Starting phenix.real_space_refine on Tue Oct 15 01:19:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q1i_18065/10_2024/8q1i_18065.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q1i_18065/10_2024/8q1i_18065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q1i_18065/10_2024/8q1i_18065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q1i_18065/10_2024/8q1i_18065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q1i_18065/10_2024/8q1i_18065.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q1i_18065/10_2024/8q1i_18065.cif" } resolution = 3.53 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 162 5.16 5 C 46026 2.51 5 N 12396 2.21 5 O 14478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 73062 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2719 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 337} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2848 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 350} Chain breaks: 1 Chain: "D" Number of atoms: 4380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4380 Classifications: {'peptide': 563} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 541} Chain breaks: 1 Chain: "E" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2230 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Restraints were copied for chains: G, I, L, Q, V, H, M, O, R, W, J, N, S, U, X, B, F, K, P, T Time building chain proxies: 18.87, per 1000 atoms: 0.26 Number of scatterers: 73062 At special positions: 0 Unit cell: (290.675, 273.763, 169.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 162 16.00 O 14478 8.00 N 12396 7.00 C 46026 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: 12.54 Conformation dependent library (CDL) restraints added in 6.8 seconds 18492 Ramachandran restraints generated. 9246 Oldfield, 0 Emsley, 9246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17328 Finding SS restraints... Secondary structure from input PDB file: 294 helices and 144 sheets defined 34.3% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.56 Creating SS restraints... Processing helix chain 'B' and resid 55 through 63 Processing helix chain 'B' and resid 66 through 78 Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 326 through 330 removed outlier: 4.198A pdb=" N HIS B 329 " --> pdb=" O LYS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 357 Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 409 through 424 removed outlier: 3.785A pdb=" N VAL B 413 " --> pdb=" O PRO B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 455 Processing helix chain 'B' and resid 485 through 490 Processing helix chain 'B' and resid 490 through 500 Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 521 through 540 Processing helix chain 'B' and resid 546 through 548 No H-bonds generated for 'chain 'B' and resid 546 through 548' Processing helix chain 'I' and resid 55 through 62 Processing helix chain 'I' and resid 66 through 78 Processing helix chain 'I' and resid 320 through 325 removed outlier: 3.865A pdb=" N ASP I 325 " --> pdb=" O ALA I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 328 No H-bonds generated for 'chain 'I' and resid 326 through 328' Processing helix chain 'I' and resid 341 through 359 Processing helix chain 'I' and resid 373 through 384 Processing helix chain 'I' and resid 409 through 424 removed outlier: 3.772A pdb=" N VAL I 413 " --> pdb=" O PRO I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 455 Processing helix chain 'I' and resid 485 through 490 Processing helix chain 'I' and resid 490 through 513 Processing helix chain 'I' and resid 520 through 539 removed outlier: 3.720A pdb=" N LYS I 526 " --> pdb=" O ALA I 522 " (cutoff:3.500A) Processing helix chain 'I' and resid 546 through 550 Processing helix chain 'O' and resid 55 through 63 Processing helix chain 'O' and resid 66 through 78 Processing helix chain 'O' and resid 113 through 118 Processing helix chain 'O' and resid 197 through 201 removed outlier: 4.281A pdb=" N TYR O 200 " --> pdb=" O GLY O 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 202 through 211 Processing helix chain 'O' and resid 229 through 233 Processing helix chain 'O' and resid 250 through 260 removed outlier: 3.522A pdb=" N ASP O 254 " --> pdb=" O ALA O 250 " (cutoff:3.500A) Processing helix chain 'O' and resid 320 through 325 Processing helix chain 'O' and resid 326 through 328 No H-bonds generated for 'chain 'O' and resid 326 through 328' Processing helix chain 'O' and resid 341 through 358 Processing