476 through 479 Processing sheet with id=AK1, first strand: chain 'Bo' and resid 74 through 78 removed outlier: 8.720A pdb=" N GLUBo 82 " --> pdb=" O ARGBo 14 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ARGBo 14 " --> pdb=" O GLUBo 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ARGBo 9 " --> pdb=" O VALBo 43 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VALBo 43 " --> pdb=" O ARGBo 9 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILEBo 11 " --> pdb=" O LEUBo 41 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILEBo 64 " --> pdb=" O ILEBo 94 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILEBo 94 " --> pdb=" O ILEBo 64 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILEBo 66 " --> pdb=" O LEUBo 92 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'Bo' and resid 21 through 22 Processing sheet with id=AK3, first strand: chain 'Bt' and resid 175 through 180 removed outlier: 6.221A pdb=" N THRBt 176 " --> pdb=" O ILEBt 379 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VALBt 381 " --> pdb=" O THRBt 176 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLUBt 178 " --> pdb=" O VALBt 381 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'Bt' and resid 194 through 195 Processing sheet with id=AK5, first strand: chain 'Bt' and resid 274 through 277 removed outlier: 6.243A pdb=" N LEUBt 247 " --> pdb=" O ALABt 274 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VALBt 276 " --> pdb=" O LEUBt 247 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILEBt 249 " --> pdb=" O VALBt 276 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHEBt 219 " --> pdb=" O LEUBt 248 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILEBt 250 " --> pdb=" O PHEBt 219 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEUBt 221 " --> pdb=" O ILEBt 250 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'Bt' and resid 411 through 413 Processing sheet with id=AK7, first strand: chain 'Bt' and resid 476 through 479 Processing sheet with id=AK8, first strand: chain 'Bu' and resid 174 through 179 removed outlier: 6.365A pdb=" N VALBu 174 " --> pdb=" O ALABu 377 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILEBu 379 " --> pdb=" O VALBu 174 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THRBu 176 " --> pdb=" O ILEBu 379 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VALBu 381 " --> pdb=" O THRBu 176 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLUBu 178 " --> pdb=" O VALBu 381 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'Bu' and resid 193 through 195 removed outlier: 6.619A pdb=" N GLYBu 335 " --> pdb=" O ALABu 320 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALABu 320 " --> pdb=" O GLYBu 335 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLYBu 318 " --> pdb=" O ILEBu 220 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALABu 251 " --> pdb=" O VALBu 276 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'Bu' and resid 213 through 216 removed outlier: 3.536A pdb=" N GLYBu 318 " --> pdb=" O ILEBu 220 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ILEBu 301 " --> pdb=" O ILEBu 220 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEUBu 222 " --> pdb=" O ILEBu 301 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'Bu' and resid 226 through 227 Processing sheet with id=AL3, first strand: chain 'Bu' and resid 411 through 413 Processing sheet with id=AL4, first strand: chain 'Bu' and resid 476 through 479 Processing sheet with id=AL5, first strand: chain 'Bv' and resid 74 through 78 removed outlier: 8.720A pdb=" N GLUBv 82 " --> pdb=" O ARGBv 14 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ARGBv 14 " --> pdb=" O GLUBv 82 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARGBv 9 " --> pdb=" O VALBv 43 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VALBv 43 " --> pdb=" O ARGBv 9 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILEBv 11 " --> pdb=" O LEUBv 41 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILEBv 64 " --> pdb=" O ILEBv 94 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILEBv 94 " --> pdb=" O ILEBv 64 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILEBv 66 " --> pdb=" O LEUBv 92 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'Bv' and resid 21 through 22 3722 hydrogen bonds defined for protein. 10722 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: 30.05 Time building geometry restraints manager: 13.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.39: 21770 1.39 - 1.60: 37534 1.60 - 1.80: 311 1.80 - 2.01: 284 2.01 - 2.22: 7 Bond restraints: 59906 Sorted by residual: bond pdb=" C PROAy 525 " pdb=" O PROAy 525 " ideal model delta sigma weight residual 1.231 2.215 -0.984 2.00e-02 2.50e+03 2.42e+03 bond pdb=" C PROBt 525 " pdb=" O PROBt 525 " ideal model delta sigma weight residual 1.231 2.215 -0.984 2.00e-02 2.50e+03 2.42e+03 bond pdb=" C PROAd 525 " pdb=" O PROAd 525 " ideal model delta sigma weight residual 1.231 2.215 -0.984 2.00e-02 2.50e+03 2.42e+03 bond pdb=" C PROBm 525 " pdb=" O PROBm 525 " ideal model delta sigma weight residual 1.231 2.215 -0.984 2.00e-02 2.50e+03 2.42e+03 bond pdb=" C PROAk 525 " pdb=" O PROAk 525 " ideal model delta sigma weight residual 1.231 2.215 -0.984 2.00e-02 2.50e+03 2.42e+03 ... (remaining 59901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.54: 80879 13.54 - 27.08: 62 27.08 - 40.63: 7 40.63 - 54.17: 0 54.17 - 67.71: 7 Bond angle restraints: 80955 Sorted by residual: angle pdb=" O PROAk 525 " pdb=" C PROAk 525 " pdb=" OXT PROAk 525 " ideal model delta sigma weight residual 118.00 50.29 67.71 3.00e+00 1.11e-01 5.09e+02 angle pdb=" O PROAy 525 " pdb=" C PROAy 525 " pdb=" OXT PROAy 525 " ideal model delta sigma weight residual 118.00 50.31 67.69 3.00e+00 1.11e-01 5.09e+02 angle pdb=" O PROAd 525 " pdb=" C PROAd 525 " pdb=" OXT PROAd 525 " ideal model delta sigma weight residual 118.00 50.32 67.68 3.00e+00 1.11e-01 5.09e+02 angle pdb=" O PROBm 525 " pdb=" C PROBm 525 " pdb=" OXT PROBm 525 " ideal model delta sigma weight residual 118.00 50.34 67.66 3.00e+00 1.11e-01 5.09e+02 angle pdb=" O PROAr 525 " pdb=" C PROAr 525 " pdb=" OXT PROAr 525 " ideal model delta sigma weight residual 118.00 50.34 67.66 3.00e+00 1.11e-01 5.09e+02 ... (remaining 80950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.92: 34874 32.92 - 65.84: 1967 65.84 - 98.76: 259 98.76 - 131.68: 14 131.68 - 164.60: 7 Dihedral angle restraints: 37121 sinusoidal: 14532 harmonic: 22589 Sorted by residual: dihedral pdb=" C VALBo 95 " pdb=" N VALBo 95 " pdb=" CA VALBo 95 " pdb=" CB VALBo 95 " ideal model delta harmonic sigma weight residual -122.00 -140.06 18.06 0 2.50e+00 1.60e-01 5.22e+01 dihedral pdb=" C VALBa 95 " pdb=" N VALBa 95 " pdb=" CA VALBa 95 " pdb=" CB VALBa 95 " ideal model delta harmonic sigma weight residual -122.00 -140.03 18.03 0 2.50e+00 1.60e-01 5.20e+01 dihedral pdb=" C VALAf 95 " pdb=" N VALAf 95 " pdb=" CA VALAf 95 " pdb=" CB VALAf 95 " ideal model delta harmonic sigma weight residual -122.00 -139.97 17.97 0 2.50e+00 1.60e-01 5.17e+01 ... (remaining 37118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 7286 0.140 - 0.281: 2243 0.281 - 0.421: 257 0.421 - 0.561: 28 0.561 - 0.701: 14 Chirality restraints: 9828 Sorted by residual: chirality pdb=" CA VALBo 95 " pdb=" N VALBo 95 " pdb=" C VALBo 95 " pdb=" CB VALBo 95 " both_signs ideal model delta sigma weight residual False 2.44 1.74 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CA VALBa 95 " pdb=" N VALBa 95 " pdb=" C VALBa 95 " pdb=" CB VALBa 95 " both_signs ideal model delta sigma weight residual False 2.44 1.74 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CA VALBh 95 " pdb=" N VALBh 95 " pdb=" C VALBh 95 " pdb=" CB VALBh 95 " both_signs ideal model delta sigma weight residual False 2.44 1.74 0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 9825 not shown) Planarity restraints: 10542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VALAk 136 " 0.028 2.00e-02 2.50e+03 5.50e-02 3.02e+01 pdb=" C VALAk 136 " -0.095 2.00e-02 2.50e+03 pdb=" O VALAk 136 " 0.035 2.00e-02 2.50e+03 pdb=" N PROAk 137 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALBm 136 " -0.028 2.00e-02 2.50e+03 5.50e-02 3.02e+01 pdb=" C VALBm 136 " 0.095 2.00e-02 2.50e+03 pdb=" O VALBm 136 " -0.035 2.00e-02 2.50e+03 pdb=" N PROBm 137 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALBf 136 " -0.028 2.00e-02 2.50e+03 5.49e-02 3.02e+01 pdb=" C VALBf 136 " 0.095 2.00e-02 2.50e+03 pdb=" O VALBf 136 " -0.035 2.00e-02 2.50e+03 pdb=" N PROBf 137 " -0.032 2.00e-02 2.50e+03 ... (remaining 10539 not shown) Histogram of nonbonded interaction distances: 0.65 - 1.50: 133 1.50 - 2.35: 388 2.35 - 3.20: 55176 3.20 - 4.05: 166430 4.05 - 4.90: 285253 Warning: very small nonbonded interaction distances. Nonbonded interactions: 507380 Sorted by model distance: nonbonded pdb=" CB ALAAd 46 " pdb=" OE2 GLUAk 76 " model vdw 0.650 3.460 nonbonded pdb=" CB ALABf 46 " pdb=" OE2 GLUBm 76 " model vdw 0.687 3.460 nonbonded pdb=" OE2 GLUBf 76 " pdb=" CB ALABt 46 " model vdw 0.689 3.460 nonbonded pdb=" OE2 GLUAr 76 " pdb=" CB ALABm 46 " model vdw 0.694 3.460 nonbonded pdb=" CB ALAAk 46 " pdb=" OE2 GLUAy 76 " model vdw 0.708 3.460 ... (remaining 507375 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'Ad' selection = chain 'Ae' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Ar' selection = chain 'As' selection = chain 'Ay' selection = chain 'Az' selection = chain 'Bf' selection = chain 'Bg' selection = chain 'Bm' selection = chain 'Bn' selection = chain 'Bt' selection = chain 'Bu' } ncs_group { reference = chain 'Af' selection = chain 'Am' selection = chain 'At' selection = chain 'Ba' selection = chain 'Bh' selection = chain 'Bo' selection = chain 'Bv' } 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: 4.760 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: 0.070 Extract box with map and model: 2.080 Check model and map are aligned: 0.350 Set scattering table: 0.450 Process input model: 104.760 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.360 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:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 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 : 0.018 0.984 59906 Z= 1.200 Angle : 2.204 67.712 80955 Z= 1.540 Chirality : 0.131 0.701 9828 Planarity : 0.011 0.169 10542 Dihedral : 19.503 164.600 22631 Min Nonbonded Distance : 0.650 Molprobity Statistics. All-atom Clashscore : 29.74 Ramachandran Plot: Outliers : 0.64 % Allowed : 2.50 % Favored : 96.86 % Rotamer: Outliers : 11.71 % Allowed : 14.64 % Favored : 73.65 % Cbeta Deviations : 1.93 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.09), residues: 7973 helix: 2.34 (0.07), residues: 4060 sheet: 0.50 (0.14), residues: 1008 loop : -0.41 (0.10), residues: 2905 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.004 HISBh 7 PHE 0.049 0.008 PHEAm 67 TYR 0.037 0.006 TYRBg 199 ARG 0.023 0.002 ARGBv 4 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 728 poor density : 508 time to evaluate : 6.