Starting phenix.real_space_refine on Thu Sep 26 05:06:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/09_2024/7pbx_13308.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/09_2024/7pbx_13308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/09_2024/7pbx_13308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/09_2024/7pbx_13308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/09_2024/7pbx_13308.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/09_2024/7pbx_13308.cif" } resolution = 3.43 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= 0.187 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 11991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 238 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 59472 Number of models: 1 Model: "" Number of chains: 5 Chain: "Ac" 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: "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: "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: {'CIS': 1, 'PTRANS': 2, 'TRANS': 93} Chain: "Ac" 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: 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} Restraints were copied for chains: Ai, Ao, Au, Ba, Bg, Bm, Aj, Ap, Av, Bb, Bh, Bn, Al, Ar, Ax, Bd, Bj, Bp Time building chain proxies: 16.76, per 1000 atoms: 0.28 Number of scatterers: 59472 At special positions: 0 Unit cell: (157.194, 158.301, 214.758, 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 11991 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: 10.80 Conformation dependent library (CDL) restraints added in 6.0 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 56.1% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.59 Creating SS restraints... Processing helix chain 'Ac' and resid 9 through 30 removed outlier: 4.212A pdb=" N THRAc 30 " --> pdb=" O ALAAc 26 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 52 through 60 removed outlier: 3.671A pdb=" N VALAc 56 " --> pdb=" O ASPAc 52 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 64 through 85 Processing helix chain 'Ac' and resid 88 through 108 Processing helix chain 'Ac' and resid 112 through 135 Processing helix chain 'Ac' and resid 140 through 152 removed outlier: 3.759A pdb=" N GLNAc 146 " --> pdb=" O LYSAc 142 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 155 through 169 removed outlier: 3.644A pdb=" N LEUAc 161 " --> pdb=" O THRAc 157 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 229 through 244 Proline residue: Ac 235 - end of helix removed outlier: 3.703A pdb=" N ALAAc 243 " --> pdb=" O ALAAc 239 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 255 through 268 removed outlier: 4.449A pdb=" N LEUAc 259 " --> pdb=" O GLUAc 255 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THRAc 261 " --> pdb=" O GLUAc 257 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VALAc 264 " --> pdb=" O ALAAc 260 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASNAc 265 " --> pdb=" O THRAc 261 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARGAc 268 " --> pdb=" O VALAc 264 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 281 through 297 Processing helix chain 'Ac' and resid 338 through 343 Processing helix chain 'Ac' and resid 343 through 353 removed outlier: 4.489A pdb=" N ALAAc 347 " --> pdb=" O GLNAc 343 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLNAc 348 " --> pdb=" O GLYAc 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEAc 353 " --> pdb=" O ILEAc 349 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 358 through 375 removed outlier: 3.758A pdb=" N ALAAc 370 " --> pdb=" O GLNAc 366 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 385 through 410 removed outlier: 3.681A pdb=" N ALAAc 394 " --> pdb=" O LYSAc 390 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARGAc 395 " --> pdb=" O GLUAc 391 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 416 through 426 Processing helix chain 'Ac' and resid 427 through 429 No H-bonds generated for 'chain 'Ac' and resid 427 through 429' Processing helix chain 'Ac' and resid 433 through 459 removed outlier: 3.688A pdb=" N GLUAc 448 " --> pdb=" O LEUAc 444 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALAAc 449 " --> pdb=" O ARGAc 445 " (cutoff:3.500A) Proline residue: Ac 450 - end of helix Processing helix chain 'Ac' and resid 461 through 472 removed outlier: 4.033A pdb=" N VALAc 465 " --> pdb=" O GLUAc 461 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 488 through 492 Processing helix chain 'Ac' and resid 497 through 516 Processing helix chain 'Ad' and resid 9 through 31 removed outlier: 4.138A pdb=" N THRAd 30 " --> pdb=" O ALAAd 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEUAd 31 " --> pdb=" O VALAd 27 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 52 through 60 Processing helix chain 'Ad' and resid 64 through 85 removed outlier: 3.620A pdb=" N GLYAd 70 " --> pdb=" O PHEAd 66 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLUAd 76 " --> pdb=" O GLNAd 72 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VALAd 77 " --> pdb=" O METAd 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALAAd 78 " --> pdb=" O VALAd 74 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 88 through 109 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 170 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 255 through 267 removed outlier: 4.072A pdb=" N THRAd 261 " --> pdb=" O GLUAd 257 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 281 through 297 removed outlier: 3.509A pdb=" N ASPAd 291 " --> pdb=" O ALAAd 287 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 308 through 312 Processing helix chain 'Ad' and resid 338 through 356 Processing helix chain 'Ad' and resid 358 through 373 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 448 removed outlier: 3.728A pdb=" N GLUAd 448 " --> pdb=" O LEUAd 444 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 448 through 459 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 removed outlier: 3.806A pdb=" N THRAd 516 " --> pdb=" O GLYAd 512 " (cutoff:3.500A) Processing helix chain 'Af' and resid 23 through 25 No H-bonds generated for 'chain 'Af' and resid 23 through 25' Processing helix chain 'Af' and resid 48 through 52 removed outlier: 3.663A pdb=" N ASNAf 51 " --> pdb=" O ILEAf 48 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLYAf 52 " --> pdb=" O LEUAf 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Af' and resid 48 through 52' Processing helix chain 'Ai' and resid 9 through 30 removed outlier: 4.212A pdb=" N THRAi 30 " --> pdb=" O ALAAi 26 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 52 through 60 removed outlier: 3.672A pdb=" N VALAi 56 " --> pdb=" O ASPAi 52 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 64 through 85 Processing helix chain 'Ai' and resid 88 through 108 Processing helix chain 'Ai' and resid 112 through 135 Processing helix chain 'Ai' and resid 140 through 152 removed outlier: 3.760A pdb=" N GLNAi 146 " --> pdb=" O LYSAi 142 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 155 through 169 removed outlier: 3.643A pdb=" N LEUAi 161 " --> pdb=" O THRAi 157 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 229 through 244 Proline residue: Ai 235 - end of helix removed outlier: 3.703A pdb=" N ALAAi 243 " --> pdb=" O ALAAi 239 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 255 through 268 removed outlier: 4.450A pdb=" N LEUAi 259 " --> pdb=" O GLUAi 255 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THRAi 261 " --> pdb=" O GLUAi 257 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VALAi 264 " --> pdb=" O ALAAi 260 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASNAi 265 " --> pdb=" O THRAi 261 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARGAi 268 " --> pdb=" O VALAi 264 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 281 through 297 Processing helix chain 'Ai' and resid 338 through 343 Processing helix chain 'Ai' and resid 343 through 353 removed outlier: 4.490A pdb=" N ALAAi 347 " --> pdb=" O GLNAi 343 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLNAi 348 " --> pdb=" O GLYAi 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEAi 353 " --> pdb=" O ILEAi 349 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 358 through 375 removed outlier: 3.758A pdb=" N ALAAi 370 " --> pdb=" O GLNAi 366 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 385 through 410 removed outlier: 3.681A pdb=" N ALAAi 394 " --> pdb=" O LYSAi 390 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARGAi 395 " --> pdb=" O GLUAi 391 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 416 through 426 Processing helix chain 'Ai' and resid 427 through 429 No H-bonds generated for 'chain 'Ai' and resid 427 through 429' Processing helix chain 'Ai' and resid 433 through 459 removed outlier: 3.688A pdb=" N GLUAi 448 " --> pdb=" O LEUAi 444 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALAAi 449 " --> pdb=" O ARGAi 445 " (cutoff:3.500A) Proline residue: Ai 450 - end of helix Processing helix chain 'Ai' and resid 461 through 472 removed outlier: 4.033A pdb=" N VALAi 465 " --> pdb=" O GLUAi 461 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 488 through 492 Processing helix chain 'Ai' and resid 497 through 516 Processing helix chain 'Aj' and resid 9 through 31 removed outlier: 4.138A pdb=" N THRAj 30 " --> pdb=" O ALAAj 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEUAj 31 " --> pdb=" O VALAj 27 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 52 through 60 Processing helix chain 'Aj' and resid 64 through 85 removed outlier: 3.621A pdb=" N GLYAj 70 " --> pdb=" O PHEAj 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLUAj 76 " --> pdb=" O GLNAj 72 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VALAj 77 " --> pdb=" O METAj 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALAAj 78 " --> pdb=" O VALAj 74 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 88 through 109 Processing helix chain 'Aj' and resid 112 through 135 Processing helix chain 'Aj' and resid 140 through 152 Processing helix chain 'Aj' and resid 155 through 170 Processing helix chain 'Aj' and resid 201 through 205 Processing helix chain 'Aj' and resid 229 through 244 Proline residue: Aj 235 - end of helix Processing helix chain 'Aj' and resid 255 through 267 removed outlier: 4.072A pdb=" N THRAj 261 " --> pdb=" O GLUAj 257 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 281 through 297 removed outlier: 3.509A pdb=" N ASPAj 291 " --> pdb=" O ALAAj 287 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 308 through 312 Processing helix chain 'Aj' and resid 338 through 356 Processing helix chain 'Aj' and resid 358 through 373 Processing helix chain 'Aj' and resid 385 through 410 Processing helix chain 'Aj' and resid 416 through 426 Processing helix chain 'Aj' and resid 433 through 448 removed outlier: 3.729A pdb=" N GLUAj 448 " --> pdb=" O LEUAj 444 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 448 through 459 Processing helix chain 'Aj' and resid 461 through 472 Processing helix chain 'Aj' and resid 488 through 492 Processing helix chain 'Aj' and resid 497 through 516 removed outlier: 3.806A pdb=" N THRAj 516 " --> pdb=" O GLYAj 512 " (cutoff:3.500A) Processing helix chain 'Al' and resid 23 through 25 No H-bonds generated for 'chain 'Al' and resid 23 through 25' Processing helix chain 'Al' and resid 48 through 52 removed outlier: 3.662A pdb=" N ASNAl 51 " --> pdb=" O ILEAl 48 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLYAl 52 " --> pdb=" O LEUAl 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Al' and resid 48 through 52' Processing helix chain 'Ao' and resid 9 through 30 removed outlier: 4.212A pdb=" N THRAo 30 " --> pdb=" O ALAAo 26 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 52 through 60 removed outlier: 3.671A pdb=" N VALAo 56 " --> pdb=" O ASPAo 52 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 64 through 85 Processing helix chain 'Ao' and resid 88 through 108 Processing helix chain 'Ao' and resid 112 through 135 Processing helix chain 'Ao' and resid 140 through 152 removed outlier: 3.760A pdb=" N GLNAo 146 " --> pdb=" O LYSAo 142 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 155 through 169 removed outlier: 3.644A pdb=" N LEUAo 161 " --> pdb=" O THRAo 157 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 229 through 244 Proline residue: Ao 235 - end of helix removed outlier: 3.703A pdb=" N ALAAo 243 " --> pdb=" O ALAAo 239 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 255 through 268 removed outlier: 4.449A pdb=" N LEUAo 259 " --> pdb=" O GLUAo 255 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THRAo 261 " --> pdb=" O GLUAo 257 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VALAo 264 " --> pdb=" O ALAAo 260 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASNAo 265 " --> pdb=" O THRAo 261 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARGAo 268 " --> pdb=" O VALAo 264 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 281 through 297 Processing helix chain 'Ao' and resid 338 through 343 Processing helix chain 'Ao' and resid 343 through 353 removed outlier: 4.489A pdb=" N ALAAo 347 " --> pdb=" O GLNAo 343 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLNAo 348 " --> pdb=" O GLYAo 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEAo 353 " --> pdb=" O ILEAo 349 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 358 through 375 removed outlier: 3.758A pdb=" N ALAAo 370 " --> pdb=" O GLNAo 366 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 385 through 410 removed outlier: 3.681A pdb=" N ALAAo 394 " --> pdb=" O LYSAo 390 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARGAo 395 " --> pdb=" O GLUAo 391 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 416 through 426 Processing helix chain 'Ao' and resid 427 through 429 No H-bonds generated for 'chain 'Ao' and resid 427 through 429' Processing helix chain 'Ao' and resid 433 through 459 removed outlier: 3.687A pdb=" N GLUAo 448 " --> pdb=" O LEUAo 444 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALAAo 449 " --> pdb=" O ARGAo 445 " (cutoff:3.500A) Proline residue: Ao 450 - end of helix Processing helix chain 'Ao' and resid 461 through 472 removed outlier: 4.034A pdb=" N VALAo 465 " --> pdb=" O GLUAo 461 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 488 through 492 Processing helix chain 'Ao' and resid 497 through 516 Processing helix chain 'Ap' and resid 9 through 31 removed outlier: 4.137A pdb=" N THRAp 30 " --> pdb=" O ALAAp 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEUAp 31 " --> pdb=" O VALAp 27 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 52 through 60 Processing helix chain 'Ap' and resid 64 through 85 removed outlier: 3.621A pdb=" N GLYAp 70 " --> pdb=" O PHEAp 66 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLUAp 76 " --> pdb=" O GLNAp 72 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VALAp 77 " --> pdb=" O METAp 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALAAp 78 " --> pdb=" O VALAp 74 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 88 through 109 Processing helix chain 'Ap' and resid 112 through 135 Processing helix chain 'Ap' and resid 140 through 152 Processing helix chain 'Ap' and resid 155 through 170 Processing helix chain 'Ap' and resid 201 through 205 Processing helix chain 'Ap' and resid 229 through 244 Proline residue: Ap 235 - end of helix Processing helix chain 'Ap' and resid 255 through 267 removed outlier: 4.072A pdb=" N THRAp 261 " --> pdb=" O GLUAp 257 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 281 through 297 removed outlier: 3.509A pdb=" N ASPAp 291 " --> pdb=" O ALAAp 287 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 308 through 