helix chain 'O' and resid 373 through 384 Processing helix chain 'O' and resid 409 through 424 removed outlier: 3.825A pdb=" N VAL O 413 " --> pdb=" O PRO O 409 " (cutoff:3.500A) Processing helix chain 'O' and resid 445 through 455 Processing helix chain 'O' and resid 485 through 490 Processing helix chain 'O' and resid 490 through 513 Processing helix chain 'O' and resid 520 through 539 Processing helix chain 'O' and resid 546 through 550 Processing helix chain 'U' and resid 5 through 23 removed outlier: 3.764A pdb=" N LYS U 15 " --> pdb=" O LEU U 11 " (cutoff:3.500A) Proline residue: U 16 - end of helix Processing helix chain 'U' and resid 24 through 32 removed outlier: 3.657A pdb=" N ILE U 28 " --> pdb=" O ASN U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 48 Processing helix chain 'U' and resid 135 through 139 Processing helix chain 'U' and resid 154 through 158 Processing helix chain 'U' and resid 194 through 213 Processing helix chain 'U' and resid 215 through 221 Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 66 through 78 Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'A' and resid 326 through 330 removed outlier: 4.199A pdb=" N HIS A 329 " --> pdb=" O LYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 357 Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 409 through 424 removed outlier: 3.785A pdb=" N VAL A 413 " --> pdb=" O PRO A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 490 through 500 Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 521 through 540 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'C' and resid 55 through 62 Processing helix chain 'C' and resid 66 through 78 Processing helix chain 'C' and resid 320 through 325 removed outlier: 3.865A pdb=" N ASP C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 328 No H-bonds generated for 'chain 'C' and resid 326 through 328' Processing helix chain 'C' and resid 341 through 359 Processing helix chain 'C' and resid 373 through 384 Processing helix chain 'C' and resid 409 through 424 removed outlier: 3.771A pdb=" N VAL C 413 " --> pdb=" O PRO C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 455 Processing helix chain 'C' and resid 485 through 490 Processing helix chain 'C' and resid 490 through 513 Processing helix chain 'C' and resid 520 through 539 removed outlier: 3.720A pdb=" N LYS C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'D' and resid 55 through 63 Processing helix chain 'D' and resid 66 through 78 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 197 through 201 removed outlier: 4.282A pdb=" N TYR D 200 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 211 Processing helix chain 'D' and resid 229 through 233 Processing helix chain 'D' and resid 250 through 260 removed outlier: 3.522A pdb=" N ASP D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 325 Processing helix chain 'D' and resid 326 through 328 No H-bonds generated for 'chain 'D' and resid 326 through 328' Processing helix chain 'D' and resid 341 through 358 Processing helix chain 'D' and resid 373 through 384 Processing helix chain 'D' and resid 409 through 424 removed outlier: 3.825A pdb=" N VAL D 413 " --> pdb=" O PRO D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 455 Processing helix chain 'D' and resid 485 through 490 Processing helix chain 'D' and resid 490 through 513 Processing helix chain 'D' and resid 520 through 539 Processing helix chain 'D' and resid 546 through 550 Processing helix chain 'E' and resid 5 through 23 removed outlier: 3.763A pdb=" N LYS E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) Proline residue: E 16 - end of helix Processing helix chain 'E' and resid 24 through 32 removed outlier: 3.657A pdb=" N ILE E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 48 Processing helix chain 'E' and resid 135 through 139 Processing helix chain 'E' and resid 154 through 158 Processing helix chain 'E' and resid 194 through 213 Processing helix chain 'E' and resid 215 through 221 Processing helix chain 'F' and resid 55 through 63 Processing helix chain 'F' and resid 66 through 78 Processing helix chain 'F' and resid 320 through 325 Processing helix chain 'F' and resid 326 through 330 removed outlier: 4.198A pdb=" N HIS F 329 " --> pdb=" O LYS F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 357 Processing helix chain 'F' and resid 373 through 384 Processing helix chain 'F' and resid 409 through 424 removed outlier: 3.785A pdb=" N VAL F 413 " --> pdb=" O PRO F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 