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ae 488 MET cc_start: 0.8277 (mmp) cc_final: 0.8042 (mmm) REVERT: Al 51 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8474 (tttp) REVERT: Al 389 MET cc_start: 0.7292 (tpp) cc_final: 0.6895 (tpp) REVERT: As 51 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8488 (tttp) REVERT: Bg 104 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8872 (mp) REVERT: Bm 518 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6224 (tp30) REVERT: Bn 51 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8577 (tttp) REVERT: Bt 73 MET cc_start: 0.7762 (mtp) cc_final: 0.7516 (mtm) REVERT: Bu 51 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8642 (tttp) outliers start: 728 outliers final: 203 residues processed: 1186 average time/residue: 0.6051 time to fit residues: 1187.2762 Evaluate side-chains 589 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 380 time to evaluate : 5.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 54 VAL Chi-restraints excluded: chain Ad residue 186 GLU Chi-restraints excluded: chain Ad residue 191 GLU Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 210 THR Chi-restraints excluded: chain Ad residue 225 LYS Chi-restraints excluded: chain Ad residue 233 MET Chi-restraints excluded: chain Ad residue 236 VAL Chi-restraints excluded: chain Ad residue 240 VAL Chi-restraints excluded: chain Ad residue 245 LYS Chi-restraints excluded: chain Ad residue 250 ILE Chi-restraints excluded: chain Ad residue 259 LEU Chi-restraints excluded: chain Ad residue 268 ARG Chi-restraints excluded: chain Ad residue 292 ILE Chi-restraints excluded: chain Ad residue 299 THR Chi-restraints excluded: chain Ad residue 300 VAL Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 308 GLU Chi-restraints excluded: chain Ad residue 321 LYS Chi-restraints excluded: chain Ad residue 336 VAL Chi-restraints excluded: chain Ad residue 351 GLN Chi-restraints excluded: chain Ad residue 354 GLU Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 357 THR Chi-restraints excluded: chain Ad residue 521 VAL Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 429 LEU Chi-restraints excluded: chain Ak residue 54 VAL Chi-restraints excluded: chain Ak residue 186 GLU Chi-restraints excluded: chain Ak residue 191 GLU Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 210 THR Chi-restraints excluded: chain Ak residue 225 LYS Chi-restraints excluded: chain Ak residue 236 VAL Chi-restraints excluded: chain Ak residue 240 VAL Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 250 ILE Chi-restraints excluded: chain Ak residue 259 LEU Chi-restraints excluded: chain Ak residue 268 ARG Chi-restraints excluded: chain Ak residue 292 ILE Chi-restraints excluded: chain Ak residue 299 THR Chi-restraints excluded: chain Ak residue 300 VAL Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 308 GLU Chi-restraints excluded: chain Ak residue 321 LYS Chi-restraints excluded: chain Ak residue 336 VAL Chi-restraints excluded: chain Ak residue 351 GLN Chi-restraints excluded: chain Ak residue 354 GLU Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 357 THR Chi-restraints excluded: chain Ak residue 521 VAL Chi-restraints excluded: chain Al residue 51 LYS Chi-restraints excluded: chain Al residue 63 GLU Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 429 LEU Chi-restraints excluded: chain Ar residue 54 VAL Chi-restraints excluded: chain Ar residue 187 LEU Chi-restraints excluded: chain Ar residue 191 GLU Chi-restraints excluded: chain Ar residue 194 GLN Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 210 THR Chi-restraints excluded: chain Ar residue 225 LYS Chi-restraints excluded: chain Ar residue 236 VAL Chi-restraints excluded: chain Ar residue 240 VAL Chi-restraints excluded: chain Ar residue 245 LYS Chi-restraints excluded: chain Ar residue 250 ILE Chi-restraints excluded: chain Ar residue 259 LEU Chi-restraints excluded: chain Ar residue 268 ARG Chi-restraints excluded: chain Ar residue 292 ILE Chi-restraints excluded: chain Ar residue 299 THR Chi-restraints excluded: chain Ar residue 300 VAL Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 308 GLU Chi-restraints excluded: chain Ar residue 321 LYS Chi-restraints excluded: chain Ar residue 336 VAL Chi-restraints excluded: chain Ar residue 351 GLN Chi-restraints excluded: chain Ar residue 354 GLU Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain Ar residue 357 THR Chi-restraints excluded: chain Ar residue 521 VAL Chi-restraints excluded: chain As residue 51 LYS Chi-restraints excluded: chain As residue 63 GLU Chi-restraints excluded: chain As residue 128 VAL Chi-restraints excluded: chain As residue 284 ARG Chi-restraints excluded: chain As residue 429 LEU Chi-restraints excluded: chain At residue 2 ASN Chi-restraints excluded: chain Ay residue 54 VAL Chi-restraints excluded: chain Ay residue 186 GLU Chi-restraints excluded: chain Ay residue 187 LEU Chi-restraints excluded: chain Ay residue 191 GLU Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 210 THR Chi-restraints excluded: chain Ay residue 225 LYS Chi-restraints excluded: chain Ay residue 233 MET Chi-restraints excluded: chain Ay residue 236 VAL Chi-restraints excluded: chain Ay residue 240 VAL Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 250 ILE Chi-restraints excluded: chain Ay residue 259 LEU Chi-restraints excluded: chain Ay residue 268 ARG Chi-restraints excluded: chain Ay residue 277 LYS Chi-restraints excluded: chain Ay residue 292 ILE Chi-restraints excluded: chain Ay residue 299 THR Chi-restraints excluded: chain Ay residue 300 VAL Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 308 GLU Chi-restraints excluded: chain Ay residue 321 LYS Chi-restraints excluded: chain Ay residue 336 VAL Chi-restraints excluded: chain Ay residue 351 GLN Chi-restraints excluded: chain Ay residue 354 GLU Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 357 THR Chi-restraints excluded: chain Ay residue 365 LEU Chi-restraints excluded: chain Ay residue 521 VAL Chi-restraints excluded: chain Az residue 63 GLU Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 429 LEU Chi-restraints excluded: chain Bf residue 54 VAL Chi-restraints excluded: chain Bf residue 186 GLU Chi-restraints excluded: chain Bf residue 191 GLU Chi-restraints excluded: chain Bf residue 194 GLN Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 210 THR Chi-restraints excluded: chain Bf residue 225 LYS Chi-restraints excluded: chain Bf residue 233 MET Chi-restraints excluded: chain Bf residue 236 VAL Chi-restraints excluded: chain Bf residue 240 VAL Chi-restraints excluded: chain Bf residue 245 LYS Chi-restraints excluded: chain Bf residue 250 ILE Chi-restraints excluded: chain Bf residue 259 LEU Chi-restraints excluded: chain Bf residue 268 ARG Chi-restraints excluded: chain Bf residue 292 ILE Chi-restraints excluded: chain Bf residue 299 THR Chi-restraints excluded: chain Bf residue 300 VAL Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 308 GLU Chi-restraints excluded: chain Bf residue 321 LYS Chi-restraints excluded: chain Bf residue 336 VAL Chi-restraints excluded: chain Bf residue 351 GLN Chi-restraints excluded: chain Bf residue 354 GLU Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 357 THR Chi-restraints excluded: chain Bf residue 365 LEU Chi-restraints excluded: chain Bf residue 521 VAL Chi-restraints excluded: chain Bg residue 63 GLU Chi-restraints excluded: chain Bg residue 104 LEU Chi-restraints excluded: chain Bg residue 284 ARG Chi-restraints excluded: chain Bg residue 429 LEU Chi-restraints excluded: chain Bh residue 2 ASN Chi-restraints excluded: chain Bm residue 186 GLU Chi-restraints excluded: chain Bm residue 187 LEU Chi-restraints excluded: chain Bm residue 191 GLU Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 210 THR Chi-restraints excluded: chain Bm residue 225 LYS Chi-restraints excluded: chain Bm residue 233 MET Chi-restraints excluded: chain Bm residue 236 VAL Chi-restraints excluded: chain Bm residue 240 VAL Chi-restraints excluded: chain Bm residue 245 LYS Chi-restraints excluded: chain Bm residue 250 ILE Chi-restraints excluded: chain Bm residue 259 LEU Chi-restraints excluded: chain Bm residue 268 ARG Chi-restraints excluded: chain Bm residue 277 LYS Chi-restraints excluded: chain Bm residue 292 ILE Chi-restraints excluded: chain Bm residue 299 THR Chi-restraints excluded: chain Bm residue 300 VAL Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 308 GLU Chi-restraints excluded: chain Bm residue 321 LYS Chi-restraints excluded: chain Bm residue 336 VAL Chi-restraints excluded: chain Bm residue 351 GLN Chi-restraints excluded: chain Bm residue 354 GLU Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 357 THR Chi-restraints excluded: chain Bm residue 518 GLU Chi-restraints excluded: chain Bm residue 521 VAL Chi-restraints excluded: chain Bn residue 51 LYS Chi-restraints excluded: chain Bn residue 63 GLU Chi-restraints excluded: chain Bn residue 284 ARG Chi-restraints excluded: chain Bn residue 429 LEU Chi-restraints excluded: chain Bt residue 54 VAL Chi-restraints excluded: chain Bt residue 