312 Processing helix chain 'Ap' and resid 338 through 356 Processing helix chain 'Ap' and resid 358 through 373 Processing helix chain 'Ap' and resid 385 through 410 Processing helix chain 'Ap' and resid 416 through 426 Processing helix chain 'Ap' and resid 433 through 448 removed outlier: 3.728A pdb=" N GLUAp 448 " --> pdb=" O LEUAp 444 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 448 through 459 Processing helix chain 'Ap' and resid 461 through 472 Processing helix chain 'Ap' and resid 488 through 492 Processing helix chain 'Ap' and resid 497 through 516 removed outlier: 3.807A pdb=" N THRAp 516 " --> pdb=" O GLYAp 512 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 23 through 25 No H-bonds generated for 'chain 'Ar' and resid 23 through 25' Processing helix chain 'Ar' and resid 48 through 52 removed outlier: 3.663A pdb=" N ASNAr 51 " --> pdb=" O ILEAr 48 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLYAr 52 " --> pdb=" O LEUAr 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ar' and resid 48 through 52' Processing helix chain 'Au' and resid 9 through 30 removed outlier: 4.211A pdb=" N THRAu 30 " --> pdb=" O ALAAu 26 " (cutoff:3.500A) Processing helix chain 'Au' and resid 52 through 60 removed outlier: 3.672A pdb=" N VALAu 56 " --> pdb=" O ASPAu 52 " (cutoff:3.500A) Processing helix chain 'Au' and resid 64 through 85 Processing helix chain 'Au' and resid 88 through 108 Processing helix chain 'Au' and resid 112 through 135 Processing helix chain 'Au' and resid 140 through 152 removed outlier: 3.759A pdb=" N GLNAu 146 " --> pdb=" O LYSAu 142 " (cutoff:3.500A) Processing helix chain 'Au' and resid 155 through 169 removed outlier: 3.644A pdb=" N LEUAu 161 " --> pdb=" O THRAu 157 " (cutoff:3.500A) Processing helix chain 'Au' and resid 229 through 244 Proline residue: Au 235 - end of helix removed outlier: 3.703A pdb=" N ALAAu 243 " --> pdb=" O ALAAu 239 " (cutoff:3.500A) Processing helix chain 'Au' and resid 255 through 268 removed outlier: 4.449A pdb=" N LEUAu 259 " --> pdb=" O GLUAu 255 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THRAu 261 " --> pdb=" O GLUAu 257 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VALAu 264 " --> pdb=" O ALAAu 260 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASNAu 265 " --> pdb=" O THRAu 261 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARGAu 268 " --> pdb=" O VALAu 264 " (cutoff:3.500A) Processing helix chain 'Au' and resid 281 through 297 Processing helix chain 'Au' and resid 338 through 343 Processing helix chain 'Au' and resid 343 through 353 removed outlier: 4.490A pdb=" N ALAAu 347 " --> pdb=" O GLNAu 343 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLNAu 348 " --> pdb=" O GLYAu 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEAu 353 " --> pdb=" O ILEAu 349 " (cutoff:3.500A) Processing helix chain 'Au' and resid 358 through 375 removed outlier: 3.758A pdb=" N ALAAu 370 " --> pdb=" O GLNAu 366 " (cutoff:3.500A) Processing helix chain 'Au' and resid 385 through 410 removed outlier: 3.681A pdb=" N ALAAu 394 " --> pdb=" O LYSAu 390 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARGAu 395 " --> pdb=" O GLUAu 391 " (cutoff:3.500A) Processing helix chain 'Au' and resid 416 through 426 Processing helix chain 'Au' and resid 427 through 429 No H-bonds generated for 'chain 'Au' and resid 427 through 429' Processing helix chain 'Au' and resid 433 through 459 removed outlier: 3.688A pdb=" N GLUAu 448 " --> pdb=" O LEUAu 444 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALAAu 449 " --> pdb=" O ARGAu 445 " (cutoff:3.500A) Proline residue: Au 450 - end of helix Processing helix chain 'Au' and resid 461 through 472 removed outlier: 4.034A pdb=" N VALAu 465 " --> pdb=" O GLUAu 461 " (cutoff:3.500A) Processing helix chain 'Au' and resid 488 through 492 Processing helix chain 'Au' and resid 497 through 516 Processing helix chain 'Av' and resid 9 through 31 removed outlier: 4.138A pdb=" N THRAv 30 " --> pdb=" O ALAAv 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEUAv 31 " --> pdb=" O VALAv 27 " (cutoff:3.500A) Processing helix chain 'Av' and resid 52 through 60 Processing helix chain 'Av' and resid 64 through 85 removed outlier: 3.620A pdb=" N GLYAv 70 " --> pdb=" O PHEAv 66 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLUAv 76 " --> pdb=" O GLNAv 72 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VALAv 77 " --> pdb=" O METAv 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALAAv 78 " --> pdb=" O VALAv 74 " (cutoff:3.500A) Processing helix chain 'Av' and resid 88 through 109 Processing helix chain 'Av' and resid 112 through 135 Processing helix chain 'Av' and resid 140 through 152 Processing helix chain 'Av' and resid 155 through 170 Processing helix chain 'Av' and resid 201 through 205 Processing helix chain 'Av' and resid 229 through 244 Proline residue: Av 235 - end of helix Processing helix chain 'Av' and resid 255 through 267 removed outlier: 4.072A pdb=" N THRAv 261 " --> pdb=" O GLUAv 257 " (cutoff:3.500A) Processing helix chain 'Av' and resid 281 through 297 removed outlier: 3.509A pdb=" N ASPAv 291 " --> pdb=" O ALAAv 287 " (cutoff:3.500A) Processing helix chain 'Av' and resid 308 through 312 Processing helix chain 'Av' and resid 338 through 356 Processing helix chain 'Av' and resid 358 through 373 Processing helix chain 'Av' and resid 385 through 410 Processing helix chain 'Av' and resid 416 through 426 Processing helix chain 'Av' and resid 433 through 448 removed outlier: 3.728A pdb=" N GLUAv 448 " --> pdb=" O LEUAv 444 " (cutoff:3.500A) Processing helix chain 'Av' and resid 448 through 459 Processing helix chain 'Av' and resid 461 through 472 Processing helix chain 'Av' and resid 488 through 492 Processing helix chain 'Av' and resid 497 through 516 removed outlier: 3.806A pdb=" N THRAv 516 " --> pdb=" O GLYAv 512 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 23 through 25 No H-bonds generated for 'chain 'Ax' and resid 23 through 25' Processing helix chain 'Ax' and resid 48 through 52 removed outlier: 3.662A pdb=" N ASNAx 51 " --> pdb=" O ILEAx 48 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLYAx 52 " --> pdb=" O LEUAx 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ax' and resid 48 through 52' Processing helix chain 'Ba' and resid 9 through 30 removed outlier: 4.212A pdb=" N THRBa 30 " --> pdb=" O ALABa 26 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 52 through 60 removed outlier: 3.670A pdb=" N VALBa 56 " --> pdb=" O ASPBa 52 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 64 through 85 Processing helix chain 'Ba' and resid 88 through 108 Processing helix chain 'Ba' and resid 112 through 135 Processing helix chain 'Ba' and resid 140 through 152 removed outlier: 3.760A pdb=" N GLNBa 146 " --> pdb=" O LYSBa 142 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 155 through 169 removed outlier: 3.644A pdb=" N LEUBa 161 " --> pdb=" O THRBa 157 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 229 through 244 Proline residue: Ba 235 - end of helix removed outlier: 3.702A pdb=" N ALABa 243 " --> pdb=" O ALABa 239 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 255 through 268 removed outlier: 4.449A pdb=" N LEUBa 259 " --> pdb=" O GLUBa 255 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THRBa 261 " --> pdb=" O GLUBa 257 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VALBa 264 " --> pdb=" O ALABa 260 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASNBa 265 " --> pdb=" O THRBa 261 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARGBa 268 " --> pdb=" O VALBa 264 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 281 through 297 Processing helix chain 'Ba' and resid 338 through 343 Processing helix chain 'Ba' and resid 343 through 353 removed outlier: 4.490A pdb=" N ALABa 347 " --> pdb=" O GLNBa 343 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLNBa 348 " --> pdb=" O GLYBa 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEBa 353 " --> pdb=" O ILEBa 349 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 358 through 375 removed outlier: 3.758A pdb=" N ALABa 370 " --> pdb=" O GLNBa 366 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 385 through 410 removed outlier: 3.681A pdb=" N ALABa 394 " --> pdb=" O LYSBa 390 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARGBa 395 " --> pdb=" O GLUBa 391 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 416 through 426 Processing helix chain 'Ba' and resid 427 through 429 No H-bonds generated for 'chain 'Ba' and resid 427 through 429' Processing helix chain 'Ba' and resid 433 through 459 removed outlier: 3.688A pdb=" N GLUBa 448 " --> pdb=" O LEUBa 444 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALABa 449 " --> pdb=" O ARGBa 445 " (cutoff:3.500A) Proline residue: Ba 450 - end of helix Processing helix chain 'Ba' and resid 461 through 472 removed outlier: 4.033A pdb=" N VALBa 465 " --> pdb=" O GLUBa 461 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 488 through 492 Processing helix chain 'Ba' and resid 497 through 516 Processing helix chain 'Bb' and resid 9 through 31 removed outlier: 4.137A pdb=" N THRBb 30 " --> pdb=" O ALABb 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEUBb 31 " --> pdb=" O VALBb 27 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 52 through 60 Processing helix chain 'Bb' and resid 64 through 85 removed outlier: 3.620A pdb=" N GLYBb 70 " --> pdb=" O PHEBb 66 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLUBb 76 " --> pdb=" O GLNBb 72 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VALBb 77 " --> pdb=" O METBb 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALABb 78 " --> pdb=" O VALBb 74 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 88 through 109 Processing helix chain 'Bb' and resid 112 through 135 Processing helix chain 'Bb' and resid 140 through 152 Processing helix chain 'Bb' and resid 155 through 170 Processing helix chain 'Bb' and resid 201 through 205 Processing helix chain 'Bb' and resid 229 through 244 Proline residue: Bb 235 - end of helix Processing helix chain 'Bb' and resid 255 through 267 removed outlier: 4.072A pdb=" N THRBb 261 " --> pdb=" O GLUBb 257 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 281 through 297 removed outlier: 3.509A pdb=" N ASPBb 291 " --> pdb=" O ALABb 287 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 308 through 312 Processing helix chain 'Bb' and resid 338 through 356 Processing helix chain 'Bb' and resid 358 through 373 Processing helix chain 'Bb' and resid 385 through 410 Processing helix chain 'Bb' and resid 416 through 426 Processing helix chain 'Bb' and resid 433 through 448 removed outlier: 3.728A pdb=" N GLUBb 448 " --> pdb=" O LEUBb 444 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 448 through 459 Processing helix chain 'Bb' and resid 461 through 472 Processing helix chain 'Bb' and resid 488 through 492 Processing helix chain 'Bb' and resid 497 through 516 removed outlier: 3.806A pdb=" N THRBb 516 " --> pdb=" O GLYBb 512 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 23 through 25 No H-bonds generated for 'chain 'Bd' and resid 23 through 25' Processing helix chain 'Bd' and resid 48 through 52 removed outlier: 3.663A pdb=" N ASNBd 51 " --> pdb=" O ILEBd 48 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLYBd 52 " --> pdb=" O LEUBd 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bd' and resid 48 through 52' Processing helix chain 'Bg' and resid 9 through 30 removed outlier: 4.211A pdb=" N THRBg 30 " --> pdb=" O ALABg 26 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 52 through 60 removed outlier: 3.672A pdb=" N VALBg 56 " --> pdb=" O ASPBg 52 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 64 through 85 Processing helix chain 'Bg' and resid 88 through 108 Processing helix chain 'Bg' and resid 112 through 135 Processing helix chain 'Bg' and resid 140 through 152 removed outlier: 3.760A pdb=" N GLNBg 146 " --> pdb=" O LYSBg 142 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 155 through 169 removed outlier: 3.644A pdb=" N LEUBg 161 " --> pdb=" O THRBg 157 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 229 through 244 Proline residue: Bg 235 - end of helix removed outlier: 3.702A pdb=" N ALABg 243 " --> pdb=" O ALABg 239 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 255 through 268 removed outlier: 4.449A pdb=" N LEUBg 259 " --> pdb=" O GLUBg 255 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THRBg 261 " --> pdb=" O GLUBg 257 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VALBg 264 " --> pdb=" O ALABg 260 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASNBg 265 " --> pdb=" O THRBg 261 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARGBg 268 " --> pdb=" O VALBg 264 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 281 through 297 Processing helix chain 'Bg' and resid 338 through 343 Processing helix chain 'Bg' and resid 343 through 353 removed outlier: 4.490A pdb=" N ALABg 347 " --> pdb=" O GLNBg 343 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLNBg 348 " --> pdb=" O GLYBg 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEBg 353 " --> pdb=" O ILEBg 349 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 358 through 375 removed outlier: 3.758A pdb=" N ALABg 370 " --> pdb=" O GLNBg 366 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 385 through 410 removed outlier: 3.682A pdb=" N ALABg 394 " --> pdb=" O LYSBg 390 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARGBg 395 " --> pdb=" O GLUBg 391 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 416 through 426 Processing helix chain 'Bg' and resid 427 through 429 No H-bonds generated for 'chain 'Bg' and resid 427 through 429' Processing helix chain 'Bg' and resid 433 through 459 removed outlier: 3.687A pdb=" N GLUBg 448 " --> pdb=" O LEUBg 444 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALABg 449 " --> pdb=" O ARGBg 445 " (cutoff:3.500A) Proline residue: Bg 450 - end of helix Processing helix chain 'Bg' and resid 461 through 472 removed outlier: 4.034A 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 9 through 31 removed outlier: 4.138A pdb=" N THRBh 30 " --> pdb=" O ALABh 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEUBh 31 " --> pdb=" O VALBh 27 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 52 through 60 Processing helix chain 'Bh' and resid 64 through 85 removed outlier: 3.620A pdb=" N GLYBh 70 " --> pdb=" O PHEBh 66 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLUBh 76 " --> pdb=" O GLNBh 72 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VALBh 77 " --> pdb=" O METBh 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALABh 78 " --> pdb=" O VALBh 74 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 88 through 109 Processing helix chain 'Bh' and resid 112 through 135 Processing helix chain 'Bh' and resid 140 through 152 Processing helix chain 'Bh' and resid 155 through 170 Processing helix chain 'Bh' and resid 201 through 205 Processing helix chain 'Bh' and resid 229 through 244 Proline residue: Bh 235 - end of helix Processing helix chain 'Bh' and resid 255 through 267 removed outlier: 4.073A pdb=" N THRBh 261 " --> pdb=" O GLUBh 257 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 281 through 297 removed outlier: 3.508A pdb=" N ASPBh 291 " --> pdb=" O ALABh 287 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 308 through 312 Processing helix chain 'Bh' and resid 338 through 356 Processing helix chain 'Bh' and resid 358 through 373 Processing helix chain 'Bh' and resid 385 through 410 Processing helix chain 'Bh' and resid 416 through 426 Processing helix chain 'Bh' and resid 433 through 448 removed outlier: 3.728A pdb=" N GLUBh 448 " --> pdb=" O LEUBh 444 