455 Processing helix chain 'F' and resid 485 through 490 Processing helix chain 'F' and resid 490 through 500 Processing helix chain 'F' and resid 513 through 517 Processing helix chain 'F' and resid 521 through 540 Processing helix chain 'F' and resid 546 through 548 No H-bonds generated for 'chain 'F' and resid 546 through 548' Processing helix chain 'G' and resid 55 through 62 Processing helix chain 'G' and resid 66 through 78 Processing helix chain 'G' and resid 320 through 325 removed outlier: 3.865A pdb=" N ASP G 325 " --> pdb=" O ALA G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 328 No H-bonds generated for 'chain 'G' and resid 326 through 328' Processing helix chain 'G' and resid 341 through 359 Processing helix chain 'G' and resid 373 through 384 Processing helix chain 'G' and resid 409 through 424 removed outlier: 3.771A pdb=" N VAL G 413 " --> pdb=" O PRO G 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 455 Processing helix chain 'G' and resid 485 through 490 Processing helix chain 'G' and resid 490 through 513 Processing helix chain 'G' and resid 520 through 539 removed outlier: 3.720A pdb=" N LYS G 526 " --> pdb=" O ALA G 522 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 550 Processing helix chain 'H' and resid 55 through 63 Processing helix chain 'H' and resid 66 through 78 Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 197 through 201 removed outlier: 4.281A pdb=" N TYR H 200 " --> pdb=" O GLY H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 211 Processing helix chain 'H' and resid 229 through 233 Processing helix chain 'H' and resid 250 through 260 removed outlier: 3.521A pdb=" N ASP H 254 " --> pdb=" O ALA H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 325 Processing helix chain 'H' and resid 326 through 328 No H-bonds generated for 'chain 'H' and resid 326 through 328' Processing helix chain 'H' and resid 341 through 358 Processing helix chain 'H' and resid 373 through 384 Processing helix chain 'H' and resid 409 through 424 removed outlier: 3.826A pdb=" N VAL H 413 " --> pdb=" O PRO H 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 445 through 455 Processing helix chain 'H' and resid 485 through 490 Processing helix chain 'H' and resid 490 through 513 Processing helix chain 'H' and resid 520 through 539 Processing helix chain 'H' and resid 546 through 550 Processing helix chain 'J' and resid 5 through 23 removed outlier: 3.763A pdb=" N LYS J 15 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Proline residue: J 16 - end of helix Processing helix chain 'J' and resid 24 through 32 removed outlier: 3.657A pdb=" N ILE J 28 " --> pdb=" O ASN J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 48 Processing helix chain 'J' and resid 135 through 139 Processing helix chain 'J' and resid 154 through 158 Processing helix chain 'J' and resid 194 through 213 Processing helix chain 'J' and resid 215 through 221 Processing helix chain 'K' and resid 55 through 63 Processing helix chain 'K' and resid 66 through 78 Processing helix chain 'K' and resid 320 through 325 Processing helix chain 'K' and resid 326 through 330 removed outlier: 4.198A pdb=" N HIS K 329 " --> pdb=" O LYS K 326 " (cutoff:3.500A) Processing helix chain 'K' and resid 341 through 357 Processing helix chain 'K' and resid 373 through 384 Processing helix chain 'K' and resid 409 through 424 removed outlier: 3.785A pdb=" N VAL K 413 " --> pdb=" O PRO K 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 445 through 455 Processing helix chain 'K' and resid 485 through 490 Processing helix chain 'K' and resid 490 through 500 Processing helix chain 'K' and resid 513 through 517 Processing helix chain 'K' and resid 521 through 540 Processing helix chain 'K' and resid 546 through 548 No H-bonds generated for 'chain 'K' and resid 546 through 548' Processing helix chain 'L' and resid 55 through 62 Processing helix chain 'L' and resid 66 through 78 Processing helix chain 'L' and resid 320 through 325 removed outlier: 3.865A pdb=" N ASP L 325 " --> pdb=" O ALA L 321 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 328 No H-bonds generated for 'chain 'L' and resid 326 through 328' Processing helix chain 'L' and resid 341 through 359 Processing helix chain 'L' and resid 373 through 384 Processing helix chain 'L' and resid 409 through 424 removed outlier: 3.772A pdb=" N VAL L 413 " --> pdb=" O PRO L 409 " (cutoff:3.500A) Processing helix chain 'L' and resid 445 through 455 Processing helix chain 