186 GLU Chi-restraints excluded: chain Bt residue 191 GLU Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 210 THR Chi-restraints excluded: chain Bt residue 225 LYS Chi-restraints excluded: chain Bt residue 233 MET Chi-restraints excluded: chain Bt residue 236 VAL Chi-restraints excluded: chain Bt residue 240 VAL Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 250 ILE Chi-restraints excluded: chain Bt residue 259 LEU Chi-restraints excluded: chain Bt residue 268 ARG Chi-restraints excluded: chain Bt residue 292 ILE Chi-restraints excluded: chain Bt residue 299 THR Chi-restraints excluded: chain Bt residue 300 VAL Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 308 GLU Chi-restraints excluded: chain Bt residue 321 LYS Chi-restraints excluded: chain Bt residue 336 VAL Chi-restraints excluded: chain Bt residue 351 GLN Chi-restraints excluded: chain Bt residue 354 GLU Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bt residue 357 THR Chi-restraints excluded: chain Bt residue 521 VAL Chi-restraints excluded: chain Bu residue 51 LYS Chi-restraints excluded: chain Bu residue 128 VAL Chi-restraints excluded: chain Bu residue 284 ARG Chi-restraints excluded: chain Bu residue 429 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 667 optimal weight: 0.7980 chunk 599 optimal weight: 8.9990 chunk 332 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 404 optimal weight: 3.9990 chunk 320 optimal weight: 0.1980 chunk 619 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 376 optimal weight: 5.9990 chunk 461 optimal weight: 0.9980 chunk 718 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 453 GLN Ae 21 ASN ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 146 GLN Ak 112 ASN ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 453 GLN Al 21 ASN ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 146 GLN Ar 112 ASN ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 453 GLN As 21 ASN ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 146 GLN As 453 GLN At 2 ASN Ay 112 ASN ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 319 GLN Ay 453 GLN Az 21 ASN ** Az 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 146 GLN Bf 112 ASN ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bf 319 GLN Bf 453 GLN Bg 21 ASN ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 146 GLN Bg 453 GLN Bh 2 ASN Bm 112 ASN ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 453 GLN Bn 21 ASN ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 146 GLN Bn 453 GLN ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bt 453 GLN Bu 21 ASN ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 146 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 59906 Z= 0.280 Angle : 0.797 11.801 80955 Z= 0.413 Chirality : 0.046 0.223 9828 Planarity : 0.005 0.052 10542 Dihedral : 12.972 153.408 9114 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.35 % Allowed : 1.93 % Favored : 97.72 % Rotamer: Outliers : 4.26 % Allowed : 18.48 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.09), residues: 7973 helix: 2.12 (0.07), residues: 4123 sheet: 0.33 (0.16), residues: 945 loop : -0.65 (0.10), residues: 2905 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HISBu 401 PHE 0.019 0.002 PHEAy 66 TYR 0.013 0.002 TYRBu 199 ARG 0.013 0.001 ARGBh 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 265 poor density : 381 time to evaluate : 5.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ae 491 MET cc_start: 0.8335 (mtp) cc_final: 0.8044 (mtm) REVERT: Ak 491 MET cc_start: 0.7506 (mtp) cc_final: 0.7289 (mtm) REVERT: As 284 ARG cc_start: 0.2611 (OUTLIER) cc_final: 0.1935 (ptm160) REVERT: Ay 514 MET cc_start: 0.8110 (mmt) cc_final: 0.7855 (mmm) REVERT: Bg 73 MET cc_start: 0.6528 (mtm) cc_final: 0.6251 (mtm) REVERT: Bm 254 VAL cc_start: 0.2350 (OUTLIER) cc_final: 0.2052 (p) REVERT: Bt 73 MET cc_start: 0.7756 (mtp) cc_final: 0.7457 (mtm) outliers start: 265 outliers final: 125 residues processed: 616 average time/residue: 0.5770 time to fit residues: 596.8352 Evaluate side-chains 469 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 342 time to evaluate : 6.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 210 THR Chi-restraints excluded: chain Ad residue 220 ILE Chi-restraints excluded: chain Ad residue 236 VAL Chi-restraints excluded: chain Ad residue 245 LYS Chi-restraints excluded: chain Ad residue 252 GLU Chi-restraints excluded: chain Ad residue 254 VAL Chi-restraints excluded: chain Ad residue 261 THR Chi-restraints excluded: chain Ad residue 268 ARG Chi-restraints excluded: chain Ad residue 300 VAL Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 310 GLU Chi-restraints excluded: chain Ad residue 351 GLN Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 360 TYR Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ak residue 191 GLU Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 210 THR Chi-restraints excluded: chain Ak residue 220 ILE Chi-restraints excluded: chain Ak residue 236 VAL Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 252 GLU Chi-restraints excluded: chain Ak residue 254 VAL Chi-restraints excluded: chain Ak residue 259 LEU Chi-restraints excluded: chain Ak residue 268 ARG Chi-restraints excluded: chain Ak residue 300 VAL Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 351 GLN Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Am residue 95 VAL Chi-restraints excluded: chain Ar residue 187 LEU Chi-restraints excluded: chain Ar residue 191 GLU Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 210 THR Chi-restraints excluded: chain Ar residue 220 ILE Chi-restraints excluded: chain Ar residue 236 VAL Chi-restraints excluded: chain Ar residue 245 LYS Chi-restraints excluded: chain Ar residue 252 GLU Chi-restraints excluded: chain Ar residue 259 LEU Chi-restraints excluded: chain Ar residue 261 THR Chi-restraints excluded: chain Ar residue 268 ARG Chi-restraints excluded: chain Ar residue 300 VAL Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 351 GLN Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain As residue 104 LEU Chi-restraints excluded: chain As residue 284 ARG Chi-restraints excluded: chain As residue 360 TYR Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain Ay residue 187 LEU Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 210 THR Chi-restraints excluded: chain Ay residue 220 ILE Chi-restraints excluded: chain Ay residue 236 VAL Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 254 VAL Chi-restraints excluded: chain Ay residue 268 ARG Chi-restraints excluded: chain Ay residue 300 VAL Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 351 GLN Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 95 VAL Chi-restraints excluded: chain Bf residue 191 GLU Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 210 THR Chi-restraints excluded: chain Bf residue 236 VAL Chi-restraints excluded: chain Bf residue 245 LYS Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 254 VAL Chi-restraints excluded: chain Bf residue 259 LEU Chi-restraints excluded: chain Bf residue 268 ARG Chi-restraints excluded: chain Bf residue 300 VAL Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 310 GLU Chi-restraints excluded: chain Bf residue 351 GLN Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bg residue 284 ARG Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bg residue 379 ILE Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bm residue 184 GLN Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 210 THR Chi-restraints excluded: chain Bm residue 220 ILE Chi-restraints excluded: chain Bm residue 236 VAL Chi-restraints excluded: chain Bm residue 245 LYS Chi-restraints excluded: chain Bm residue 252 GLU Chi-restraints excluded: chain Bm residue 254 VAL Chi-restraints excluded: chain Bm residue 261 THR Chi-restraints excluded: chain Bm residue 268 ARG Chi-restraints excluded: chain Bm residue 300 VAL Chi-restraints excluded: chain Bm residue 302 SER Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 351 GLN Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 284 ARG Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bt residue 63 GLU Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 210 THR Chi-restraints excluded: chain Bt residue 220 ILE Chi-restraints excluded: chain Bt residue 236 VAL Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 252 GLU Chi-restraints excluded: chain Bt residue 254 VAL Chi-restraints excluded: chain Bt residue 259 LEU Chi-restraints excluded: chain Bt residue 268 ARG Chi-restraints excluded: chain Bt residue 300 VAL Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 351 GLN Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bu residue 284 ARG Chi-restraints excluded: chain Bu residue 360 TYR Chi-restraints excluded: chain Bv residue 71 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 6.9990 chunk 222 optimal weight: 30.0000 chunk 597 optimal weight: 30.0000 chunk 489 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 719 optimal weight: 2.9990 chunk 777 optimal weight: 0.9990 chunk 640 optimal weight: 0.9990 chunk 713 optimal weight: 5.9990 chunk 245 optimal weight: 40.0000 chunk 577 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 319 GLN Ae 72 GLN ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 112 ASN Ae 290 GLN ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 290 GLN ** Am 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 112 ASN As 290 GLN ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 72 GLN ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 319 GLN ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bo 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bv 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 59906 Z= 0.367 Angle : 0.715 9.627 80955 Z= 0.371 Chirality : 0.046 0.170 9828 Planarity : 0.004 0.044 10542 Dihedral : 10.884 135.333 8820 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.93 % Favored : 96.81 % Rotamer: Outliers : 3.57 % Allowed : 18.85 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 7973 helix: 1.82 (0.08), residues: 4165 sheet: 0.46 (0.16), residues: 980 loop : -0.68 (0.11), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HISAz 401 PHE 0.013 0.002 PHEAd 66 TYR 0.012 0.002 TYRBg 199 ARG 0.008 0.001 ARGBu 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 354 time to evaluate : 5.