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 448 through 459 Processing helix chain 'Bh' and resid 461 through 472 Processing helix chain 'Bh' and resid 488 through 492 Processing helix chain 'Bh' and resid 497 through 516 removed outlier: 3.806A pdb=" N THRBh 516 " --> pdb=" O GLYBh 512 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 23 through 25 No H-bonds generated for 'chain 'Bj' and resid 23 through 25' Processing helix chain 'Bj' and resid 48 through 52 removed outlier: 3.662A pdb=" N ASNBj 51 " --> pdb=" O ILEBj 48 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLYBj 52 " --> pdb=" O LEUBj 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bj' and resid 48 through 52' Processing helix chain 'Bm' and resid 9 through 30 removed outlier: 4.211A pdb=" N THRBm 30 " --> pdb=" O ALABm 26 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 52 through 60 removed outlier: 3.672A 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 108 Processing helix chain 'Bm' and resid 112 through 135 Processing helix chain 'Bm' and resid 140 through 152 removed outlier: 3.760A pdb=" N GLNBm 146 " --> pdb=" O LYSBm 142 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 155 through 169 removed outlier: 3.643A pdb=" N LEUBm 161 " --> pdb=" O THRBm 157 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 229 through 244 Proline residue: Bm 235 - end of helix removed outlier: 3.703A pdb=" N ALABm 243 " --> pdb=" O ALABm 239 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 255 through 268 removed outlier: 4.449A pdb=" N LEUBm 259 " --> pdb=" O GLUBm 255 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THRBm 261 " --> pdb=" O GLUBm 257 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VALBm 264 " --> pdb=" O ALABm 260 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASNBm 265 " --> pdb=" O THRBm 261 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARGBm 268 " --> pdb=" O VALBm 264 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 281 through 297 Processing helix chain 'Bm' and resid 338 through 343 Processing helix chain 'Bm' and resid 343 through 353 removed outlier: 4.489A pdb=" N ALABm 347 " --> pdb=" O GLNBm 343 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLNBm 348 " --> pdb=" O GLYBm 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEBm 353 " --> pdb=" O ILEBm 349 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 358 through 375 removed outlier: 3.757A pdb=" N ALABm 370 " --> pdb=" O GLNBm 366 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 385 through 410 removed outlier: 3.682A pdb=" N ALABm 394 " --> pdb=" O LYSBm 390 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARGBm 395 " --> pdb=" O GLUBm 391 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 416 through 426 Processing helix chain 'Bm' and resid 427 through 429 No H-bonds generated for 'chain 'Bm' and resid 427 through 429' Processing helix chain 'Bm' and resid 433 through 459 removed outlier: 3.688A pdb=" N GLUBm 448 " --> pdb=" O LEUBm 444 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALABm 449 " --> pdb=" O ARGBm 445 " (cutoff:3.500A) Proline residue: Bm 450 - end of helix Processing helix chain 'Bm' and resid 461 through 472 removed outlier: 4.034A pdb=" N VALBm 465 " --> pdb=" O GLUBm 461 " (cutoff:3.500A) 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 31 removed outlier: 4.137A pdb=" N THRBn 30 " --> pdb=" O ALABn 26 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEUBn 31 " --> pdb=" O VALBn 27 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 52 through 60 Processing helix chain 'Bn' and resid 64 through 85 removed outlier: 3.620A pdb=" N GLYBn 70 " --> pdb=" O PHEBn 66 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLUBn 76 " --> pdb=" O GLNBn 72 " (cutoff:3.500A) removed outlier: 4.215A 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 Processing helix chain 'Bn' and resid 229 through 244 Proline residue: Bn 235 - end of helix Processing helix chain 'Bn' and resid 255 through 267 removed outlier: 4.072A pdb=" N THRBn 261 " --> pdb=" O GLUBn 257 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 281 through 297 removed outlier: 3.508A pdb=" N ASPBn 291 " --> pdb=" O ALABn 287 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 308 through 312 Processing helix chain 'Bn' and resid 338 through 356 Processing helix chain 'Bn' and resid 358 through 373 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 448 removed outlier: 3.728A pdb=" N GLUBn 448 " --> pdb=" O LEUBn 444 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 448 through 459 Processing helix chain 'Bn' and resid 461 through 472 Processing helix chain 'Bn' and resid 488 through 492 Processing helix chain 'Bn' and resid 497 through 516 removed outlier: 3.806A pdb=" N THRBn 516 " --> pdb=" O GLYBn 512 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 23 through 25 No H-bonds generated for 'chain 'Bp' and resid 23 through 25' Processing helix chain 'Bp' and resid 48 through 52 removed outlier: 3.662A pdb=" N ASNBp 51 " --> pdb=" O ILEBp 48 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLYBp 52 " --> pdb=" O LEUBp 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bp' and resid 48 through 52' Processing sheet with id=AA1, first strand: chain 'Ac' and resid 4 through 8 Processing sheet with id=AA2, first strand: chain 'Ac' and resid 48 through 50 removed outlier: 6.392A pdb=" N VALAc 39 " --> pdb=" O VALAi 521 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASPAi 523 " --> pdb=" O VALAc 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Ac' and resid 174 through 179 removed outlier: 6.375A pdb=" N VALAc 174 " --> pdb=" O ALAAc 377 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILEAc 379 " --> pdb=" O VALAc 174 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THRAc 176 " --> pdb=" O ILEAc 379 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VALAc 381 " --> pdb=" O THRAc 176 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLUAc 178 " --> pdb=" O VALAc 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Ac' and resid 193 through 195 Processing sheet with id=AA5, first strand: chain 'Ac' and resid 273 through 277 removed outlier: 6.488A pdb=" N LEUAc 247 " --> pdb=" O ALAAc 274 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VALAc 276 " --> pdb=" O LEUAc 247 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILEAc 249 " --> pdb=" O VALAc 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Ac' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'Ac' and resid 476 through 479 Processing sheet with id=AA8, first strand: chain 'Ad' and resid 4 through 8 removed outlier: 7.501A pdb=" N VALAj 39 " --> pdb=" O GLUAd 518 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N METAd 520 " --> pdb=" O VALAj 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Ad' and resid 48 through 50 removed outlier: 7.299A pdb=" N ASNAd 37 " --> pdb=" O GLUAp 518 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N METAp 520 " --> pdb=" O ASNAd 37 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VALAd 39 " --> pdb=" O METAp 520 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N THRAp 522 " --> pdb=" O VALAd 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Ad' and resid 174 through 180 removed outlier: 3.724A pdb=" N VALAd 376 " --> pdb=" O VALAd 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Ad' and resid 193 through 195 removed outlier: 3.860A pdb=" N METAd 193 " --> pdb=" O ILEAd 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGAd 322 " --> pdb=" O ILEAd 333 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLYAd 335 " --> pdb=" O ALAAd 320 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALAAd 320 " --> pdb=" O GLYAd 335 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEUAd 247 " --> pdb=" O ALAAd 274 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VALAd 276 " --> pdb=" O LEUAd 247 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILEAd 249 " --> pdb=" O VALAd 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Ad' and resid 213 through 216 removed outlier: 8.055A pdb=" N ILEAd 301 " --> pdb=" O ILEAd 220 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEUAd 222 " --> pdb=" O ILEAd 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Ad' and resid 411 through 413 Processing sheet with id=AB5, first strand: chain 'Ad' and resid 476 through 479 Processing sheet with id=AB6, first strand: chain 'Af' and resid 74 through 78 removed outlier: 8.475A pdb=" N GLUAf 82 " --> pdb=" O ARGAf 14 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARGAf 14 " --> pdb=" O GLUAf 82 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARGAf 9 " --> pdb=" O VALAf 43 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VALAf 43 " --> pdb=" O ARGAf 9 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILEAf 11 " --> pdb=" O LEUAf 41 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILEAf 66 " --> pdb=" O LEUAf 92 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Af' and resid 21 through 22 Processing sheet with id=AB8, first strand: chain 'Af' and resid 46 through 47 Processing sheet with id=AB9, first strand: chain 'Ai' and resid 48 through 50 removed outlier: 6.418A pdb=" N VALAi 39 " --> pdb=" O VALAu 521 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ASPAu 523 " --> pdb=" O VALAi 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Ai' and resid 174 through 179 removed outlier: 6.374A pdb=" N VALAi 174 " --> pdb=" O ALAAi 377 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILEAi 379 " --> pdb=" O VALAi 174 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THRAi 176 " --> pdb=" O ILEAi 379 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VALAi 381 " --> pdb=" O THRAi 176 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLUAi 178 " --> pdb=" O VALAi 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Ai' and resid 193 through 195 Processing sheet with id=AC3, first strand: chain 'Ai' and resid 273 through 277 removed outlier: 6.488A pdb=" N LEUAi 247 " --> pdb=" O ALAAi 274 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VALAi 276 " --> pdb=" O LEUAi 247 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILEAi 249 " --> pdb=" O VALAi 276 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Ai' and resid 411 through 413 Processing sheet with id=AC5, first strand: chain 'Ai' and resid 476 through 479 Processing sheet with id=AC6, first strand: chain 'Aj' and resid 4 through 8 removed outlier: 7.538A pdb=" N VALAv 39 " --> pdb=" O GLUAj 518 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N METAj 520 " --> pdb=" O VALAv 39 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Aj' and resid 174 through 180 removed outlier: 3.724A pdb=" N VALAj 376 " --> pdb=" O VALAj 190 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Aj' and resid 193 through 195 removed outlier: 3.859A pdb=" N METAj 193 " --> pdb=" O ILEAj 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGAj 322 " --> pdb=" O ILEAj 333 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLYAj 335 " --> pdb=" O ALAAj 320 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALAAj 320 " --> pdb=" O GLYAj 335 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEUAj 247 " --> pdb=" O ALAAj 274 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VALAj 276 " --> pdb=" O LEUAj 247 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILEAj 249 " --> pdb=" O VALAj 276 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Aj' and resid 213 through 216 removed outlier: 8.055A pdb=" N ILEAj 301 " --> pdb=" O ILEAj 220 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEUAj 222 " --> pdb=" O ILEAj 301 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Aj' and resid 411 through 413 Processing sheet with id=AD2, first strand: chain 'Aj' and resid 476 through 479 Processing sheet with id=AD3, first strand: chain 'Al' and resid 74 through 78 removed outlier: 8.475A pdb=" N GLUAl 82 " --> pdb=" O ARGAl 14 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARGAl 14 " --> pdb=" O GLUAl 82 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARGAl 9 " --> pdb=" O VALAl 43 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VALAl 43 " --> pdb=" O ARGAl 9 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILEAl 11 " --> pdb=" O LEUAl 41 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILEAl 66 " --> pdb=" O LEUAl 92 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Al' and resid 21 through 22 Processing sheet with id=AD5, first strand: chain 'Al' and resid 46 through 47 Processing sheet with id=AD6, first strand: chain 'Ao' and resid 4 through 8 Processing sheet with id=AD7, first strand: chain 'Ao' and resid 174 through 179 removed outlier: 6.375A pdb=" N VALAo 174 " --> pdb=" O ALAAo 377 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILEAo 379 " --> pdb=" O VALAo 174 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THRAo 176 " --> pdb=" O ILEAo 379 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VALAo 381 " --> pdb=" O THRAo 176 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLUAo 178 " --> pdb=" O VALAo 381 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Ao' and resid 193 through 195 Processing sheet with id=AD9, first strand: chain 'Ao' and resid 273 through 277 removed outlier: 6.488A pdb=" N LEUAo 247 " --> pdb=" O ALAAo 274 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VALAo 276 " --> pdb=" O LEUAo 247 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILEAo 249 " --> pdb=" O VALAo 276 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Ao' and resid 411 through 413 Processing sheet with id=AE2, first strand: chain 'Ao' and resid 476 through 479 Processing sheet with id=AE3, first strand: chain 'Ap' and resid 48 through 50 removed outlier: 7.272A pdb=" N ASNAp 37 " --> pdb=" O GLUBb 518 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N METBb 520 " --> pdb=" O ASNAp 37 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VALAp 39 " --> pdb=" O METBb 520 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N THRBb 522 " --> pdb=" O VALAp 39 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Ap' and resid 174 through 180 removed outlier: 3.723A pdb=" N VALAp 376 " --> pdb=" O VALAp 190 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Ap' and resid 193 through 195 removed outlier: 3.860A pdb=" N METAp 193 " --> pdb=" O ILEAp 332 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARGAp 322 " --> pdb=" O ILEAp 333 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLYAp 335 " --> pdb=" O ALAAp 320 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALAAp 320 " --> pdb=" O GLYAp 335 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEUAp 247 " --> pdb=" O ALAAp 274 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VALAp 276 " --> pdb=" O LEUAp 247 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILEAp 249 " --> pdb=" O VALAp 276 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Ap' and resid 213 through 216 removed outlier: 8.055A pdb=" N ILEAp 301 " --> pdb=" O ILEAp 220 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEUAp 222 " --> pdb=" O ILEAp 301 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Ap' and resid 411 through 413 Processing sheet with id=AE8, first strand: chain 'Ap' and resid 476 through 479 Processing sheet with id=AE9, first strand: chain 'Ar' and resid 74 through 78 removed outlier: 8.474A pdb=" N GLUAr 82 " --> pdb=" O ARGAr 14 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARGAr 14 " --> pdb=" O GLUAr 82 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARGAr 9 " --> pdb=" O VALAr 43 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VALAr 43 " --> pdb=" O ARGAr 9 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILEAr 11 " --> pdb=" O LEUAr 41 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILEAr 66 " --> pdb=" O LEUAr 92 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Ar' and resid 21 through 22 Processing sheet with id=AF2, first strand: chain 'Ar' and resid 46 through 47 Processing sheet with id=AF3, first strand: chain 'Au' and resid 48 through 50 removed outlier: 6.424A pdb=" N VALAu 39 " --> pdb=" O VALBg 521 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ASPBg 523 " --> pdb=" O VALAu 39 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Au' and resid 174 through 179 removed outlier: 6.375A pdb=" N VALAu 174 " --> pdb=" O ALAAu 377 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILEAu 379 " --> pdb=" O VALAu 174 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THRAu 176 " --> pdb=" O ILEAu 379 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VALAu 381 " --> pdb=" O THRAu 176 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLUAu 178 " --> pdb=" O VALAu 381 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Au' and resid 193 through 195 Processing sheet with id=AF6, first strand: chain 'Au' and resid 273 through 277 removed outlier: 6.487A pdb=" N LEUAu 247 " --> pdb=" O ALAAu 274 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VALAu 276 " --> pdb=" O LEUAu 247 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILEAu 249 " --> pdb=" O VALAu 276 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Au' and resid 411 through 413 Processing sheet with id=AF8, first strand: chain 'Au' and resid 476 through 479 Processing sheet with id=AF9, first strand: chain 'Av' and resid 4 through 8 removed outlier: 7.536A pdb=" N VALBh 39 " --> pdb=" O GLUAv 518 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N METAv 520 " --> pdb=" O VALBh 39 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Av' and resid 174 through 180 removed outlier: 3.724A pdb=" N VALAv 376 " --> pdb=" O VALAv 190 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Av' and resid 193 through 195 removed outlier: 3.860A pdb=" N METAv 193 " --> pdb=" O ILEAv 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGAv 322 " --> pdb=" O ILEAv 333 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLYAv 335 " --> pdb=" O ALAAv 320 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALAAv 320 " --> pdb=" O GLYAv 335 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEUAv 247 " --> pdb=" O ALAAv 274 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VALAv 276 " --> pdb=" O LEUAv 247 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILEAv 249 " --> pdb=" O VALAv 276 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Av' and resid 213 through 216 removed outlier: 8.055A pdb=" N ILEAv 301 " --> pdb=" O ILEAv 220 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEUAv 222 " --> pdb=" O ILEAv 301 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Av' and resid 411 through 413 Processing sheet with id=AG5, first strand: chain 'Av' and resid 476 through 479 Processing sheet with id=AG6, first strand: chain 'Ax' and resid 74 through 78 removed outlier: 8.475A pdb=" N GLUAx 82 " --> pdb=" O ARGAx 14 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARGAx 14 " --> pdb=" O GLUAx 82 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARGAx 9 " --> pdb=" O VALAx 43 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VALAx 43 " --> pdb=" O ARGAx 9 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILEAx 11 " --> pdb=" O LEUAx 41 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILEAx 66 " --> pdb=" O LEUAx 92 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Ax' and resid 21 through 22 Processing sheet with id=AG8, first strand: chain 'Ax' and resid 46 through 47 Processing sheet with id=AG9, first strand: chain 'Ba' and resid 4 through 8 Processing sheet with id=AH1, first strand: chain 'Ba' and resid 174 through 179 removed outlier: 6.375A pdb=" N VALBa 174 " --> pdb=" O ALABa 377 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILEBa 379 " --> pdb=" O VALBa 174 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THRBa 176 " --> pdb=" O ILEBa 379 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VALBa 381 " --> pdb=" O THRBa 176 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLUBa 178 " --> pdb=" O VALBa 381 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Ba' and resid 193 through 195 Processing sheet with id=AH3, first strand: chain 'Ba' and resid 273 through 277 removed outlier: 6.488A pdb=" N LEUBa 247 " --> pdb=" O ALABa 274 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VALBa 276 " --> pdb=" O LEUBa 247 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILEBa 249 " --> pdb=" O VALBa 276 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Ba' and resid 411 through 413 Processing sheet with id=AH5, first strand: chain 'Ba' and resid 476 through 479 Processing sheet with id=AH6, first strand: chain 'Bb' and resid 48 through 50 removed outlier: 7.268A pdb=" N ASNBb 37 " --> pdb=" O GLUBn 518 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N METBn 520 " --> pdb=" O ASNBb 37 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VALBb 39 " --> pdb=" O METBn 520 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N THRBn 522 " --> pdb=" O VALBb 39 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Bb' and resid 174 through 180 removed outlier: 3.724A pdb=" N VALBb 376 " --> pdb=" O VALBb 190 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Bb' and resid 193 through 195 removed outlier: 3.860A pdb=" N METBb 193 " --> pdb=" O ILEBb 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGBb 322 " --> pdb=" O ILEBb 333 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLYBb 335 " --> pdb=" O ALABb 320 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALABb 320 " --> pdb=" O GLYBb 335 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEUBb 247 " --> pdb=" O ALABb 274 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VALBb 276 " --> pdb=" O LEUBb 247 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILEBb 249 " --> pdb=" O VALBb 276 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Bb' and resid 213 through 216 removed outlier: 8.055A pdb=" N ILEBb 301 " --> pdb=" O ILEBb 220 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEUBb 222 " --> pdb=" O ILEBb 301 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Bb' and resid 411 through 413 Processing sheet with id=AI2, first strand: chain 'Bb' and resid 476 through 479 Processing sheet with id=AI3, first strand: chain 'Bd' and resid 74 through 78 removed outlier: 8.475A pdb=" N GLUBd 82 " --> pdb=" O ARGBd 14 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARGBd 14 " --> pdb=" O GLUBd 82 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ARGBd 9 " --> pdb=" O VALBd 43 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VALBd 43 " --> pdb=" O ARGBd 9 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILEBd 11 " --> pdb=" O LEUBd 41 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILEBd 66 " --> pdb=" O LEUBd 92 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Bd' and resid 21 through 22 Processing sheet with id=AI5, first strand: chain 'Bd' and resid 46 through 47 Processing sheet with id=AI6, first strand: chain 'Bg' and resid 48 through 50 removed outlier: 6.424A pdb=" N VALBg 39 " --> pdb=" O VALBm 521 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ASPBm 523 " --> pdb=" O VALBg 39 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Bg' and resid 174 through 179 removed outlier: 6.374A pdb=" N VALBg 174 " --> pdb=" O ALABg 377 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILEBg 379 " --> pdb=" O VALBg 174 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THRBg 176 " --> pdb=" O ILEBg 379 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VALBg 381 " --> pdb=" O THRBg 176 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLUBg 178 " --> pdb=" O VALBg 381 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Bg' and resid 193 through 195 Processing sheet with id=AI9, first strand: chain 'Bg' and resid 273 through 277 removed outlier: 6.487A pdb=" N LEUBg 247 " --> pdb=" O ALABg 274 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VALBg 276 " --> pdb=" O LEUBg 247 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILEBg 249 " --> pdb=" O VALBg 276 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Bg' and resid 411 through 413 Processing sheet with id=AJ2, first strand: chain 'Bg' and resid 476 through 479 Processing sheet with id=AJ3, first strand: chain 'Bh' and resid 4 through 8 removed outlier: 7.525A pdb=" N VALBn 39 " --> pdb=" O GLUBh 518 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N METBh 520 " --> pdb=" O VALBn 39 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Bh' and resid 174 through 180 removed outlier: 3.724A pdb=" N VALBh 376 " --> pdb=" O VALBh 190 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Bh' and resid 193 through 195 removed outlier: 3.859A pdb=" N METBh 193 " --> pdb=" O ILEBh 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGBh 322 " --> pdb=" O ILEBh 333 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLYBh 335 " --> pdb=" O ALABh 320 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALABh 320 " --> pdb=" O GLYBh 335 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEUBh 247 " --> pdb=" O ALABh 274 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VALBh 276 " --> pdb=" O LEUBh 247 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILEBh 249 " --> pdb=" O VALBh 276 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Bh' and resid 213 through 216 removed outlier: 8.056A pdb=" N ILEBh 301 " --> pdb=" O ILEBh 220 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEUBh 222 " --> pdb=" O ILEBh 301 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Bh' and resid 411 through 413 Processing sheet with id=AJ8, first strand: chain 'Bh' and resid 476 through 479 Processing sheet with id=AJ9, first strand: chain 'Bj' and resid 74 through 78 removed outlier: 8.476A pdb=" N GLUBj 82 " --> pdb=" O ARGBj 14 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARGBj 14 " --> pdb=" O GLUBj 82 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARGBj 9 " --> pdb=" O VALBj 43 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VALBj 43 " --> pdb=" O ARGBj 9 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILEBj 11 " --> pdb=" O LEUBj 41 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILEBj 66 " --> pdb=" O LEUBj 92 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Bj' and resid 21 through 22 Processing sheet with id=AK2, first strand: chain 'Bj' and resid 46 through 47 Processing sheet with id=AK3, first strand: chain 'Bm' and resid 174 through 179 removed outlier: 6.375A pdb=" N VALBm 174 " --> pdb=" O ALABm 377 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILEBm 379 " --> pdb=" O VALBm 174 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THRBm 176 " --> pdb=" O ILEBm 379 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VALBm 381 " --> pdb=" O THRBm 176 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLUBm 178 " --> pdb=" O VALBm 381 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'Bm' and resid 193 through 195 Processing sheet with id=AK5, first strand: chain 'Bm' and resid 273 through 277 removed outlier: 6.488A pdb=" N LEUBm 247 " --> pdb=" O ALABm 274 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VALBm 276 " --> pdb=" O LEUBm 247 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILEBm 249 " --> pdb=" O VALBm 276 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'Bm' and resid 411 through 413 Processing sheet with id=AK7, first strand: chain 'Bm' and resid 476 through 479 Processing sheet with id=AK8, first strand: chain 'Bn' and resid 174 through 180 removed outlier: 3.725A pdb=" N VALBn 376 " --> pdb=" O VALBn 190 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'Bn' and resid 193 through 195 removed outlier: 3.860A pdb=" N METBn 193 " --> pdb=" O ILEBn 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGBn 322 " --> pdb=" O ILEBn 333 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLYBn 335 " --> pdb=" O ALABn 320 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALABn 320 " --> pdb=" O GLYBn 335 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEUBn 247 " --> pdb=" O ALABn 274 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VALBn 276 " --> pdb=" O LEUBn 247 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILEBn 249 " --> pdb=" O VALBn 276 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'Bn' and resid 213 through 216 removed outlier: 8.055A pdb=" N ILEBn 301 " --> pdb=" O ILEBn 220 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEUBn 222 " --> pdb=" O ILEBn 301 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'Bn' and resid 411 through 413 Processing sheet with id=AL3, first strand: chain 'Bn' and resid 476 through 479 Processing sheet with id=AL4, first strand: chain 'Bp' and resid 74 through 78 removed outlier: 8.476A pdb=" N GLUBp 82 " --> pdb=" O ARGBp 14 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARGBp 14 " --> pdb=" O GLUBp 82 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARGBp 9 " --> pdb=" O VALBp 43 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VALBp 43 " --> pdb=" O ARGBp 9 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILEBp 11 " --> pdb=" O LEUBp 41 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILEBp 66 " --> pdb=" O LEUBp 92 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'Bp' and resid 21 through 22 Processing sheet with id=AL6, first strand: chain 'Bp' and resid 46 through 47 3734 hydrogen bonds defined for protein. 10677 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: 26.91 Time building geometry restraints manager: 12.