'L' and resid 485 through 490 Processing helix chain 'L' and resid 490 through 513 Processing helix chain 'L' and resid 520 through 539 removed outlier: 3.720A pdb=" N LYS L 526 " --> pdb=" O ALA L 522 " (cutoff:3.500A) Processing helix chain 'L' and resid 546 through 550 Processing helix chain 'M' and resid 55 through 63 Processing helix chain 'M' and resid 66 through 78 Processing helix chain 'M' and resid 113 through 118 Processing helix chain 'M' and resid 197 through 201 removed outlier: 4.281A pdb=" N TYR M 200 " --> pdb=" O GLY M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 202 through 211 Processing helix chain 'M' and resid 229 through 233 Processing helix chain 'M' and resid 250 through 260 removed outlier: 3.522A pdb=" N ASP M 254 " --> pdb=" O ALA M 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 325 Processing helix chain 'M' and resid 326 through 328 No H-bonds generated for 'chain 'M' and resid 326 through 328' Processing helix chain 'M' and resid 341 through 358 Processing helix chain 'M' and resid 373 through 384 Processing helix chain 'M' and resid 409 through 424 removed outlier: 3.825A pdb=" N VAL M 413 " --> pdb=" O PRO M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 445 through 455 Processing helix chain 'M' and resid 485 through 490 Processing helix chain 'M' and resid 490 through 513 Processing helix chain 'M' and resid 520 through 539 Processing helix chain 'M' and resid 546 through 550 Processing helix chain 'N' and resid 5 through 23 removed outlier: 3.764A pdb=" N LYS N 15 " --> pdb=" O LEU N 11 " (cutoff:3.500A) Proline residue: N 16 - end of helix Processing helix chain 'N' and resid 24 through 32 removed outlier: 3.657A pdb=" N ILE N 28 " --> pdb=" O ASN N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 48 Processing helix chain 'N' and resid 135 through 139 Processing helix chain 'N' and resid 154 through 158 Processing helix chain 'N' and resid 194 through 213 Processing helix chain 'N' and resid 215 through 221 Processing helix chain 'P' and resid 55 through 63 Processing helix chain 'P' and resid 66 through 78 Processing helix chain 'P' and resid 320 through 325 Processing helix chain 'P' and resid 326 through 330 removed outlier: 4.199A pdb=" N HIS P 329 " --> pdb=" O LYS P 326 " (cutoff:3.500A) Processing helix chain 'P' and resid 341 through 357 Processing helix chain 'P' and resid 373 through 384 Processing helix chain 'P' and resid 409 through 424 removed outlier: 3.785A pdb=" N VAL P 413 " --> pdb=" O PRO P 409 " (cutoff:3.500A) Processing helix chain 'P' and resid 445 through 455 Processing helix chain 'P' and resid 485 through 490 Processing helix chain 'P' and resid 490 through 500 Processing helix chain 'P' and resid 513 through 517 Processing helix chain 'P' and resid 521 through 540 Processing helix chain 'P' and resid 546 through 548 No H-bonds generated for 'chain 'P' and resid 546 through 548' Processing helix chain 'Q' and resid 55 through 62 Processing helix chain 'Q' and resid 66 through 78 Processing helix chain 'Q' and resid 320 through 325 removed outlier: 3.865A pdb=" N ASP Q 325 " --> pdb=" O ALA Q 321 " (cutoff:3.500A) Processing helix chain 'Q' and resid 326 through 328 No H-bonds generated for 'chain 'Q' and resid 326 through 328' Processing helix chain 'Q' and resid 341 through 359 Processing helix chain 'Q' and resid 373 through 384 Processing helix chain 'Q' and resid 409 through 424 removed outlier: 3.771A pdb=" N VAL Q 413 " --> pdb=" O PRO Q 409 " (cutoff:3.500A) Processing helix chain 'Q' and resid 445 through 455 Processing helix chain 'Q' and resid 485 through 490 Processing helix chain 'Q' and resid 490 through 513 Processing helix chain 'Q' and resid 520 through 539 removed outlier: 3.720A pdb=" N LYS Q 526 " --> pdb=" O ALA Q 522 " (cutoff:3.500A) Processing helix chain 'Q' and resid 546 through 550 Processing helix chain 'R' and resid 55 through 63 Processing helix chain 'R' and resid 66 through 78 Processing helix chain 'R' and resid 113 through 118 Processing helix chain 'R' and resid 197 through 201 removed outlier: 4.282A pdb=" N TYR R 200 " --> pdb=" O GLY R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 211 Processing helix chain 'R' and resid 229 through 233 Processing helix chain 'R' and resid 250 through 260 removed outlier: 3.522A pdb=" N ASP R 254 " --> pdb=" O ALA R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 325 Processing helix chain 'R' and resid 326 through 328 No H-bonds generated for 'chain 'R' and resid 326 