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ae 491 MET cc_start: 0.8535 (mtp) cc_final: 0.8307 (mtm) REVERT: Bg 73 MET cc_start: 0.6567 (mtm) cc_final: 0.6291 (mtm) REVERT: Bm 389 MET cc_start: 0.4608 (mmm) cc_final: 0.4348 (mmt) outliers start: 222 outliers final: 127 residues processed: 547 average time/residue: 0.5558 time to fit residues: 521.4108 Evaluate side-chains 456 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 329 time to evaluate : 5.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 150 ILE Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 210 THR Chi-restraints excluded: chain Ad residue 220 ILE Chi-restraints excluded: chain Ad residue 236 VAL Chi-restraints excluded: chain Ad residue 245 LYS Chi-restraints excluded: chain Ad residue 254 VAL Chi-restraints excluded: chain Ad residue 261 THR Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 351 GLN Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 483 GLU Chi-restraints excluded: chain Ad residue 517 THR Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 360 TYR Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ak residue 191 GLU Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 210 THR Chi-restraints excluded: chain Ak residue 220 ILE Chi-restraints excluded: chain Ak residue 236 VAL Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 254 VAL Chi-restraints excluded: chain Ak residue 259 LEU Chi-restraints excluded: chain Ak residue 261 THR Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 351 GLN Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 366 GLN Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Al residue 442 VAL Chi-restraints excluded: chain Am residue 60 LYS Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Am residue 79 ASP Chi-restraints excluded: chain Ar residue 91 THR Chi-restraints excluded: chain Ar residue 150 ILE Chi-restraints excluded: chain Ar residue 191 GLU Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 210 THR Chi-restraints excluded: chain Ar residue 220 ILE Chi-restraints excluded: chain Ar residue 236 VAL Chi-restraints excluded: chain Ar residue 245 LYS Chi-restraints excluded: chain Ar residue 252 GLU Chi-restraints excluded: chain Ar residue 259 LEU Chi-restraints excluded: chain Ar residue 261 THR Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 351 GLN Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain As residue 104 LEU Chi-restraints excluded: chain As residue 360 TYR Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain At residue 79 ASP Chi-restraints excluded: chain At residue 80 ASN Chi-restraints excluded: chain At residue 95 VAL Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 210 THR Chi-restraints excluded: chain Ay residue 220 ILE Chi-restraints excluded: chain Ay residue 236 VAL Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 261 THR Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 351 GLN Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 517 THR Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 94 ILE Chi-restraints excluded: chain Ba residue 95 VAL Chi-restraints excluded: chain Bf residue 11 ASP Chi-restraints excluded: chain Bf residue 91 THR Chi-restraints excluded: chain Bf residue 191 GLU Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 210 THR Chi-restraints excluded: chain Bf residue 236 VAL Chi-restraints excluded: chain Bf residue 245 LYS Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 254 VAL Chi-restraints excluded: chain Bf residue 259 LEU Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 351 GLN Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bg residue 114 MET Chi-restraints excluded: chain Bg residue 284 ARG Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 79 ASP Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 210 THR Chi-restraints excluded: chain Bm residue 220 ILE Chi-restraints excluded: chain Bm residue 236 VAL Chi-restraints excluded: chain Bm residue 245 LYS Chi-restraints excluded: chain Bm residue 252 GLU Chi-restraints excluded: chain Bm residue 261 THR Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 351 GLN Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 517 THR Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 80 ASN Chi-restraints excluded: chain Bt residue 63 GLU Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 210 THR Chi-restraints excluded: chain Bt residue 220 ILE Chi-restraints excluded: chain Bt residue 236 VAL Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 252 GLU Chi-restraints excluded: chain Bt residue 254 VAL Chi-restraints excluded: chain Bt residue 259 LEU Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 351 GLN Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bt residue 517 THR Chi-restraints excluded: chain Bu residue 284 ARG Chi-restraints excluded: chain Bu residue 360 TYR Chi-restraints excluded: chain Bu residue 367 GLU Chi-restraints excluded: chain Bu residue 442 VAL Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 79 ASP Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 7.9990 chunk 541 optimal weight: 2.9990 chunk 373 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 343 optimal weight: 3.9990 chunk 483 optimal weight: 5.9990 chunk 722 optimal weight: 3.9990 chunk 764 optimal weight: 1.9990 chunk 377 optimal weight: 8.9990 chunk 684 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 72 GLN ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bo 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 72 GLN ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 59906 Z= 0.307 Angle : 0.666 11.365 80955 Z= 0.342 Chirality : 0.045 0.264 9828 Planarity : 0.004 0.057 10542 Dihedral : 9.826 117.418 8773 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.97 % Favored : 96.89 % Rotamer: Outliers : 3.59 % Allowed : 18.97 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.09), residues: 7973 helix: 1.80 (0.08), residues: 4158 sheet: 0.44 (0.16), residues: 1043 loop : -0.72 (0.11), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HISBo 7 PHE 0.014 0.002 PHEAs 281 TYR 0.010 0.001 TYRBu 199 ARG 0.021 0.001 ARGAe 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 338 time to evaluate : 5.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ad 389 MET cc_start: 0.5033 (mmt) cc_final: 0.4710 (tpt) REVERT: Ak 389 MET cc_start: 0.5844 (tpp) cc_final: 0.5462 (mmm) REVERT: Al 284 ARG cc_start: 0.2970 (OUTLIER) cc_final: 0.2121 (ptm160) REVERT: Ar 73 MET cc_start: 0.7500 (mtm) cc_final: 0.7141 (mtm) REVERT: Az 49 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8614 (mm) REVERT: Bg 73 MET cc_start: 0.6634 (mtm) cc_final: 0.6114 (mtm) REVERT: Bn 514 MET cc_start: 0.7790 (mtp) cc_final: 0.7490 (mtp) REVERT: Bu 284 ARG cc_start: 0.2878 (OUTLIER) cc_final: 0.2247 (ptm160) outliers start: 223 outliers final: 118 residues processed: 535 average time/residue: 0.5346 time to fit residues: 496.5731 Evaluate side-chains 443 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 322 time to evaluate : 5.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 91 THR Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 236 VAL Chi-restraints excluded: chain Ad residue 245 LYS Chi-restraints excluded: chain Ad residue 254 VAL Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 351 GLN Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Ad residue 517 THR Chi-restraints excluded: chain Ae residue 49 ILE Chi-restraints excluded: chain Ae residue 281 PHE Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 360 TYR Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Ak residue 91 THR Chi-restraints excluded: chain Ak residue 150 ILE Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 236 VAL Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 254 VAL Chi-restraints excluded: chain Ak residue 261 THR Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 351 GLN Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 366 GLN Chi-restraints excluded: chain Al residue 114 MET Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Al residue 442 VAL Chi-restraints excluded: chain Am residue 60 LYS Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Am residue 95 VAL Chi-restraints excluded: chain Ar residue 23 LEU Chi-restraints excluded: chain Ar residue 191 GLU Chi-restraints excluded: chain Ar residue 193 MET Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 236 VAL Chi-restraints excluded: chain Ar residue 245 LYS Chi-restraints excluded: chain Ar residue 252 GLU Chi-restraints excluded: chain Ar residue 259 LEU Chi-restraints excluded: chain Ar residue 261 THR Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 351 GLN Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain As residue 104 LEU Chi-restraints excluded: chain As residue 281 PHE Chi-restraints excluded: chain As residue 360 TYR Chi-restraints excluded: chain At residue 58 ASP Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain At residue 79 ASP Chi-restraints excluded: chain Ay residue 23 LEU Chi-restraints excluded: chain Ay residue 150 ILE Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 236 VAL Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 366 GLN Chi-restraints excluded: chain Ay residue 517 THR Chi-restraints excluded: chain Az residue 49 ILE Chi-restraints excluded: chain Az residue 281 PHE Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Ba residue 60 LYS Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 94 ILE Chi-restraints excluded: chain Bf residue 23 LEU Chi-restraints excluded: chain Bf residue 150 ILE Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 236 VAL Chi-restraints excluded: chain Bf residue 245 LYS Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 261 THR Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 351 