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.58: 59081 1.58 - 1.96: 776 1.96 - 2.33: 35 2.33 - 2.71: 7 2.71 - 3.09: 7 Bond restraints: 59906 Sorted by residual: bond pdb=" C PROBm 525 " pdb=" O PROBm 525 " ideal model delta sigma weight residual 1.231 2.610 -1.379 2.00e-02 2.50e+03 4.75e+03 bond pdb=" C PROBg 525 " pdb=" O PROBg 525 " ideal model delta sigma weight residual 1.231 2.609 -1.378 2.00e-02 2.50e+03 4.75e+03 bond pdb=" C PROAu 525 " pdb=" O PROAu 525 " ideal model delta sigma weight residual 1.231 2.609 -1.378 2.00e-02 2.50e+03 4.75e+03 bond pdb=" C PROAi 525 " pdb=" O PROAi 525 " ideal model delta sigma weight residual 1.231 2.609 -1.378 2.00e-02 2.50e+03 4.75e+03 bond pdb=" C PROBa 525 " pdb=" O PROBa 525 " ideal model delta sigma weight residual 1.231 2.609 -1.378 2.00e-02 2.50e+03 4.75e+03 ... (remaining 59901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.31: 80808 15.31 - 30.61: 126 30.61 - 45.92: 14 45.92 - 61.22: 0 61.22 - 76.53: 7 Bond angle restraints: 80955 Sorted by residual: angle pdb=" O PROAo 525 " pdb=" C PROAo 525 " pdb=" OXT PROAo 525 " ideal model delta sigma weight residual 118.00 41.47 76.53 3.00e+00 1.11e-01 6.51e+02 angle pdb=" O PROAu 525 " pdb=" C PROAu 525 " pdb=" OXT PROAu 525 " ideal model delta sigma weight residual 118.00 41.48 76.52 3.00e+00 1.11e-01 6.51e+02 angle pdb=" O PROBm 525 " pdb=" C PROBm 525 " pdb=" OXT PROBm 525 " ideal model delta sigma weight residual 118.00 41.49 76.51 3.00e+00 1.11e-01 6.50e+02 angle pdb=" O PROAi 525 " pdb=" C PROAi 525 " pdb=" OXT PROAi 525 " ideal model delta sigma weight residual 118.00 41.49 76.51 3.00e+00 1.11e-01 6.50e+02 angle pdb=" O PROAc 525 " pdb=" C PROAc 525 " pdb=" OXT PROAc 525 " ideal model delta sigma weight residual 118.00 41.49 76.51 3.00e+00 1.11e-01 6.50e+02 ... (remaining 80950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.64: 35018 32.64 - 65.28: 1830 65.28 - 97.92: 245 97.92 - 130.56: 7 130.56 - 163.21: 21 Dihedral angle restraints: 37121 sinusoidal: 14532 harmonic: 22589 Sorted by residual: dihedral pdb=" CA ILEAx 3 " pdb=" C ILEAx 3 " pdb=" N ARGAx 4 " pdb=" CA ARGAx 4 " ideal model delta harmonic sigma weight residual -180.00 -48.77 -131.23 0 5.00e+00 4.00e-02 6.89e+02 dihedral pdb=" CA ILEAf 3 " pdb=" C ILEAf 3 " pdb=" N ARGAf 4 " pdb=" CA ARGAf 4 " ideal model delta harmonic sigma weight residual -180.00 -48.88 -131.12 0 5.00e+00 4.00e-02 6.88e+02 dihedral pdb=" CA ILEAr 3 " pdb=" C ILEAr 3 " pdb=" N ARGAr 4 " pdb=" CA ARGAr 4 " ideal model delta harmonic sigma weight residual -180.00 -48.93 -131.07 0 5.00e+00 4.00e-02 6.87e+02 ... (remaining 37118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.915: 9786 0.915 - 1.830: 28 1.830 - 2.745: 7 2.745 - 3.660: 0 3.660 - 4.574: 7 Chirality restraints: 9828 Sorted by residual: chirality pdb=" C1' ADPAj 601 " pdb=" C2' ADPAj 601 " pdb=" N9 ADPAj 601 " pdb=" O4' ADPAj 601 " both_signs ideal model delta sigma weight residual False 2.48 -2.09 4.57 2.00e-01 2.50e+01 5.23e+02 chirality pdb=" C1' ADPBh 601 " pdb=" C2' ADPBh 601 " pdb=" N9 ADPBh 601 " pdb=" O4' ADPBh 601 " both_signs ideal model delta sigma weight residual False 2.48 -2.09 4.57 2.00e-01 2.50e+01 5.23e+02 chirality pdb=" C1' ADPAp 601 " pdb=" C2' ADPAp 601 " pdb=" N9 ADPAp 601 " pdb=" O4' ADPAp 601 " both_signs ideal model delta sigma weight residual False 2.48 -2.09 4.57 2.00e-01 2.50e+01 5.23e+02 ... (remaining 9825 not shown) Planarity restraints: 10542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PROBg 525 " 0.142 2.00e-02 2.50e+03 2.83e-01 8.02e+02 pdb=" C PROBg 525 " -0.404 2.00e-02 2.50e+03 pdb=" O PROBg 525 " -0.097 2.00e-02 2.50e+03 pdb=" OXT PROBg 525 " 0.358 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PROAu 525 " 0.142 2.00e-02 2.50e+03 2.83e-01 8.02e+02 pdb=" C PROAu 525 " -0.403 2.00e-02 2.50e+03 pdb=" O PROAu 525 " -0.097 2.00e-02 2.50e+03 pdb=" OXT PROAu 525 " 0.359 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PROAi 525 " 0.142 2.00e-02 2.50e+03 2.83e-01 8.01e+02 pdb=" C PROAi 525 " -0.403 2.00e-02 2.50e+03 pdb=" O PROAi 525 " -0.097 2.00e-02 2.50e+03 pdb=" OXT PROAi 525 " 0.358 2.00e-02 2.50e+03 ... (remaining 10539 not shown) Histogram of nonbonded interaction distances: 0.60 - 1.46: 75 1.46 - 2.32: 496 2.32 - 3.18: 53166 3.18 - 4.04: 165463 4.04 - 4.90: 282189 Warning: very small nonbonded interaction distances. Nonbonded interactions: 501389 Sorted by model distance: nonbonded pdb=" CD2 PHEAc 281 " pdb=" CD GLUAo 386 " model vdw 0.597 3.570 nonbonded pdb=" CD2 PHEBa 281 " pdb=" CD GLUBm 386 " model vdw 0.600 3.570 nonbonded pdb=" CD2 PHEAo 281 " pdb=" CD GLUBa 386 " model vdw 0.607 3.570 nonbonded pdb=" CD GLUAu 386 " pdb=" CD2 PHEBg 281 " model vdw 0.614 3.570 nonbonded pdb=" OE2 GLUAc 386 " pdb=" CD2 PHEAi 281 " model vdw 0.618 3.340 ... (remaining 501384 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 'Ac' selection = chain 'Ad' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Au' selection = chain 'Av' selection = chain 'Ba' selection = chain 'Bb' selection = chain 'Bg' selection = chain 'Bh' selection = chain 'Bm' selection = chain 'Bn' } ncs_group { reference = chain 'Af' selection = chain 'Al' selection = chain 'Ar' selection = chain 'Ax' selection = chain 'Bd' selection = chain 'Bj' selection = chain 'Bp' } 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: 4.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 1.680 Check model and map are aligned: 0.350 Set scattering table: 0.410 Process input model: 99.000 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.280 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: 0.020 Load rotamer database and sin/cos tables:2.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 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 : 0.032 1.566 59906 Z= 2.088 Angle : 2.527 76.526 80955 Z= 1.715 Chirality : 0.208 4.574 9828 Planarity : 0.016 0.283 10542 Dihedral : 19.429 163.205 22631 Min Nonbonded Distance : 0.597 Molprobity Statistics. All-atom Clashscore : 32.75 Ramachandran Plot: Outliers : 1.58 % Allowed : 3.11 % Favored : 95.31 % Rotamer: Outliers : 11.71 % Allowed : 13.84 % Favored : 74.45 % Cbeta Deviations : 2.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: 1.29 (0.09), residues: 7973 helix: 2.33 (0.08), residues: 4032 sheet: 0.07 (0.16), residues: 966 loop : -0.97 (0.11), residues: 2975 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HISBd 7 PHE 0.062 0.011 PHEAj 219 TYR 0.144 0.011 TYRBg 360 ARG 0.027 0.002 ARGAu 322 *********************** 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 1227 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 728 poor density : 499 time to evaluate : 5.034 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: Ad 389 MET cc_start: 0.7138 (tpp) cc_final: 0.6510 (tpp) REVERT: Aj 389 MET cc_start: 0.7111 (tpp) cc_final: 0.6857 (tpp) REVERT: Av 417 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8716 (m) REVERT: Av 483 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6910 (mm-30) REVERT: Bn 483 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6981 (mm-30) outliers start: 728 outliers final: 170 residues processed: 1131 average time/residue: 0.5831 time to fit residues: 1091.5995 Evaluate side-chains 545 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 372 time to evaluate : 5.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 55 SER Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 79 SER Chi-restraints excluded: chain Ac residue 90 THR Chi-restraints excluded: chain Ac residue 116 LEU Chi-restraints excluded: chain Ac residue 184 GLN Chi-restraints excluded: chain Ac residue 358 SER Chi-restraints excluded: chain Ac residue 366 GLN Chi-restraints excluded: chain Ac residue 432 GLN Chi-restraints excluded: chain Ac residue 518 GLU Chi-restraints excluded: chain Ad residue 201 SER Chi-restraints excluded: chain Ad residue 313 THR Chi-restraints excluded: chain Ad residue 380 LYS Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Ad residue 509 SER Chi-restraints excluded: chain Af residue 1 MET Chi-restraints excluded: chain Af residue 2 ASN Chi-restraints excluded: chain Af residue 34 LYS Chi-restraints excluded: chain Af residue 54 VAL Chi-restraints excluded: chain Af residue 77 LYS Chi-restraints excluded: chain Af residue 94 ILE Chi-restraints excluded: chain Af residue 96 GLU Chi-restraints excluded: chain Ai residue 55 SER Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 79 SER Chi-restraints excluded: chain Ai residue 89 THR Chi-restraints excluded: chain Ai residue 90 THR Chi-restraints excluded: chain Ai residue 139 SER Chi-restraints excluded: chain Ai residue 184 GLN Chi-restraints excluded: chain Ai residue 358 SER Chi-restraints excluded: chain Ai residue 366 GLN Chi-restraints excluded: chain Ai residue 432 GLN Chi-restraints excluded: chain Ai residue 518 GLU Chi-restraints excluded: chain Aj residue 87 ASP Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 313 THR Chi-restraints excluded: chain Aj residue 379 ILE Chi-restraints excluded: chain Aj residue 380 LYS Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 420 ILE Chi-restraints excluded: chain Aj residue 483 GLU Chi-restraints excluded: chain Al residue 1 MET Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 34 LYS Chi-restraints excluded: chain Al residue 54 VAL Chi-restraints excluded: chain Al residue 77 LYS Chi-restraints excluded: chain Al residue 78 ILE Chi-restraints excluded: chain Al residue 94 ILE Chi-restraints excluded: chain Al residue 96 GLU Chi-restraints excluded: chain Ao residue 55 SER Chi-restraints excluded: chain Ao residue 90 THR Chi-restraints excluded: chain Ao residue 184 GLN Chi-restraints excluded: chain Ao residue 358 SER Chi-restraints excluded: chain Ao residue 366 GLN Chi-restraints excluded: chain Ao residue 432 GLN Chi-restraints excluded: chain Ao residue 518 GLU Chi-restraints excluded: chain Ap residue 157 THR Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 286 LYS Chi-restraints excluded: chain Ap residue 308 GLU Chi-restraints excluded: chain Ap residue 313 THR Chi-restraints excluded: chain Ap residue 380 LYS Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ap residue 420 ILE Chi-restraints excluded: chain Ap residue 483 GLU Chi-restraints excluded: chain Ap residue 509 SER Chi-restraints excluded: chain Ar residue 1 MET Chi-restraints excluded: chain Ar residue 2 ASN Chi-restraints excluded: chain Ar residue 13 LYS Chi-restraints excluded: chain Ar residue 54 VAL Chi-restraints excluded: chain Ar residue 64 ILE Chi-restraints excluded: chain Ar residue 77 LYS Chi-restraints excluded: chain Ar residue 78 ILE Chi-restraints excluded: chain Ar residue 96 GLU Chi-restraints excluded: chain Au residue 55 SER Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Au residue 90 THR Chi-restraints excluded: chain Au residue 184 GLN Chi-restraints excluded: chain Au residue 358 SER Chi-restraints excluded: chain Au residue 366 GLN Chi-restraints excluded: chain Au residue 432 GLN Chi-restraints excluded: chain Au residue 518 GLU Chi-restraints excluded: chain Av residue 87 ASP Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 286 LYS Chi-restraints excluded: chain Av residue 308 GLU Chi-restraints excluded: chain Av residue 313 THR Chi-restraints excluded: chain Av residue 380 LYS Chi-restraints excluded: chain Av residue 417 VAL Chi-restraints excluded: chain Av residue 420 ILE Chi-restraints excluded: chain Av residue 483 GLU Chi-restraints excluded: chain Av residue 509 SER Chi-restraints excluded: chain Ax residue 1 MET Chi-restraints excluded: chain Ax residue 2 ASN Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 77 LYS Chi-restraints excluded: chain Ax residue 78 ILE Chi-restraints excluded: chain Ax residue 94 ILE Chi-restraints excluded: chain Ax residue 96 GLU Chi-restraints excluded: chain Ba residue 55 SER Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 90 THR Chi-restraints excluded: chain Ba residue 139 SER Chi-restraints excluded: chain Ba residue 358 SER Chi-restraints excluded: chain Ba residue 366 GLN Chi-restraints excluded: chain Ba residue 432 GLN Chi-restraints excluded: chain Ba residue 518 GLU Chi-restraints excluded: chain Bb residue 157 THR Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 313 THR Chi-restraints excluded: chain Bb residue 379 ILE Chi-restraints excluded: chain Bb residue 380 LYS Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bb residue 483 GLU Chi-restraints excluded: chain Bb residue 509 SER Chi-restraints excluded: chain Bd residue 1 MET Chi-restraints excluded: chain Bd residue 2 ASN Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 34 LYS Chi-restraints excluded: chain Bd residue 54 VAL Chi-restraints excluded: chain Bd residue 64 ILE Chi-restraints excluded: chain Bd residue 77 LYS Chi-restraints excluded: chain Bd residue 94 ILE Chi-restraints excluded: chain Bd residue 96 GLU Chi-restraints excluded: chain Bg residue 55 SER Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 90 THR Chi-restraints excluded: chain Bg residue 116 LEU Chi-restraints excluded: chain Bg residue 358 SER Chi-restraints excluded: chain Bg residue 366 GLN Chi-restraints excluded: chain Bg residue 432 GLN Chi-restraints excluded: chain Bg residue 518 GLU Chi-restraints excluded: chain Bh residue 87 ASP Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 313 THR Chi-restraints excluded: chain Bh residue 380 LYS Chi-restraints excluded: chain Bh residue 417 VAL Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bh residue 483 GLU Chi-restraints excluded: chain Bj residue 1 MET Chi-restraints excluded: chain Bj residue 2 ASN Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 34 LYS Chi-restraints excluded: chain Bj residue 77 LYS Chi-restraints excluded: chain Bj residue 94 ILE Chi-restraints excluded: chain Bj residue 96 GLU Chi-restraints excluded: chain Bm residue 55 SER Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 90 THR Chi-restraints excluded: chain Bm residue 184 GLN Chi-restraints excluded: chain Bm residue 358 SER Chi-restraints excluded: chain Bm residue 366 GLN Chi-restraints excluded: chain Bm residue 432 GLN Chi-restraints excluded: chain Bm residue 518 GLU Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 308 GLU Chi-restraints excluded: chain Bn residue 313 THR Chi-restraints excluded: chain Bn residue 380 LYS Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bn residue 483 GLU Chi-restraints excluded: chain Bn residue 509 SER Chi-restraints excluded: chain Bp residue 1 MET Chi-restraints excluded: chain Bp residue 2 ASN Chi-restraints excluded: chain Bp residue 54 VAL Chi-restraints excluded: chain Bp residue 77 LYS Chi-restraints excluded: chain Bp residue 78 ILE Chi-restraints excluded: chain Bp residue 94 ILE Chi-restraints excluded: chain Bp residue 96 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 667 optimal weight: 0.9990 chunk 599 optimal weight: 6.9990 chunk 332 optimal weight: 10.0000 chunk 204 optimal weight: 0.8980 chunk 404 optimal weight: 4.9990 chunk 320 optimal weight: 0.9980 chunk 619 optimal weight: 0.7980 chunk 239 optimal weight: 0.9980 chunk 376 optimal weight: 8.9990 chunk 461 optimal weight: 0.9980 chunk 718 optimal weight: 6.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 21 ASN Ac 37 ASN Ac 112 ASN Ac 366 GLN Ac 432 GLN ** Ad 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 82 ASN Ad 146 GLN Ad 351 GLN Ad 366 GLN Ad 453 GLN Ad 457 ASN Ai 21 ASN Ai 366 GLN Ai 432 GLN ** Aj 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 82 ASN Aj 146 GLN Aj 351 GLN Aj 366 GLN Aj 453 GLN Aj 457 ASN Ao 21 ASN Ao 37 ASN Ao 112 ASN Ao 366 GLN Ao 432 GLN ** Ap 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 82 ASN Ap 146 GLN Ap 351 GLN Ap 366 GLN Ap 457 ASN Au 21 ASN Au 112 ASN Au 366 GLN Au 432 GLN ** Av 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 37 ASN Av 82 ASN Av 146 GLN Av 351 GLN Av 366 GLN Av 457 ASN Ba 21 ASN Ba 112 ASN Ba 366 GLN Ba 432 GLN ** Bb 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 82 ASN Bb 146 GLN Bb 351 GLN Bb 366 GLN Bg 21 ASN Bg 112 ASN Bg 184 GLN Bg 366 GLN Bg 432 GLN ** Bh 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 82 ASN Bh 146 GLN Bh 351 GLN Bh 366 GLN Bm 21 ASN Bm 37 ASN Bm 112 ASN Bm 366 GLN Bm 432 GLN ** Bn 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 82 ASN Bn 146 GLN Bn 351 GLN Bn 366 GLN Bn 453 GLN Bn 457 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.278 59906 Z= 0.363 Angle : 1.012 39.464 80955 Z= 0.538 Chirality : 0.071 1.789 9828 Planarity : 0.006 0.145 10542 Dihedral : 12.543 177.667 8986 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.44 % Allowed : 3.11 % Favored : 96.45 % Rotamer: Outliers : 4.63 % Allowed : 17.07 % Favored : 78.30 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.32 (0.09), residues: 7973 helix: 2.26 (0.08), residues: 4088 sheet: 0.16 (0.14), residues: 1204 loop : -1.01 (0.12), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HISAx 7 PHE 0.020 0.002 PHEAj 66 TYR 0.034 0.002 TYRAc 360 ARG 0.013 0.001 ARGAf 4 *********************** 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 659 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 371 time to evaluate : 5.067 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: Ac 107 VAL cc_start: 0.8863 (OUTLIER) cc_final: 0.8654 (t) REVERT: Ad 10 ASN cc_start: 0.6932 (m-40) cc_final: 0.6547 (m-40) REVERT: Ad 491 MET cc_start: 0.7962 (mtm) cc_final: 0.7724 (mtm) REVERT: Af 19 THR cc_start: 0.3687 (p) cc_final: 0.3482 (p) REVERT: Ai 199 TYR cc_start: 0.4007 (OUTLIER) cc_final: 0.3241 (p90) REVERT: Al 59 VAL cc_start: 0.3671 (OUTLIER) cc_final: 0.3165 (m) REVERT: Av 104 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8965 (mt) REVERT: Bb 28 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8183 (mtmt) REVERT: Bh 491 MET cc_start: 0.8073 (mtm) cc_final: 0.7666 (mtm) REVERT: Bj 59 VAL cc_start: 0.3289 (OUTLIER) cc_final: 0.3068 (m) REVERT: Bm 520 MET cc_start: 0.7678 (mtm) cc_final: 0.7408 (mtm) REVERT: Bn 10 ASN cc_start: 0.6820 (m-40) cc_final: 0.6524 (m-40) REVERT: Bn 28 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7990 (mtpt) REVERT: Bn 491 MET cc_start: 0.8079 (mtm) cc_final: 0.7873 (mtm) REVERT: Bp 59 VAL cc_start: 0.3409 (OUTLIER) cc_final: 0.2588 (m) outliers start: 288 outliers final: 102 residues processed: 625 average time/residue: 0.5393 time to fit residues: 579.7247 Evaluate side-chains 447 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 337 time to evaluate : 5.