through 328' Processing helix chain 'R' and resid 341 through 358 Processing helix chain 'R' and resid 373 through 384 Processing helix chain 'R' and resid 409 through 424 removed outlier: 3.825A pdb=" N VAL R 413 " --> pdb=" O PRO R 409 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 455 Processing helix chain 'R' and resid 485 through 490 Processing helix chain 'R' and resid 490 through 513 Processing helix chain 'R' and resid 520 through 539 Processing helix chain 'R' and resid 546 through 550 Processing helix chain 'S' and resid 5 through 23 removed outlier: 3.763A pdb=" N LYS S 15 " --> pdb=" O LEU S 11 " (cutoff:3.500A) Proline residue: S 16 - end of helix Processing helix chain 'S' and resid 24 through 32 removed outlier: 3.657A pdb=" N ILE S 28 " --> pdb=" O ASN S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 48 Processing helix chain 'S' and resid 135 through 139 Processing helix chain 'S' and resid 154 through 158 Processing helix chain 'S' and resid 194 through 213 Processing helix chain 'S' and resid 215 through 221 Processing helix chain 'T' and resid 55 through 63 Processing helix chain 'T' and resid 66 through 78 Processing helix chain 'T' and resid 320 through 325 Processing helix chain 'T' and resid 326 through 330 removed outlier: 4.198A pdb=" N HIS T 329 " --> pdb=" O LYS T 326 " (cutoff:3.500A) Processing helix chain 'T' and resid 341 through 357 Processing helix chain 'T' and resid 373 through 384 Processing helix chain 'T' and resid 409 through 424 removed outlier: 3.785A pdb=" N VAL T 413 " --> pdb=" O PRO T 409 " (cutoff:3.500A) Processing helix chain 'T' and resid 445 through 455 Processing helix chain 'T' and resid 485 through 490 Processing helix chain 'T' and resid 490 through 500 Processing helix chain 'T' and resid 513 through 517 Processing helix chain 'T' and resid 521 through 540 Processing helix chain 'T' and resid 546 through 548 No H-bonds generated for 'chain 'T' and resid 546 through 548' Processing helix chain 'V' and resid 55 through 62 Processing helix chain 'V' and resid 66 through 78 Processing helix chain 'V' and resid 320 through 325 removed outlier: 3.865A pdb=" N ASP V 325 " --> pdb=" O ALA V 321 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 328 No H-bonds generated for 'chain 'V' and resid 326 through 328' Processing helix chain 'V' and resid 341 through 359 Processing helix chain 'V' and resid 373 through 384 Processing helix chain 'V' and resid 409 through 424 removed outlier: 3.771A pdb=" N VAL V 413 " --> pdb=" O PRO V 409 " (cutoff:3.500A) Processing helix chain 'V' and resid 445 through 455 Processing helix chain 'V' and resid 485 through 490 Processing helix chain 'V' and resid 490 through 513 Processing helix chain 'V' and resid 520 through 539 removed outlier: 3.720A pdb=" N LYS V 526 " --> pdb=" O ALA V 522 " (cutoff:3.500A) Processing helix chain 'V' and resid 546 through 550 Processing helix chain 'W' and resid 55 through 63 Processing helix chain 'W' and resid 66 through 78 Processing helix chain 'W' and resid 113 through 118 Processing helix chain 'W' and resid 197 through 201 removed outlier: 4.281A pdb=" N TYR W 200 " --> pdb=" O GLY W 197 " (cutoff:3.500A) Processing helix chain 'W' and resid 202 through 211 Processing helix chain 'W' and resid 229 through 233 Processing helix chain 'W' and resid 250 through 260 removed outlier: 3.521A pdb=" N ASP W 254 " --> pdb=" O ALA W 250 " (cutoff:3.500A) Processing helix chain 'W' and resid 320 through 325 Processing helix chain 'W' and resid 326 through 328 No H-bonds generated for 'chain 'W' and resid 326 through 328' Processing helix chain 'W' and resid 341 through 358 Processing helix chain 'W' and resid 373 through 384 Processing helix chain 'W' and resid 409 through 424 removed outlier: 3.826A pdb=" N VAL W 413 " --> pdb=" O PRO W 409 " (cutoff:3.500A) Processing helix chain 'W' and resid 445 through 455 Processing helix chain 'W' and resid 485 through 490 Processing helix chain 'W' and resid 490 through 513 Processing helix chain 'W' and resid 520 through 539 Processing helix chain 'W' and resid 546 through 550 Processing helix chain 'X' and resid 5 through 23 removed outlier: 3.763A pdb=" N LYS X 15 " --> pdb=" O LEU X 11 " (cutoff:3.500A) Proline residue: X 16 - end of helix Processing helix chain 'X' and resid 24 through 32 removed outlier: 3.657A pdb=" N ILE X 28 " --> pdb=" O ASN X 24 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 48 Processing helix chain 'X' and resid 135 through 139 Processing