GLN Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bg residue 155 ASP Chi-restraints excluded: chain Bg residue 281 PHE Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bg residue 509 SER Chi-restraints excluded: chain Bh residue 58 ASP Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 91 THR Chi-restraints excluded: chain Bm residue 104 LEU Chi-restraints excluded: chain Bm residue 150 ILE Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 236 VAL Chi-restraints excluded: chain Bm residue 245 LYS Chi-restraints excluded: chain Bm residue 261 THR Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 351 GLN Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 517 THR Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 155 ASP Chi-restraints excluded: chain Bn residue 281 PHE Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bo residue 58 ASP Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 79 ASP Chi-restraints excluded: chain Bo residue 95 VAL Chi-restraints excluded: chain Bt residue 150 ILE Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 236 VAL Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 252 GLU Chi-restraints excluded: chain Bt residue 254 VAL Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 351 GLN Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bu residue 284 ARG Chi-restraints excluded: chain Bu residue 360 TYR Chi-restraints excluded: chain Bu residue 367 GLU Chi-restraints excluded: chain Bu residue 442 VAL Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 79 ASP Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 636 optimal weight: 10.0000 chunk 434 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 569 optimal weight: 0.9980 chunk 315 optimal weight: 10.0000 chunk 652 optimal weight: 8.9990 chunk 528 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 390 optimal weight: 0.9980 chunk 686 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bo 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 59906 Z= 0.395 Angle : 0.686 19.515 80955 Z= 0.351 Chirality : 0.046 0.231 9828 Planarity : 0.004 0.077 10542 Dihedral : 9.486 131.465 8747 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 3.27 % Allowed : 19.35 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.09), residues: 7973 helix: 1.62 (0.08), residues: 4165 sheet: 0.47 (0.16), residues: 973 loop : -0.86 (0.11), residues: 2835 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISAe 401 PHE 0.014 0.002 PHEBm 44 TYR 0.012 0.001 TYRBu 199 ARG 0.016 0.001 ARGAk 368 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 324 time to evaluate : 5.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ae 491 MET cc_start: 0.8102 (mtp) cc_final: 0.7804 (mtm) REVERT: Ak 514 MET cc_start: 0.8331 (tpp) cc_final: 0.8007 (mmm) REVERT: Al 284 ARG cc_start: 0.2921 (OUTLIER) cc_final: 0.2083 (ptm160) REVERT: Az 49 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8656 (mm) REVERT: Bg 73 MET cc_start: 0.6480 (mtm) cc_final: 0.6230 (mtm) outliers start: 203 outliers final: 142 residues processed: 504 average time/residue: 0.5345 time to fit residues: 469.9866 Evaluate side-chains 463 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 319 time to evaluate : 6.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 91 THR Chi-restraints excluded: chain Ad residue 150 ILE Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 236 VAL Chi-restraints excluded: chain Ad residue 254 VAL Chi-restraints excluded: chain Ad residue 261 THR Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 351 GLN Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 483 GLU Chi-restraints excluded: chain Ad residue 517 THR Chi-restraints excluded: chain Ae residue 49 ILE Chi-restraints excluded: chain Ae residue 210 THR Chi-restraints excluded: chain Ae residue 281 PHE Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 360 TYR Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ak residue 54 VAL Chi-restraints excluded: chain Ak residue 91 THR Chi-restraints excluded: chain Ak residue 150 ILE Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 236 VAL Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 261 THR Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 310 GLU Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 420 ILE Chi-restraints excluded: chain Al residue 114 MET Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Al residue 387 VAL Chi-restraints excluded: chain Al residue 442 VAL Chi-restraints excluded: chain Am residue 25 ILE Chi-restraints excluded: chain Am residue 60 LYS Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Am residue 79 ASP Chi-restraints excluded: chain Am residue 95 VAL Chi-restraints excluded: chain Ar residue 23 LEU Chi-restraints excluded: chain Ar residue 91 THR Chi-restraints excluded: chain Ar residue 150 ILE Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 245 LYS Chi-restraints excluded: chain Ar residue 252 GLU Chi-restraints excluded: chain Ar residue 259 LEU Chi-restraints excluded: chain Ar residue 261 THR Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 351 GLN Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain Ar residue 420 ILE Chi-restraints excluded: chain As residue 104 LEU Chi-restraints excluded: chain As residue 281 PHE Chi-restraints excluded: chain As residue 360 TYR Chi-restraints excluded: chain As residue 420 ILE Chi-restraints excluded: chain As residue 509 SER Chi-restraints excluded: chain At residue 58 ASP Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain At residue 95 VAL Chi-restraints excluded: chain Ay residue 23 LEU Chi-restraints excluded: chain Ay residue 91 THR Chi-restraints excluded: chain Ay residue 150 ILE Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 236 VAL Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 366 GLN Chi-restraints excluded: chain Ay residue 420 ILE Chi-restraints excluded: chain Ay residue 483 GLU Chi-restraints excluded: chain Ay residue 517 THR Chi-restraints excluded: chain Az residue 49 ILE Chi-restraints excluded: chain Az residue 281 PHE Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Ba residue 60 LYS Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 94 ILE Chi-restraints excluded: chain Bf residue 11 ASP Chi-restraints excluded: chain Bf residue 23 LEU Chi-restraints excluded: chain Bf residue 91 THR Chi-restraints excluded: chain Bf residue 150 ILE Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 236 VAL Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 261 THR Chi-restraints excluded: chain Bf residue 300 VAL Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 351 GLN Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 420 ILE Chi-restraints excluded: chain Bg residue 155 ASP Chi-restraints excluded: chain Bg residue 213 VAL Chi-restraints excluded: chain Bg residue 281 PHE Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bg residue 442 VAL Chi-restraints excluded: chain Bg residue 509 SER Chi-restraints excluded: chain Bg residue 521 VAL Chi-restraints excluded: chain Bh residue 25 ILE Chi-restraints excluded: chain Bh residue 58 ASP Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 79 ASP Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 14 VAL Chi-restraints excluded: chain Bm residue 23 LEU Chi-restraints excluded: chain Bm residue 91 THR Chi-restraints excluded: chain Bm residue 104 LEU Chi-restraints excluded: chain Bm residue 150 ILE Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 236 VAL Chi-restraints excluded: chain Bm residue 261 THR Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 351 GLN Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 420 ILE Chi-restraints excluded: chain Bm residue 517 THR Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 281 PHE Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bo residue 58 ASP Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 95 VAL Chi-restraints excluded: chain Bt residue 23 LEU Chi-restraints excluded: chain Bt residue 54 VAL Chi-restraints excluded: chain Bt residue 63 GLU Chi-restraints excluded: chain Bt residue 150 ILE Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 236 VAL Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 351 GLN Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bt residue 420 ILE Chi-restraints excluded: chain Bt residue 517 THR Chi-restraints excluded: chain Bu residue 284 ARG Chi-restraints excluded: chain Bu residue 360 TYR Chi-restraints excluded: chain Bu residue 442 VAL Chi-restraints excluded: chain Bv residue 66 ILE Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 79 ASP Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 0.5980 chunk 688 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 448 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 765 optimal weight: 7.9990 chunk 635 optimal weight: 1.9990 chunk 354 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 253 optimal weight: 50.0000 chunk 401 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 453 GLN ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 453 GLN ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 59906 Z= 0.270 Angle : 0.641 18.156 80955 Z= 0.326 Chirality : 0.044 0.266 9828 Planarity : 0.004 0.068 10542 Dihedral : 9.167 136.362 8728 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.16 % Favored : 96.74 % Rotamer: Outliers : 2.82 % Allowed : 19.77 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.09), residues: 7973 helix: 1.74 (0.08), residues: 4207 sheet: 0.28 (0.16), residues: 1043 loop : -0.81 (0.11), residues: 2723 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISAk 401 PHE 0.016 0.002 PHEBf 219 TYR 0.010 0.001 TYRAl 199 ARG 0.007 0.000 ARGBf 368 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 324 time to evaluate : 5.