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 107 VAL Chi-restraints excluded: chain Ac residue 252 GLU Chi-restraints excluded: chain Ac residue 327 LYS Chi-restraints excluded: chain Ac residue 358 SER Chi-restraints excluded: chain Ad residue 87 ASP Chi-restraints excluded: chain Ad residue 104 LEU Chi-restraints excluded: chain Ad residue 201 SER Chi-restraints excluded: chain Ad residue 313 THR Chi-restraints excluded: chain Ad residue 379 ILE Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Af residue 2 ASN Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 54 VAL Chi-restraints excluded: chain Af residue 64 ILE Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Af residue 77 LYS Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 107 VAL Chi-restraints excluded: chain Ai residue 199 TYR Chi-restraints excluded: chain Ai residue 358 SER Chi-restraints excluded: chain Ai residue 521 VAL Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 313 THR Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 54 VAL Chi-restraints excluded: chain Al residue 59 VAL Chi-restraints excluded: chain Al residue 64 ILE Chi-restraints excluded: chain Ao residue 327 LYS Chi-restraints excluded: chain Ao residue 358 SER Chi-restraints excluded: chain Ao residue 489 ILE Chi-restraints excluded: chain Ap residue 16 MET Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 286 LYS Chi-restraints excluded: chain Ap residue 313 THR Chi-restraints excluded: chain Ap residue 360 TYR Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ap residue 420 ILE Chi-restraints excluded: chain Ar residue 2 ASN Chi-restraints excluded: chain Ar residue 3 ILE Chi-restraints excluded: chain Ar residue 21 SER Chi-restraints excluded: chain Ar residue 54 VAL Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Ar residue 77 LYS Chi-restraints excluded: chain Au residue 40 LEU Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Au residue 304 GLU Chi-restraints excluded: chain Au residue 327 LYS Chi-restraints excluded: chain Au residue 358 SER Chi-restraints excluded: chain Au residue 521 VAL Chi-restraints excluded: chain Av residue 104 LEU Chi-restraints excluded: chain Av residue 286 LYS Chi-restraints excluded: chain Av residue 313 THR Chi-restraints excluded: chain Av residue 360 TYR Chi-restraints excluded: chain Ax residue 2 ASN Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 64 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ax residue 75 SER Chi-restraints excluded: chain Ax residue 77 LYS Chi-restraints excluded: chain Ba residue 54 VAL Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 304 GLU Chi-restraints excluded: chain Ba residue 327 LYS Chi-restraints excluded: chain Ba residue 358 SER Chi-restraints excluded: chain Ba residue 456 LEU Chi-restraints excluded: chain Bb residue 28 LYS Chi-restraints excluded: chain Bb residue 87 ASP Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 313 THR Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bd residue 2 ASN Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bd residue 78 ILE Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 79 SER Chi-restraints excluded: chain Bg residue 327 LYS Chi-restraints excluded: chain Bg residue 358 SER Chi-restraints excluded: chain Bh residue 313 THR Chi-restraints excluded: chain Bh residue 360 TYR Chi-restraints excluded: chain Bh residue 380 LYS Chi-restraints excluded: chain Bh residue 417 VAL Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bj residue 2 ASN Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 59 VAL Chi-restraints excluded: chain Bj residue 65 VAL Chi-restraints excluded: chain Bj residue 77 LYS Chi-restraints excluded: chain Bj residue 78 ILE Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 107 VAL Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 327 LYS Chi-restraints excluded: chain Bm residue 358 SER Chi-restraints excluded: chain Bn residue 28 LYS Chi-restraints excluded: chain Bn residue 87 ASP Chi-restraints excluded: chain Bn residue 313 THR Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bn residue 380 LYS Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bp residue 2 ASN Chi-restraints excluded: chain Bp residue 3 ILE Chi-restraints excluded: chain Bp residue 21 SER Chi-restraints excluded: chain Bp residue 59 VAL Chi-restraints excluded: chain Bp residue 65 VAL 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: 2.9990 chunk 597 optimal weight: 0.9980 chunk 489 optimal weight: 8.9990 chunk 198 optimal weight: 10.0000 chunk 719 optimal weight: 8.9990 chunk 777 optimal weight: 0.8980 chunk 640 optimal weight: 8.9990 chunk 713 optimal weight: 2.9990 chunk 245 optimal weight: 40.0000 chunk 577 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 21 ASN Ad 37 ASN Af 7 HIS Ai 37 ASN Aj 21 ASN Ao 453 GLN Ap 21 ASN Ap 37 ASN Av 21 ASN Ax 7 HIS Bb 21 ASN Bb 37 ASN Bd 7 HIS Bh 21 ASN Bh 453 GLN Bn 21 ASN Bp 7 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 59906 Z= 0.287 Angle : 0.843 26.402 80955 Z= 0.444 Chirality : 0.072 1.994 9828 Planarity : 0.005 0.119 10542 Dihedral : 10.400 143.951 8708 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.50 % Favored : 96.07 % Rotamer: Outliers : 3.12 % Allowed : 18.63 % Favored : 78.25 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.16 (0.09), residues: 7973 helix: 2.13 (0.08), residues: 4109 sheet: 0.02 (0.15), residues: 1176 loop : -1.04 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HISAx 7 PHE 0.017 0.002 PHEBg 44 TYR 0.027 0.002 TYRAo 199 ARG 0.014 0.001 ARGBj 14 *********************** 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 548 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 354 time to evaluate : 5.064 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: Ad 10 ASN cc_start: 0.6908 (m-40) cc_final: 0.6536 (m-40) REVERT: Ad 491 MET cc_start: 0.8099 (mtm) cc_final: 0.7836 (mtm) REVERT: Af 2 ASN cc_start: 0.1621 (OUTLIER) cc_final: 0.1416 (m110) REVERT: Ai 491 MET cc_start: 0.6515 (mtp) cc_final: 0.6303 (mtm) REVERT: Aj 389 MET cc_start: 0.7166 (tpp) cc_final: 0.6607 (tpp) REVERT: Al 80 ASN cc_start: 0.4526 (p0) cc_final: 0.4300 (p0) REVERT: Ax 19 THR cc_start: 0.3917 (OUTLIER) cc_final: 0.3704 (p) REVERT: Ax 59 VAL cc_start: 0.3894 (OUTLIER) cc_final: 0.3155 (p) REVERT: Ba 491 MET cc_start: 0.7169 (mtm) cc_final: 0.6914 (mtm) REVERT: Bd 59 VAL cc_start: 0.5481 (OUTLIER) cc_final: 0.5207 (p) REVERT: Bh 491 MET cc_start: 0.8193 (mtm) cc_final: 0.7943 (mtm) REVERT: Bm 90 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7844 (m) outliers start: 194 outliers final: 80 residues processed: 522 average time/residue: 0.5318 time to fit residues: 482.6046 Evaluate side-chains 412 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 327 time to evaluate : 5.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 90 THR Chi-restraints excluded: chain Ad residue 379 ILE Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Af residue 2 ASN Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Ai residue 37 ASN Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 90 THR Chi-restraints excluded: chain Ai residue 157 THR Chi-restraints excluded: chain Ai residue 177 VAL Chi-restraints excluded: chain Aj residue 385 THR Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 483 GLU Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 54 VAL Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Al residue 75 SER Chi-restraints excluded: chain Ao residue 90 THR Chi-restraints excluded: chain Ao residue 177 VAL Chi-restraints excluded: chain Ao residue 358 SER Chi-restraints excluded: chain Ao residue 435 ASP Chi-restraints excluded: chain Ao residue 489 ILE Chi-restraints excluded: chain Ap residue 16 MET Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 286 LYS Chi-restraints excluded: chain Ap residue 360 TYR Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ap residue 420 ILE Chi-restraints excluded: chain Ap residue 483 GLU Chi-restraints excluded: chain Ar residue 3 ILE Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Ar residue 77 LYS Chi-restraints excluded: chain Ar residue 94 ILE Chi-restraints excluded: chain Au residue 40 LEU Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Au residue 177 VAL Chi-restraints excluded: chain Au residue 358 SER Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 104 LEU Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 286 LYS Chi-restraints excluded: chain Av residue 360 TYR Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 19 THR Chi-restraints excluded: chain Ax residue 25 ILE Chi-restraints excluded: chain Ax residue 59 VAL Chi-restraints excluded: chain Ax residue 77 LYS Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 90 THR Chi-restraints excluded: chain Ba residue 456 LEU Chi-restraints excluded: chain Bb residue 16 MET Chi-restraints excluded: chain Bb residue 305 ILE Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 59 VAL Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 90 THR Chi-restraints excluded: chain Bg residue 358 SER Chi-restraints excluded: chain Bg residue 435 ASP Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 360 TYR Chi-restraints excluded: chain Bh residue 417 VAL Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 65 VAL Chi-restraints excluded: chain Bj residue 77 LYS Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 90 THR Chi-restraints excluded: chain Bm residue 358 SER Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 305 ILE Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bn residue 380 LYS Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bp residue 3 ILE Chi-restraints excluded: chain Bp residue 21 SER Chi-restraints excluded: chain Bp residue 25 ILE Chi-restraints excluded: chain Bp residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 0.9990 chunk 541 optimal weight: 9.9990 chunk 373 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 343 optimal weight: 7.9990 chunk 483 optimal weight: 6.9990 chunk 722 optimal weight: 8.9990 chunk 764 optimal weight: 0.9990 chunk 377 optimal weight: 3.9990 chunk 684 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Al 7 HIS Ar 7 HIS Au 290 GLN Bb 453 GLN Bb 457 ASN Bg 290 GLN Bh 457 ASN Bj 2 ASN Bj 7 HIS Bm 290 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 59906 Z= 0.287 Angle : 0.763 17.801 80955 Z= 0.390 Chirality : 0.050 0.772 9828 Planarity : 0.004 0.107 10542 Dihedral : 9.433 130.137 8675 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.75 % Favored : 95.97 % Rotamer: Outliers : 2.40 % Allowed : 19.93 % Favored : 77.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: 1.23 (0.09), residues: 7973 helix: 2.18 (0.08), residues: 4067 sheet: 0.04 (0.16), residues: 1141 loop : -0.93 (0.12), residues: 2765 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HISAl 7 PHE 0.014 0.002 PHEAd 66 TYR 0.021 0.001 TYRBa 199 ARG 0.008 0.001 ARGAx 37 *********************** 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 489 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 340 time to evaluate : 5.077 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: Ad 10 ASN cc_start: 0.6845 (m-40) cc_final: 0.6478 (m-40) REVERT: Aj 447 MET cc_start: 0.7966 (mtt) cc_final: 0.7736 (mtt) REVERT: Al 80 ASN cc_start: 0.4663 (p0) cc_final: 0.4428 (p0) REVERT: Ao 69 MET cc_start: 0.7798 (mtm) cc_final: 0.7580 (mtm) REVERT: Ba 491 MET cc_start: 0.6988 (mtm) cc_final: 0.6628 (mtm) REVERT: Bb 69 MET cc_start: 0.8262 (mtt) cc_final: 0.7729 (mtt) REVERT: Bb 483 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7206 (mm-30) REVERT: Bb 491 MET cc_start: 0.7998 (mtm) cc_final: 0.7523 (mtm) REVERT: Bh 491 MET cc_start: 0.8242 (mtm) cc_final: 0.7883 (mtm) REVERT: Bn 28 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7862 (mtpt) REVERT: Bn 100 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.8999 (mt) REVERT: Bn 483 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7265 (mm-30) outliers start: 149 outliers final: 89 residues processed: 469 average time/residue: 0.5230 time to fit residues: 435.2603 Evaluate side-chains 417 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 324 time to evaluate : 4.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 435 ASP Chi-restraints excluded: chain Ad residue 77 VAL Chi-restraints excluded: chain Ad residue 104 LEU Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Af residue 2 ASN Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ai residue 37 ASN Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 157 THR Chi-restraints excluded: chain Ai residue 358 SER Chi-restraints excluded: chain Ai residue 521 VAL Chi-restraints excluded: chain Aj residue 77 VAL Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 385 THR Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 420 ILE Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 54 VAL Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Al residue 95 VAL Chi-restraints excluded: chain Ao residue 107 VAL Chi-restraints excluded: chain Ao residue 489 ILE Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 286 LYS Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ap residue 420 ILE Chi-restraints excluded: chain Ap residue 483 GLU Chi-restraints excluded: chain Ar residue 3 ILE Chi-restraints excluded: chain Ar residue 25 ILE Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Ar residue 77 LYS Chi-restraints excluded: chain Ar residue 94 ILE Chi-restraints excluded: chain Au residue 40 LEU Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 77 VAL Chi-restraints excluded: chain Av residue 104 LEU Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Ax residue 1 MET Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 25 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ax residue 77 LYS Chi-restraints excluded: chain Ax residue 95 VAL Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 358 SER Chi-restraints excluded: chain Ba residue 435 ASP Chi-restraints excluded: chain Ba residue 456 LEU Chi-restraints excluded: chain Bb residue 185 ASP Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 305 ILE Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bb residue 483 GLU Chi-restraints excluded: chain Bb residue 504 LEU Chi-restraints excluded: chain Bd residue 1 MET Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 25 ILE Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 79 SER Chi-restraints excluded: chain Bg residue 435 ASP Chi-restraints excluded: chain Bh residue 77 VAL Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 417 VAL Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bh residue 483 GLU Chi-restraints excluded: chain Bh residue 504 LEU Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 25 ILE Chi-restraints excluded: chain Bj residue 77 LYS Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 107 VAL Chi-restraints