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ae 491 MET cc_start: 0.7871 (mtp) cc_final: 0.7527 (mtm) REVERT: Ak 514 MET cc_start: 0.8322 (tpp) cc_final: 0.7988 (mmm) REVERT: Al 284 ARG cc_start: 0.2878 (OUTLIER) cc_final: 0.2010 (ptm160) REVERT: As 524 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8236 (mt) REVERT: Bg 73 MET cc_start: 0.6382 (mtm) cc_final: 0.6134 (mtm) REVERT: Bh 1 MET cc_start: 0.2639 (tpp) cc_final: 0.2318 (tpt) REVERT: Bt 514 MET cc_start: 0.8159 (mmt) cc_final: 0.7880 (mtt) outliers start: 175 outliers final: 135 residues processed: 476 average time/residue: 0.5468 time to fit residues: 455.7187 Evaluate side-chains 455 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 318 time to evaluate : 5.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 150 ILE Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 254 VAL Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 319 GLN Chi-restraints excluded: chain Ad residue 351 GLN Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Ad residue 483 GLU Chi-restraints excluded: chain Ae residue 49 ILE Chi-restraints excluded: chain Ae residue 281 PHE Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 360 TYR Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ak residue 54 VAL Chi-restraints excluded: chain Ak residue 150 ILE Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 261 THR Chi-restraints excluded: chain Ak residue 271 VAL Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 420 ILE Chi-restraints excluded: chain Al residue 14 VAL Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Al residue 387 VAL Chi-restraints excluded: chain Am residue 25 ILE Chi-restraints excluded: chain Am residue 60 LYS Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Am residue 95 VAL Chi-restraints excluded: chain Ar residue 150 ILE Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 259 LEU Chi-restraints excluded: chain Ar residue 261 THR Chi-restraints excluded: chain Ar residue 271 VAL Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 351 GLN Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain Ar residue 420 ILE Chi-restraints excluded: chain As residue 104 LEU Chi-restraints excluded: chain As residue 281 PHE Chi-restraints excluded: chain As residue 360 TYR Chi-restraints excluded: chain As residue 420 ILE Chi-restraints excluded: chain As residue 509 SER Chi-restraints excluded: chain As residue 524 LEU Chi-restraints excluded: chain At residue 25 ILE Chi-restraints excluded: chain At residue 58 ASP Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain At residue 79 ASP Chi-restraints excluded: chain At residue 95 VAL Chi-restraints excluded: chain Ay residue 23 LEU Chi-restraints excluded: chain Ay residue 150 ILE Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 236 VAL Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 271 VAL Chi-restraints excluded: chain Ay residue 300 VAL Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 420 ILE Chi-restraints excluded: chain Ay residue 483 GLU Chi-restraints excluded: chain Ay residue 517 THR Chi-restraints excluded: chain Az residue 213 VAL Chi-restraints excluded: chain Az residue 281 PHE Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Az residue 387 VAL Chi-restraints excluded: chain Ba residue 60 LYS Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 94 ILE Chi-restraints excluded: chain Ba residue 95 VAL Chi-restraints excluded: chain Bf residue 14 VAL Chi-restraints excluded: chain Bf residue 150 ILE Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 236 VAL Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 261 THR Chi-restraints excluded: chain Bf residue 271 VAL Chi-restraints excluded: chain Bf residue 300 VAL Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 420 ILE Chi-restraints excluded: chain Bg residue 14 VAL Chi-restraints excluded: chain Bg residue 155 ASP Chi-restraints excluded: chain Bg residue 213 VAL Chi-restraints excluded: chain Bg residue 281 PHE Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bg residue 387 VAL Chi-restraints excluded: chain Bg residue 509 SER Chi-restraints excluded: chain Bh residue 25 ILE Chi-restraints excluded: chain Bh residue 58 ASP Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 14 VAL Chi-restraints excluded: chain Bm residue 23 LEU Chi-restraints excluded: chain Bm residue 91 THR Chi-restraints excluded: chain Bm residue 104 LEU Chi-restraints excluded: chain Bm residue 150 ILE Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 261 THR Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 319 GLN Chi-restraints excluded: chain Bm residue 351 GLN Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 420 ILE Chi-restraints excluded: chain Bm residue 517 THR Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 281 PHE Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bo residue 25 ILE Chi-restraints excluded: chain Bo residue 58 ASP Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 95 VAL Chi-restraints excluded: chain Bt residue 150 ILE Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 236 VAL Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 261 THR Chi-restraints excluded: chain Bt residue 271 VAL Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 351 GLN Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bt residue 420 ILE Chi-restraints excluded: chain Bt residue 517 THR Chi-restraints excluded: chain Bu residue 284 ARG Chi-restraints excluded: chain Bu residue 360 TYR Chi-restraints excluded: chain Bu residue 387 VAL Chi-restraints excluded: chain Bu residue 442 VAL Chi-restraints excluded: chain Bv residue 58 ASP Chi-restraints excluded: chain Bv residue 66 ILE Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 737 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 436 optimal weight: 0.7980 chunk 558 optimal weight: 0.9980 chunk 433 optimal weight: 3.9990 chunk 644 optimal weight: 7.9990 chunk 427 optimal weight: 2.9990 chunk 762 optimal weight: 4.9990 chunk 477 optimal weight: 20.0000 chunk 464 optimal weight: 2.9990 chunk 351 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bt 453 GLN ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 59906 Z= 0.219 Angle : 0.622 17.062 80955 Z= 0.316 Chirality : 0.043 0.269 9828 Planarity : 0.003 0.052 10542 Dihedral : 8.921 138.116 8718 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 2.35 % Allowed : 20.03 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 7973 helix: 1.87 (0.08), residues: 4207 sheet: 0.24 (0.15), residues: 1106 loop : -0.73 (0.11), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISAk 401 PHE 0.011 0.001 PHEAs 281 TYR 0.009 0.001 TYRBg 199 ARG 0.006 0.000 ARGAr 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 323 time to evaluate : 5.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ae 491 MET cc_start: 0.7784 (mtp) cc_final: 0.7393 (mtm) REVERT: Al 284 ARG cc_start: 0.2910 (OUTLIER) cc_final: 0.2057 (ptm160) REVERT: As 524 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8215 (mt) REVERT: Bm 514 MET cc_start: 0.8264 (mmt) cc_final: 0.8022 (mmm) outliers start: 146 outliers final: 122 residues processed: 446 average time/residue: 0.5295 time to fit residues: 412.2355 Evaluate side-chains 441 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 317 time to evaluate : 5.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 150 ILE Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 254 VAL Chi-restraints excluded: chain Ad residue 271 VAL Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 351 GLN Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Ad residue 483 GLU Chi-restraints excluded: chain Ae residue 49 ILE Chi-restraints excluded: chain Ae residue 210 THR Chi-restraints excluded: chain Ae residue 281 PHE Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 360 TYR Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ak residue 150 ILE Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 261 THR Chi-restraints excluded: chain Ak residue 271 VAL Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 420 ILE Chi-restraints excluded: chain Ak residue 517 THR Chi-restraints excluded: chain Al residue 213 VAL Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Al residue 387 VAL Chi-restraints excluded: chain Al residue 442 VAL Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Am residue 95 VAL Chi-restraints excluded: chain Ar residue 150 ILE Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 259 LEU Chi-restraints excluded: chain Ar residue 271 VAL Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain Ar residue 420 ILE Chi-restraints excluded: chain As residue 104 LEU Chi-restraints excluded: chain As residue 213 VAL Chi-restraints excluded: chain As residue 281 PHE Chi-restraints excluded: chain As residue 360 TYR Chi-restraints excluded: chain As residue 420 ILE Chi-restraints excluded: chain As residue 509 SER Chi-restraints excluded: chain As residue 524 LEU Chi-restraints excluded: chain At residue 25 ILE Chi-restraints excluded: chain At residue 30 SER Chi-restraints excluded: chain At residue 58 ASP Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain Ay residue 150 ILE Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 271 VAL Chi-restraints excluded: chain Ay residue 300 VAL Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 420 ILE Chi-restraints excluded: chain Ay residue 514 MET Chi-restraints excluded: chain Ay residue 517 THR Chi-restraints excluded: chain Az residue 213 VAL Chi-restraints excluded: chain Az residue 281 PHE Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Ba residue 60 LYS Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 94 ILE Chi-restraints excluded: chain Ba residue 95 VAL Chi-restraints excluded: chain Bf residue 150 ILE Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 261 THR Chi-restraints excluded: chain Bf residue 271 VAL Chi-restraints excluded: chain Bf residue 300 VAL Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 420 ILE Chi-restraints excluded: chain Bg residue 155 ASP Chi-restraints excluded: chain Bg residue 213 VAL Chi-restraints excluded: chain Bg residue 281 PHE Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bg residue 387 VAL Chi-restraints excluded: chain Bg residue 442 VAL Chi-restraints excluded: chain Bg residue 509 SER Chi-restraints excluded: chain Bh residue 25 ILE Chi-restraints excluded: chain Bh residue 58 ASP Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 14 VAL Chi-restraints excluded: chain Bm residue 91 THR Chi-restraints excluded: chain Bm residue 150 ILE Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 261 THR Chi-restraints excluded: chain Bm residue 271 VAL Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 319 GLN Chi-restraints excluded: chain Bm residue 351 GLN Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 420 ILE Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bn residue 387 VAL Chi-restraints excluded: chain Bo residue 58 ASP Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 95 VAL Chi-restraints excluded: chain Bt residue 150 ILE Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 261 THR Chi-restraints excluded: chain Bt residue 271 VAL Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bt residue 420 ILE Chi-restraints excluded: chain Bu residue 284 ARG Chi-restraints excluded: chain Bu residue 360 TYR Chi-restraints excluded: chain Bu residue 387 VAL Chi-restraints excluded: chain Bu residue 442 VAL Chi-restraints excluded: chain Bv residue 25 ILE Chi-restraints excluded: chain Bv residue 58 ASP Chi-restraints excluded: chain Bv residue 66 ILE Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 30.0000 chunk 304 optimal weight: 3.9990 chunk 455 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 484 optimal weight: 7.9990 chunk 519 optimal weight: 0.9980 chunk 376 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 599 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 453 GLN ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 82 ASN ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 475 ASN ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bt 453 GLN ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 59906 Z= 0.469 Angle : 0.713 16.565 80955 Z= 0.362 Chirality : 0.046 0.240 9828 Planarity : 0.004 0.058 10542 Dihedral : 8.921 143.918 8701 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.46 % Rotamer: Outliers : 2.65 % Allowed : 20.16 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.09), residues: 7973 helix: 1.47 (0.08), residues: 4186 sheet: 0.31 (0.16), residues: 931 loop : -0.89 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISAe 401 PHE 0.012 0.002 PHEBu 8 TYR 0.014 0.002 TYRBg 199 ARG 0.013 0.001 ARGAk 368 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 318 time to evaluate : 5.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ae 491 MET cc_start: 0.8357 (mtp) cc_final: 0.7850 (mtm) REVERT: Al 284 ARG cc_start: 0.2945 (OUTLIER) cc_final: 0.2070 (ptm160) REVERT: At 25 ILE cc_start: 0.4687 (OUTLIER) cc_final: 0.4467 (tt) REVERT: Bh 1 MET cc_start: 0.2979 (tpp) cc_final: 0.1922 (tpt) outliers start: 165 outliers final: 142 residues processed: 455 average time/residue: 0.5270 time to fit residues: 421.1585 Evaluate side-chains 459 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 315 time to evaluate : 5.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 150 ILE Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 254 VAL Chi-restraints excluded: chain Ad residue 271 VAL Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Ad residue 483 GLU Chi-restraints excluded: chain Ad residue 517 THR Chi-restraints excluded: chain Ae residue 49 ILE Chi-restraints excluded: chain Ae residue 210 THR Chi-restraints excluded: chain Ae residue 281 PHE Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 360 TYR Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ak residue 54 VAL Chi-restraints excluded: chain Ak residue 150 ILE Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 261 THR Chi-restraints excluded: chain Ak residue 271 VAL Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 420 ILE Chi-restraints excluded: chain Al residue 14 VAL Chi-restraints excluded: chain Al residue 114 MET Chi-restraints excluded: chain Al residue 213 VAL Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Al residue 442 VAL Chi-restraints excluded: chain Am residue 60 LYS Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Ar residue 91 THR Chi-restraints excluded: chain Ar residue 150 ILE Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 259 LEU Chi-restraints excluded: chain Ar residue 271 VAL Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 351 GLN Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain Ar residue 420 ILE Chi-restraints excluded: chain As residue 14 VAL Chi-restraints excluded: chain As residue 104 LEU Chi-restraints excluded: chain As residue 210 THR Chi-restraints excluded: chain As residue 213 VAL Chi-restraints excluded: chain As residue 281 PHE Chi-restraints excluded: chain As residue 301 ILE Chi-restraints excluded: chain As residue 360 TYR Chi-restraints excluded: chain As residue 420 ILE Chi-restraints excluded: chain As residue 509 SER Chi-restraints excluded: chain At residue 25 ILE Chi-restraints excluded: chain At residue 30 SER Chi-restraints excluded: chain At residue 58 ASP Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain Ay residue 14 VAL Chi-restraints excluded: chain Ay residue 23 LEU Chi-restraints excluded: chain Ay residue 91 THR Chi-restraints excluded: chain Ay residue 150 ILE Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 271 VAL Chi-restraints excluded: chain Ay residue 300 VAL Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 420 ILE Chi-restraints excluded: chain Ay residue 514 MET Chi-restraints excluded: chain Ay residue 517 THR Chi-restraints excluded: chain Az residue 213 VAL Chi-restraints excluded: chain Az residue 281 PHE Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Ba residue 60 LYS Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 94 ILE Chi-restraints excluded: chain Bf residue 23 LEU Chi-restraints excluded: chain Bf residue 54 VAL Chi-restraints excluded: chain Bf residue 91 THR Chi-restraints excluded: chain Bf residue 150 ILE Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 261 THR Chi-restraints excluded: chain Bf residue 271 VAL Chi-restraints excluded: chain Bf residue 300 VAL Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 420 ILE Chi-restraints excluded: chain Bg residue 14 VAL Chi-restraints excluded: chain Bg residue 114 MET Chi-restraints excluded: chain Bg residue 213 VAL Chi-restraints excluded: chain Bg residue 281 PHE Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bg residue 387 VAL Chi-restraints excluded: chain Bg residue 442 VAL Chi-restraints excluded: chain Bg residue 509 SER Chi-restraints excluded: chain Bg residue 521 VAL Chi-restraints excluded: chain Bh residue 25 ILE Chi-restraints excluded: chain Bh residue 58 ASP Chi-restraints excluded: chain Bh residue 64 ILE Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 14 VAL Chi-restraints excluded: chain Bm residue 23 LEU Chi-restraints excluded: chain Bm residue 91 THR Chi-restraints excluded: chain Bm residue 104 LEU Chi-restraints excluded: chain Bm residue 150 ILE Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 261 THR Chi-restraints excluded: chain Bm residue 271 VAL Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 319 GLN Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 420 ILE Chi-restraints excluded: chain Bm residue 517 THR Chi-restraints excluded: chain Bn residue 14 VAL Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 176 THR Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 281 PHE Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bo residue 58 ASP Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 95 VAL Chi-restraints excluded: chain Bt residue 23 LEU Chi-restraints excluded: chain Bt residue 54 VAL Chi-restraints excluded: chain Bt residue 150 ILE Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 261 THR Chi-restraints excluded: chain Bt residue 271 VAL Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bt residue 420 ILE Chi-restraints excluded: chain Bu residue 44 PHE Chi-restraints excluded: chain Bu residue 284 ARG Chi-restraints excluded: chain Bu residue 360 TYR Chi-restraints excluded: chain Bu residue 387 VAL Chi-restraints excluded: chain Bu residue 442 VAL Chi-restraints excluded: chain Bv residue 25 ILE Chi-restraints excluded: chain Bv residue 66 ILE Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 79 ASP Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 6.9990 chunk 730 optimal weight: 0.8980 chunk 666 optimal weight: 0.7980 chunk 710 optimal weight: 0.9990 chunk 427 optimal weight: 4.9990 chunk 309 optimal weight: 7.9990 chunk 557 optimal weight: 20.0000 chunk 218 optimal weight: 0.8980 chunk 641 optimal weight: 0.9990 chunk 671 optimal weight: 8.9990 chunk 707 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 68 ASN ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 453 GLN ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 68 ASN ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 68 ASN ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 453 GLN Bn 82 ASN Bo 68 ASN ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bt 453 GLN Bu 82 ASN Bv 68 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 59906 Z= 0.185 Angle : 0.623 17.118 80955 Z= 0.314 Chirality : 0.043 0.232 9828 Planarity : 0.003 0.050 10542 Dihedral : 8.564 140.769 8695 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.54 % Rotamer: Outliers : 1.83 % Allowed : 21.16 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.09), residues: 7973 helix: 1.87 (0.08), residues: 4214 sheet: 0.37 (0.15), residues: 1036 loop : -0.76 (0.11), residues: 2723 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HISAz 401 PHE 0.013 0.001 PHEAz 195 TYR 0.009 0.001 TYRBu 476 ARG 0.007 0.000 ARGAk 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 327 time to evaluate : 5.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Al 284 ARG cc_start: 0.2873 (OUTLIER) cc_final: 0.2044 (ptm160) REVERT: Az 518 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6664 (pt0) REVERT: Ba 86 MET cc_start: 0.6246 (pmm) cc_final: 0.5951 (ptt) REVERT: Bm 514 MET cc_start: 0.8177 (mmt) cc_final: 0.7939 (mmm) outliers start: 114 outliers final: 97 residues processed: 425 average time/residue: 0.5396 time to fit residues: 397.5211 Evaluate side-chains 418 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 319 time to evaluate : 5.