excluded: chain Bm residue 177 VAL Chi-restraints excluded: chain Bn residue 28 LYS Chi-restraints excluded: chain Bn residue 100 ILE Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bn residue 483 GLU Chi-restraints excluded: chain Bp residue 3 ILE Chi-restraints excluded: chain Bp residue 25 ILE Chi-restraints excluded: chain Bp residue 65 VAL Chi-restraints excluded: chain Bp 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: 20.0000 chunk 434 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 569 optimal weight: 9.9990 chunk 315 optimal weight: 10.0000 chunk 652 optimal weight: 10.0000 chunk 528 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 390 optimal weight: 1.9990 chunk 686 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 343 GLN Ac 453 GLN Ad 82 ASN Ai 343 GLN Aj 82 ASN Al 2 ASN Ao 343 GLN Ap 82 ASN Ar 2 ASN Au 343 GLN Av 82 ASN ** Ax 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 343 GLN Bg 343 GLN Bh 82 ASN Bm 343 GLN Bn 82 ASN ** Bp 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 59906 Z= 0.317 Angle : 0.764 20.515 80955 Z= 0.387 Chirality : 0.048 0.527 9828 Planarity : 0.004 0.074 10542 Dihedral : 9.228 142.658 8663 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.08 % Favored : 95.75 % Rotamer: Outliers : 2.72 % Allowed : 20.06 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 1.16 (0.09), residues: 7973 helix: 2.07 (0.08), residues: 4095 sheet: 0.07 (0.15), residues: 1232 loop : -0.98 (0.12), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISAr 7 PHE 0.016 0.002 PHEBm 44 TYR 0.032 0.002 TYRAo 203 ARG 0.010 0.000 ARGAl 14 *********************** 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 503 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 334 time to evaluate : 5.082 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: Ac 491 MET cc_start: 0.6996 (mtm) cc_final: 0.6698 (mtm) REVERT: Ad 10 ASN cc_start: 0.6926 (m-40) cc_final: 0.6638 (m-40) REVERT: Ad 491 MET cc_start: 0.8153 (mtm) cc_final: 0.7890 (mtm) REVERT: Af 51 ASN cc_start: 0.5227 (OUTLIER) cc_final: 0.4994 (m110) REVERT: Al 80 ASN cc_start: 0.4627 (p0) cc_final: 0.4418 (p0) REVERT: Ba 488 MET cc_start: 0.8122 (mmm) cc_final: 0.7874 (mmm) REVERT: Ba 491 MET cc_start: 0.7190 (mtm) cc_final: 0.6748 (mtm) REVERT: Bb 10 ASN cc_start: 0.7154 (m-40) cc_final: 0.6811 (m-40) REVERT: Bb 483 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: Bh 491 MET cc_start: 0.8326 (mtm) cc_final: 0.8024 (mtm) REVERT: Bn 483 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7267 (mm-30) outliers start: 169 outliers final: 80 residues processed: 488 average time/residue: 0.5359 time to fit residues: 459.1633 Evaluate side-chains 402 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 319 time to evaluate : 5.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 494 LEU Chi-restraints excluded: chain Ad residue 77 VAL Chi-restraints excluded: chain Ad residue 185 ASP Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Af residue 2 ASN Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 51 ASN Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 157 THR Chi-restraints excluded: chain Ai residue 358 SER Chi-restraints excluded: chain Ai residue 521 VAL Chi-restraints excluded: chain Aj residue 77 VAL Chi-restraints excluded: chain Aj residue 185 ASP Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 385 THR Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 420 ILE Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 25 ILE Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Ao residue 107 VAL Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 286 LYS Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ap residue 420 ILE Chi-restraints excluded: chain Ap residue 483 GLU Chi-restraints excluded: chain Ap residue 499 VAL Chi-restraints excluded: chain Ar residue 25 ILE Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Au residue 40 LEU Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Au residue 116 LEU Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 77 VAL Chi-restraints excluded: chain Av residue 104 LEU Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 417 VAL Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 25 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 358 SER Chi-restraints excluded: chain Ba residue 456 LEU Chi-restraints excluded: chain Bb residue 77 VAL Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 305 ILE Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bb residue 483 GLU Chi-restraints excluded: chain Bb residue 504 LEU Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 25 ILE Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 79 SER Chi-restraints excluded: chain Bg residue 435 ASP Chi-restraints excluded: chain Bh residue 77 VAL Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 233 MET Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bh residue 483 GLU Chi-restraints excluded: chain Bh residue 499 VAL Chi-restraints excluded: chain Bh residue 504 LEU Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 25 ILE Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 107 VAL Chi-restraints excluded: chain Bn residue 77 VAL Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bn residue 483 GLU Chi-restraints excluded: chain Bn residue 499 VAL Chi-restraints excluded: chain Bp residue 6 LEU Chi-restraints excluded: chain Bp residue 25 ILE Chi-restraints excluded: chain Bp residue 65 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 9.9990 chunk 688 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 448 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 765 optimal weight: 8.9990 chunk 635 optimal weight: 7.9990 chunk 354 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 253 optimal weight: 0.5980 chunk 401 optimal weight: 0.6980 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 352 GLN ** Af 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 453 GLN Al 51 ASN Ar 51 ASN Au 37 ASN Ax 51 ASN Bb 82 ASN Bd 51 ASN Bj 51 ASN Bp 51 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 59906 Z= 0.383 Angle : 0.786 20.139 80955 Z= 0.400 Chirality : 0.049 0.504 9828 Planarity : 0.004 0.074 10542 Dihedral : 9.065 138.977 8649 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.62 % Favored : 95.21 % Rotamer: Outliers : 2.41 % Allowed : 20.56 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.88 (0.09), residues: 7973 helix: 1.82 (0.08), residues: 4123 sheet: -0.05 (0.16), residues: 1148 loop : -1.07 (0.12), residues: 2702 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HISBj 7 PHE 0.017 0.002 PHEBd 67 TYR 0.037 0.002 TYRAi 203 ARG 0.007 0.001 ARGAr 4 *********************** 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 481 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 331 time to evaluate : 5.087 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: Ac 514 MET cc_start: 0.7379 (mmm) cc_final: 0.7171 (mmm) REVERT: Ad 10 ASN cc_start: 0.7011 (m-40) cc_final: 0.6770 (m-40) REVERT: Al 80 ASN cc_start: 0.4521 (p0) cc_final: 0.4308 (p0) REVERT: Ba 488 MET cc_start: 0.8160 (mmm) cc_final: 0.7915 (mmm) REVERT: Ba 491 MET cc_start: 0.7294 (mtm) cc_final: 0.6900 (mtm) REVERT: Bb 483 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7199 (mm-30) REVERT: Bn 483 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7343 (mm-30) REVERT: Bn 491 MET cc_start: 0.8170 (mtm) cc_final: 0.7823 (mtm) outliers start: 150 outliers final: 99 residues processed: 465 average time/residue: 0.5061 time to fit residues: 420.6396 Evaluate side-chains 422 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 321 time to evaluate : 5.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 89 THR Chi-restraints excluded: chain Ac residue 116 LEU Chi-restraints excluded: chain Ad residue 77 VAL Chi-restraints excluded: chain Ad residue 185 ASP Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Af residue 2 ASN Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 157 THR Chi-restraints excluded: chain Ai residue 358 SER Chi-restraints excluded: chain Ai residue 521 VAL Chi-restraints excluded: chain Aj residue 77 VAL Chi-restraints excluded: chain Aj residue 134 LEU Chi-restraints excluded: chain Aj residue 185 ASP Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 385 THR Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 420 ILE Chi-restraints excluded: chain Aj residue 499 VAL Chi-restraints excluded: chain Aj residue 524 LEU Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 6 LEU Chi-restraints excluded: chain Al residue 25 ILE Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Ao residue 107 VAL Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ap residue 420 ILE Chi-restraints excluded: chain Ap residue 483 GLU Chi-restraints excluded: chain Ap residue 499 VAL Chi-restraints excluded: chain Ar residue 3 ILE Chi-restraints excluded: chain Ar residue 6 LEU Chi-restraints excluded: chain Ar residue 25 ILE Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Au residue 37 ASN Chi-restraints excluded: chain Au residue 40 LEU Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Au residue 116 LEU Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 77 VAL Chi-restraints excluded: chain Av residue 104 LEU Chi-restraints excluded: chain Av residue 134 LEU Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 213 VAL Chi-restraints excluded: chain Av residue 273 VAL Chi-restraints excluded: chain Av residue 417 VAL Chi-restraints excluded: chain Av residue 420 ILE Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 25 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ax residue 77 LYS Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 116 LEU Chi-restraints excluded: chain Ba residue 358 SER Chi-restraints excluded: chain Ba residue 494 LEU Chi-restraints excluded: chain Bb residue 77 VAL Chi-restraints excluded: chain Bb residue 185 ASP Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bb residue 483 GLU Chi-restraints excluded: chain Bb residue 499 VAL Chi-restraints excluded: chain Bb residue 504 LEU Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 25 ILE Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 79 SER Chi-restraints excluded: chain Bg residue 521 VAL Chi-restraints excluded: chain Bh residue 77 VAL Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 233 MET Chi-restraints excluded: chain Bh residue 417 VAL Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bh residue 483 GLU Chi-restraints excluded: chain Bh residue 499 VAL Chi-restraints excluded: chain Bh residue 504 LEU Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 6 LEU Chi-restraints excluded: chain Bj residue 25 ILE Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 107 VAL Chi-restraints excluded: chain Bm residue 494 LEU Chi-restraints excluded: chain Bn residue 44 PHE Chi-restraints excluded: chain Bn residue 77 VAL Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bn residue 442 VAL Chi-restraints excluded: chain Bn residue 483 GLU Chi-restraints excluded: chain Bn residue 499 VAL Chi-restraints excluded: chain Bp residue 25 ILE Chi-restraints excluded: chain Bp residue 65 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: 9.9990 chunk 436 optimal weight: 0.6980 chunk 558 optimal weight: 20.0000 chunk 433 optimal weight: 3.9990 chunk 644 optimal weight: 8.9990 chunk 427 optimal weight: 6.9990 chunk 762 optimal weight: 0.7980 chunk 477 optimal weight: 0.0980 chunk 464 optimal weight: 5.9990 chunk 351 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 72 GLN Af 51 ASN Ai 37 ASN Ai 112 ASN Ai 457 ASN Al 2 ASN Au 37 ASN Au 453 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 59906 Z= 0.200 Angle : 0.725 20.626 80955 Z= 0.365 Chirality : 0.046 0.514 9828 Planarity : 0.003 0.074 10542 Dihedral : 8.558 138.100 8645 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.15 % Favored : 95.67 % Rotamer: Outliers : 2.04 % Allowed : 21.62 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 1.16 (0.09), residues: 7973 helix: 2.06 (0.08), residues: 4137 sheet: 0.08 (0.16), residues: 1120 loop : -0.97 (0.12), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISBj 7 PHE 0.011 0.001 PHEAd 66 TYR 0.045 0.002 TYRAo 203 ARG 0.004 0.000 ARGAl 4 *********************** 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 458 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 331 time to evaluate : 5.132 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: Ac 514 MET cc_start: 0.7353 (mmm) cc_final: 0.7150 (mmm) REVERT: Ad 10 ASN cc_start: 0.6774 (m-40) cc_final: 0.6557 (m-40) REVERT: Ad 491 MET cc_start: 0.8052 (mtm) cc_final: 0.7607 (mtm) REVERT: Al 80 ASN cc_start: 0.4791 (p0) cc_final: 0.4556 (p0) REVERT: Ba 491 MET cc_start: 0.6999 (mtm) cc_final: 0.6474 (mtm) REVERT: Bb 10 ASN cc_start: 0.7037 (m-40) cc_final: 0.6763 (m-40) REVERT: Bh 491 MET cc_start: 0.8101 (mtm) cc_final: 0.7762 (mtm) outliers start: 127 outliers final: 82 residues processed: 447 average time/residue: 0.5141 time to fit residues: 411.9116 Evaluate side-chains 402 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 320 time to evaluate : 5.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 89 THR Chi-restraints excluded: chain Ac residue 494 LEU Chi-restraints excluded: chain Ad residue 77 VAL Chi-restraints excluded: chain Ad residue 185 ASP Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Af residue 2 ASN Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 64 ILE Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Ai residue 37 ASN Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 157 THR Chi-restraints excluded: chain Ai residue 358 SER Chi-restraints excluded: chain Ai residue 494 LEU Chi-restraints excluded: chain Aj residue 77 VAL Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 420 ILE Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 25 ILE Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Ao residue 107 VAL Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ap residue 483 GLU Chi-restraints excluded: chain Ar residue 2 ASN Chi-restraints excluded: chain Ar residue 3 ILE Chi-restraints excluded: chain Ar residue 25 ILE Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Ar residue 95 VAL Chi-restraints excluded: chain Au residue 37 ASN Chi-restraints excluded: chain Au residue 40 LEU Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 79 SER Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 104 LEU Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 420 ILE Chi-restraints excluded: chain Av residue 524 LEU Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 25 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 494 LEU Chi-restraints excluded: chain Bb residue 77 VAL Chi-restraints excluded: chain Bb residue 185 ASP Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 25 ILE Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 79 SER Chi-restraints excluded: chain Bg residue 199 TYR Chi-restraints excluded: chain Bg residue 494 LEU Chi-restraints excluded: chain Bg residue 521 VAL Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bh residue 483 GLU Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 25 ILE Chi-restraints excluded: chain Bj residue 65 VAL Chi-restraints excluded: chain Bj residue 95 VAL Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 199 TYR Chi-restraints excluded: chain Bm residue 494 LEU Chi-restraints excluded: chain Bn residue 77 VAL Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bn residue 442 VAL Chi-restraints excluded: chain Bp residue 3 ILE Chi-restraints excluded: chain Bp residue 25 ILE Chi-restraints excluded: chain Bp residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 5.9990 chunk 304 optimal weight: 8.9990 chunk 455 optimal weight: 0.9980 chunk 229 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 484 optimal weight: 30.0000 chunk 519 optimal weight: 0.9990 chunk 376 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 599 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Af 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 2 ASN Au 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 59906 Z= 0.295 Angle : 0.748 21.056 80955 Z= 0.377 Chirality : 0.047 0.527 9828 Planarity : 0.004 0.072 10542 Dihedral : 8.537 139.605 8643 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.53 % Favored : 95.30 % Rotamer: Outliers : 1.91 % Allowed : 21.88 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 1.06 (0.09), residues: 7973 helix: 1.97 (0.08), residues: 4151 sheet: 0.13 (0.16), residues: 1155 loop : -1.08 (0.12), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISBj 7 PHE 0.014 0.001 PHEAd 66 TYR 0.051 0.002 TYRAi 203 ARG 0.005 0.000 ARGAi 36 *********************** 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 442 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 323 time to evaluate : 6.003 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: Ad 10 ASN cc_start: 0.6935 (m-40) cc_final: 0.6687 (m-40) REVERT: Ad 491 MET cc_start: 0.8257 (mtm) cc_final: 0.7789 (mtm) REVERT: Al 80 ASN cc_start: 0.4813 (p0) cc_final: 0.4557 (p0) REVERT: Ba 491 MET cc_start: 0.6994 (mtm) cc_final: 0.6548 (mtm) REVERT: Bb 10 ASN cc_start: 0.7104 (m-40) cc_final: 0.6853 (m-40) REVERT: Bh 491 MET cc_start: 0.8375 (mtm) cc_final: 0.7871 (mtm) REVERT: Bn 483 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7299 (mm-30) outliers start: 119 outliers final: 88 residues processed: 431 average time/residue: 0.5229 time to fit residues: 405.8698 Evaluate side-chains 409 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 320 time to evaluate : 5.