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 150 ILE Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 271 VAL Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Ae residue 210 THR Chi-restraints excluded: chain Ae residue 281 PHE Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ak residue 150 ILE Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 261 THR Chi-restraints excluded: chain Ak residue 271 VAL Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 420 ILE Chi-restraints excluded: chain Al residue 213 VAL Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Am residue 68 ASN Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Ar residue 91 THR Chi-restraints excluded: chain Ar residue 150 ILE Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 261 THR Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain Ar residue 420 ILE Chi-restraints excluded: chain As residue 14 VAL Chi-restraints excluded: chain As residue 104 LEU Chi-restraints excluded: chain As residue 210 THR Chi-restraints excluded: chain As residue 213 VAL Chi-restraints excluded: chain As residue 281 PHE Chi-restraints excluded: chain As residue 420 ILE Chi-restraints excluded: chain At residue 30 SER Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain Ay residue 150 ILE Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 300 VAL Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 420 ILE Chi-restraints excluded: chain Ay residue 514 MET Chi-restraints excluded: chain Ay residue 517 THR Chi-restraints excluded: chain Az residue 44 PHE Chi-restraints excluded: chain Az residue 213 VAL Chi-restraints excluded: chain Az residue 281 PHE Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 518 GLU Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 94 ILE Chi-restraints excluded: chain Bf residue 150 ILE Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 261 THR Chi-restraints excluded: chain Bf residue 271 VAL Chi-restraints excluded: chain Bf residue 300 VAL Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 420 ILE Chi-restraints excluded: chain Bg residue 213 VAL Chi-restraints excluded: chain Bg residue 281 PHE Chi-restraints excluded: chain Bg residue 387 VAL Chi-restraints excluded: chain Bg residue 442 VAL Chi-restraints excluded: chain Bh residue 25 ILE Chi-restraints excluded: chain Bh residue 58 ASP Chi-restraints excluded: chain Bh residue 68 ASN Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 150 ILE Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 261 THR Chi-restraints excluded: chain Bm residue 271 VAL Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 319 GLN Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 420 ILE Chi-restraints excluded: chain Bn residue 14 VAL Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bo residue 58 ASP Chi-restraints excluded: chain Bo residue 68 ASN Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 95 VAL Chi-restraints excluded: chain Bt residue 150 ILE Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 271 VAL Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bt residue 420 ILE Chi-restraints excluded: chain Bu residue 284 ARG Chi-restraints excluded: chain Bu residue 387 VAL Chi-restraints excluded: chain Bv residue 66 ILE Chi-restraints excluded: chain Bv residue 68 ASN Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 466 optimal weight: 0.9980 chunk 751 optimal weight: 10.0000 chunk 458 optimal weight: 5.9990 chunk 356 optimal weight: 0.9990 chunk 522 optimal weight: 9.9990 chunk 788 optimal weight: 0.0370 chunk 725 optimal weight: 6.9990 chunk 627 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 484 optimal weight: 7.9990 chunk 384 optimal weight: 0.6980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 68 ASN ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 82 ASN ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 68 ASN ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bo 68 ASN ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 59906 Z= 0.177 Angle : 0.630 18.217 80955 Z= 0.315 Chirality : 0.043 0.292 9828 Planarity : 0.003 0.059 10542 Dihedral : 8.425 140.069 8689 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.26 % Favored : 96.65 % Rotamer: Outliers : 1.58 % Allowed : 21.44 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.09), residues: 7973 helix: 1.96 (0.08), residues: 4200 sheet: 0.39 (0.15), residues: 1036 loop : -0.72 (0.11), residues: 2737 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISAk 401 PHE 0.020 0.001 PHEBv 67 TYR 0.008 0.001 TYRAy 360 ARG 0.008 0.000 ARGBt 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 321 time to evaluate : 5.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ae 491 MET cc_start: 0.7690 (mtp) cc_final: 0.7150 (mtm) REVERT: Al 284 ARG cc_start: 0.2782 (OUTLIER) cc_final: 0.1911 (ptm160) REVERT: Az 518 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6644 (pt0) REVERT: Ba 86 MET cc_start: 0.6234 (pmm) cc_final: 0.5941 (ptt) REVERT: Bh 1 MET cc_start: 0.3030 (tpp) cc_final: 0.1913 (tpt) REVERT: Bm 447 MET cc_start: 0.7559 (mtt) cc_final: 0.7119 (mtt) REVERT: Bm 514 MET cc_start: 0.8171 (mmt) cc_final: 0.7960 (mmm) outliers start: 98 outliers final: 90 residues processed: 406 average time/residue: 0.5466 time to fit residues: 387.4358 Evaluate side-chains 411 residues out of total 6216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 319 time to evaluate : 5.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 49 ILE Chi-restraints excluded: chain Ad residue 150 ILE Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 271 VAL Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Ad residue 483 GLU Chi-restraints excluded: chain Ae residue 210 THR Chi-restraints excluded: chain Ae residue 281 PHE Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 442 VAL Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ak residue 150 ILE Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 261 THR Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 420 ILE Chi-restraints excluded: chain Al residue 213 VAL Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Ar residue 150 ILE Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 252 GLU Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain Ar residue 420 ILE Chi-restraints excluded: chain As residue 14 VAL Chi-restraints excluded: chain As residue 104 LEU Chi-restraints excluded: chain As residue 213 VAL Chi-restraints excluded: chain As residue 281 PHE Chi-restraints excluded: chain As residue 420 ILE Chi-restraints excluded: chain At residue 30 SER Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain Ay residue 150 ILE Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 300 VAL Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 420 ILE Chi-restraints excluded: chain Ay residue 514 MET Chi-restraints excluded: chain Ay residue 517 THR Chi-restraints excluded: chain Az residue 213 VAL Chi-restraints excluded: chain Az residue 281 PHE Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 518 GLU Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 94 ILE Chi-restraints excluded: chain Bf residue 150 ILE Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 261 THR Chi-restraints excluded: chain Bf residue 271 VAL Chi-restraints excluded: chain Bf residue 300 VAL Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 420 ILE Chi-restraints excluded: chain Bg residue 213 VAL Chi-restraints excluded: chain Bg residue 281 PHE Chi-restraints excluded: chain Bg residue 387 VAL Chi-restraints excluded: chain Bg residue 442 VAL Chi-restraints excluded: chain Bh residue 25 ILE Chi-restraints excluded: chain Bh residue 58 ASP Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 150 ILE Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 261 THR Chi-restraints excluded: chain Bm residue 271 VAL Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 420 ILE Chi-restraints excluded: chain Bn residue 14 VAL Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 176 THR Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bo residue 58 ASP Chi-restraints excluded: chain Bo residue 68 ASN Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 95 VAL Chi-restraints excluded: chain Bt residue 150 ILE Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 271 VAL Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bt residue 420 ILE Chi-restraints excluded: chain Bu residue 284 ARG Chi-restraints excluded: chain Bu residue 387 VAL Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 0.7980 chunk 668 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 chunk 578 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 628 optimal weight: 7.9990 chunk 263 optimal weight: 5.9990 chunk 645 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 68 ASN ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 2 ASN Ba 68 ASN ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bf 453 GLN ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.069067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.049591 restraints weight = 264620.603| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.92 r_work: 0.2966 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 59906 Z= 0.183 Angle : 0.622 18.999 80955 Z= 0.310 Chirality : 0.042 0.340 9828 Planarity : 0.003 0.049 10542 Dihedral : 8.206 139.919 8689 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 1.54 % Allowed : 21.46 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.09), residues: 7973 helix: 1.98 (0.08), residues: 4228 sheet: 0.41 (0.15), residues: 1036 loop : -0.73 (0.11), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISAk 401 PHE 0.014 0.001 PHEBo 67 TYR 0.010 0.001 TYRAr 360 ARG 0.007 0.000 ARGBt 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10297.59 seconds wall clock time: 183 minutes 15.70 seconds (10995.70 seconds total)