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 89 THR Chi-restraints excluded: chain Ac residue 494 LEU Chi-restraints excluded: chain Ad residue 77 VAL Chi-restraints excluded: chain Ad residue 185 ASP Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Af residue 2 ASN Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 157 THR Chi-restraints excluded: chain Ai residue 358 SER Chi-restraints excluded: chain Ai residue 494 LEU Chi-restraints excluded: chain Aj residue 77 VAL Chi-restraints excluded: chain Aj residue 185 ASP Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 385 THR Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 420 ILE Chi-restraints excluded: chain Aj residue 524 LEU Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 25 ILE Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Ao residue 107 VAL Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 483 GLU Chi-restraints excluded: chain Ar residue 3 ILE Chi-restraints excluded: chain Ar residue 6 LEU Chi-restraints excluded: chain Ar residue 25 ILE Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Ar residue 95 VAL Chi-restraints excluded: chain Au residue 37 ASN Chi-restraints excluded: chain Au residue 40 LEU Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 79 SER Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 104 LEU Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 420 ILE Chi-restraints excluded: chain Av residue 524 LEU Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 25 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 116 LEU Chi-restraints excluded: chain Ba residue 494 LEU Chi-restraints excluded: chain Bb residue 77 VAL Chi-restraints excluded: chain Bb residue 185 ASP Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bd residue 2 ASN Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 25 ILE Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 79 SER Chi-restraints excluded: chain Bg residue 199 TYR Chi-restraints excluded: chain Bg residue 494 LEU Chi-restraints excluded: chain Bg residue 521 VAL Chi-restraints excluded: chain Bh residue 77 VAL Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 417 VAL Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bh residue 483 GLU Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 6 LEU Chi-restraints excluded: chain Bj residue 25 ILE Chi-restraints excluded: chain Bj residue 65 VAL Chi-restraints excluded: chain Bj residue 95 VAL Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 199 TYR Chi-restraints excluded: chain Bm residue 494 LEU Chi-restraints excluded: chain Bn residue 44 PHE Chi-restraints excluded: chain Bn residue 77 VAL Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bn residue 442 VAL Chi-restraints excluded: chain Bn residue 483 GLU Chi-restraints excluded: chain Bp residue 2 ASN Chi-restraints excluded: chain Bp residue 3 ILE Chi-restraints excluded: chain Bp residue 25 ILE Chi-restraints excluded: chain Bp residue 65 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 30.0000 chunk 730 optimal weight: 2.9990 chunk 666 optimal weight: 3.9990 chunk 710 optimal weight: 8.9990 chunk 427 optimal weight: 6.9990 chunk 309 optimal weight: 6.9990 chunk 557 optimal weight: 0.9980 chunk 218 optimal weight: 8.9990 chunk 641 optimal weight: 0.8980 chunk 671 optimal weight: 0.9980 chunk 707 optimal weight: 8.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ai 37 ASN Aj 72 GLN Au 37 ASN ** Bp 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 59906 Z= 0.234 Angle : 0.730 20.683 80955 Z= 0.366 Chirality : 0.045 0.509 9828 Planarity : 0.003 0.076 10542 Dihedral : 8.282 138.213 8640 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.35 % Favored : 95.56 % Rotamer: Outliers : 1.71 % Allowed : 22.27 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 1.08 (0.09), residues: 7973 helix: 2.00 (0.08), residues: 4179 sheet: 0.13 (0.16), residues: 1148 loop : -1.13 (0.11), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HISBp 7 PHE 0.011 0.001 PHEAd 66 TYR 0.022 0.002 TYRAc 203 ARG 0.017 0.000 ARGAu 36 *********************** 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 429 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 323 time to evaluate : 5.153 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: Ad 10 ASN cc_start: 0.6794 (m-40) cc_final: 0.6581 (m-40) REVERT: Ad 491 MET cc_start: 0.8211 (mtm) cc_final: 0.7729 (mtm) REVERT: Al 2 ASN cc_start: 0.3352 (OUTLIER) cc_final: 0.1950 (m110) REVERT: Al 80 ASN cc_start: 0.4712 (p0) cc_final: 0.4488 (p0) REVERT: Ap 483 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: Bb 10 ASN cc_start: 0.7059 (m-40) cc_final: 0.6836 (m-40) REVERT: Bb 483 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7032 (mm-30) REVERT: Bh 491 MET cc_start: 0.8308 (mtm) cc_final: 0.7766 (mtm) REVERT: Bn 483 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7266 (mm-30) outliers start: 106 outliers final: 85 residues processed: 419 average time/residue: 0.5151 time to fit residues: 388.3267 Evaluate side-chains 410 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 321 time to evaluate : 5.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 89 THR Chi-restraints excluded: chain Ac residue 494 LEU Chi-restraints excluded: chain Ad residue 77 VAL Chi-restraints excluded: chain Ad residue 185 ASP Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 157 THR Chi-restraints excluded: chain Ai residue 358 SER Chi-restraints excluded: chain Ai residue 494 LEU Chi-restraints excluded: chain Aj residue 77 VAL Chi-restraints excluded: chain Aj residue 185 ASP Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 420 ILE Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 25 ILE Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Al residue 95 VAL Chi-restraints excluded: chain Ao residue 107 VAL Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 483 GLU Chi-restraints excluded: chain Ar residue 3 ILE Chi-restraints excluded: chain Ar residue 6 LEU Chi-restraints excluded: chain Ar residue 25 ILE Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Ar residue 95 VAL Chi-restraints excluded: chain Au residue 37 ASN Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 79 SER Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 77 VAL Chi-restraints excluded: chain Av residue 104 LEU Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 420 ILE Chi-restraints excluded: chain Av residue 524 LEU Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 25 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 116 LEU Chi-restraints excluded: chain Ba residue 358 SER Chi-restraints excluded: chain Ba residue 494 LEU Chi-restraints excluded: chain Bb residue 77 VAL Chi-restraints excluded: chain Bb residue 185 ASP Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bb residue 483 GLU Chi-restraints excluded: chain Bd residue 2 ASN Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 25 ILE Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 79 SER Chi-restraints excluded: chain Bg residue 199 TYR Chi-restraints excluded: chain Bg residue 494 LEU Chi-restraints excluded: chain Bg residue 521 VAL Chi-restraints excluded: chain Bh residue 77 VAL Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 417 VAL Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bh residue 483 GLU Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 6 LEU Chi-restraints excluded: chain Bj residue 25 ILE Chi-restraints excluded: chain Bj residue 65 VAL Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 199 TYR Chi-restraints excluded: chain Bm residue 494 LEU Chi-restraints excluded: chain Bn residue 44 PHE Chi-restraints excluded: chain Bn residue 77 VAL Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bn residue 442 VAL Chi-restraints excluded: chain Bn residue 483 GLU Chi-restraints excluded: chain Bp residue 2 ASN Chi-restraints excluded: chain Bp residue 3 ILE Chi-restraints excluded: chain Bp residue 6 LEU Chi-restraints excluded: chain Bp residue 25 ILE Chi-restraints excluded: chain Bp residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 466 optimal weight: 9.9990 chunk 751 optimal weight: 1.9990 chunk 458 optimal weight: 5.9990 chunk 356 optimal weight: 7.9990 chunk 522 optimal weight: 10.0000 chunk 788 optimal weight: 0.9980 chunk 725 optimal weight: 6.9990 chunk 627 optimal weight: 0.9980 chunk 65 optimal weight: 0.0070 chunk 484 optimal weight: 10.0000 chunk 384 optimal weight: 5.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Au 37 ASN Bp 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 59906 Z= 0.236 Angle : 0.731 20.967 80955 Z= 0.366 Chirality : 0.045 0.494 9828 Planarity : 0.003 0.075 10542 Dihedral : 8.168 138.382 8638 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 1.54 % Allowed : 22.46 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 1.09 (0.09), residues: 7973 helix: 2.02 (0.08), residues: 4179 sheet: 0.09 (0.16), residues: 1155 loop : -1.12 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HISBj 7 PHE 0.012 0.001 PHEAd 66 TYR 0.028 0.001 TYRAo 203 ARG 0.015 0.000 ARGAu 36 ********************** 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 421 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 325 time to evaluate : 5.095 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: Ad 10 ASN cc_start: 0.6826 (m-40) cc_final: 0.6608 (m-40) REVERT: Ad 491 MET cc_start: 0.8228 (mtm) cc_final: 0.7748 (mtm) REVERT: Al 80 ASN cc_start: 0.4859 (p0) cc_final: 0.4607 (p0) REVERT: Ap 483 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: Bb 483 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7035 (mm-30) REVERT: Bh 491 MET cc_start: 0.8310 (mtm) cc_final: 0.7793 (mtm) REVERT: Bn 483 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7261 (mm-30) outliers start: 96 outliers final: 80 residues processed: 413 average time/residue: 0.5507 time to fit residues: 395.8886 Evaluate side-chains 404 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 321 time to evaluate : 5.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 89 THR Chi-restraints excluded: chain Ac residue 494 LEU Chi-restraints excluded: chain Ad residue 77 VAL Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 157 THR Chi-restraints excluded: chain Ai residue 358 SER Chi-restraints excluded: chain Ai residue 494 LEU Chi-restraints excluded: chain Aj residue 77 VAL Chi-restraints excluded: chain Aj residue 185 ASP Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 420 ILE Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 25 ILE Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Ao residue 107 VAL Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 483 GLU Chi-restraints excluded: chain Ar residue 3 ILE Chi-restraints excluded: chain Ar residue 6 LEU Chi-restraints excluded: chain Ar residue 25 ILE Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Au residue 37 ASN Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 79 SER Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 77 VAL Chi-restraints excluded: chain Av residue 104 LEU Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 420 ILE Chi-restraints excluded: chain Av residue 524 LEU Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 25 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 358 SER Chi-restraints excluded: chain Ba residue 494 LEU Chi-restraints excluded: chain Bb residue 77 VAL Chi-restraints excluded: chain Bb residue 185 ASP Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 311 LYS Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bb residue 483 GLU Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 25 ILE Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 79 SER Chi-restraints excluded: chain Bg residue 199 TYR Chi-restraints excluded: chain Bg residue 494 LEU Chi-restraints excluded: chain Bg residue 521 VAL Chi-restraints excluded: chain Bh residue 77 VAL Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 417 VAL Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bh residue 483 GLU Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 6 LEU Chi-restraints excluded: chain Bj residue 25 ILE Chi-restraints excluded: chain Bj residue 65 VAL Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 199 TYR Chi-restraints excluded: chain Bm residue 494 LEU Chi-restraints excluded: chain Bn residue 44 PHE Chi-restraints excluded: chain Bn residue 77 VAL Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bn residue 483 GLU Chi-restraints excluded: chain Bp residue 3 ILE Chi-restraints excluded: chain Bp residue 6 LEU Chi-restraints excluded: chain Bp residue 25 ILE Chi-restraints excluded: chain Bp residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 4.9990 chunk 668 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 578 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 628 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 645 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Au 37 ASN Bn 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.062665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.045326 restraints weight = 323007.181| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.24 r_work: 0.2912 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 59906 Z= 0.229 Angle : 0.724 18.871 80955 Z= 0.362 Chirality : 0.045 0.365 9828 Planarity : 0.003 0.076 10542 Dihedral : 8.010 138.144 8638 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.37 % Rotamer: Outliers : 1.46 % Allowed : 22.65 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 2.16 (0.08), residues: 4095 sheet: 0.08 (0.16), residues: 1155 loop : -1.09 (0.11), residues: 2723 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.000 HISAf 7 PHE 0.011 0.001 PHEAd 66 TYR 0.023 0.002 TYRAi 203 ARG 0.009 0.000 ARGAu 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10758.45 seconds wall clock time: 191 minutes 9.57 seconds (11469.57 seconds total)