helix chain 'X' and resid 154 through 158 Processing helix chain 'X' and resid 194 through 213 Processing helix chain 'X' and resid 215 through 221 Processing sheet with id=1, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=2, first strand: chain 'B' and resid 50 through 53 removed outlier: 6.344A pdb=" N PHE B 36 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N MET B 90 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU B 38 " --> pdb=" O MET B 90 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 39 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE B 335 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N GLY B 367 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ILE B 458 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU B 391 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 405 through 408 removed outlier: 3.659A pdb=" N GLY B 396 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 439 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 434 through 435 removed outlier: 4.488A pdb=" N PHE B 471 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 470 " --> pdb=" O VAL B 463 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 558 through 563 Processing sheet with id=6, first strand: chain 'B' and resid 573 through 580 removed outlier: 6.511A pdb=" N LYS B 573 " --> pdb=" O ALA I 559 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE I 561 " --> pdb=" O LYS B 573 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER B 575 " --> pdb=" O ILE I 561 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET I 563 " --> pdb=" O SER B 575 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER B 577 " --> pdb=" O MET I 563 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL I 565 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 579 " --> pdb=" O VAL I 565 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=8, first strand: chain 'I' and resid 51 through 53 removed outlier: 6.307A pdb=" N PHE I 36 " --> pdb=" O LEU I 88 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N MET I 90 " --> pdb=" O PHE I 36 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU I 38 " --> pdb=" O MET I 90 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY I 367 " --> pdb=" O PRO I 337 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ILE I 458 " --> pdb=" O VAL I 389 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU I 391 " --> pdb=" O ILE I 458 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'I' and resid 43 through 44 removed outlier: 3.783A pdb=" N GLU I 43 " --> pdb=" O ARG I 64 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'I' and resid 404 through 407 removed outlier: 3.585A pdb=" N ARG I 404 " --> pdb=" O MET I 400 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'I' and resid 434 through 435 removed outlier: 4.224A pdb=" N PHE I 471 " --> pdb=" O LEU I 435 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE I 470 " --> pdb=" O VAL I 463 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=13, first strand: chain 'O' and resid 50 through 53 removed outlier: 3.564A pdb=" N ILE O 39 " --> pdb=" O VAL O 336 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE O 335 " --> pdb=" O ILE O 365 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLY O 367 " --> pdb=" O ILE O 335 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'O' and resid 95 through 96 Processing sheet with id=15, first strand: chain 'O' and resid 99 through 102 Processing sheet with id=16, first strand: chain 'O' and resid 143 through 150 removed outlier: 3.681A pdb=" N ASN O 149 " --> pdb=" O LEU O 132 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU O 132 " --> pdb=" O ASN O 149 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU O 123 " --> pdb=" O GLU O 304 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU O 304 " --> pdb=" O LEU O 123 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'O' and resid 216 through 220 removed outlier: 3.780A pdb=" N PHE O 154 " --> pdb=" O VAL O 248 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'O' and resid 165 through 171 removed outlier: 4.055A pdb=" N ARG O 180 " --> pdb=" O GLU O 170 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS O 191 " --> pdb=" O LEU O 183 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL O 185 " --> pdb=" O GLU O 189 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU O 189 " --> pdb=" O VAL O 185 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'O' and resid 405 through 408 removed outlier: 3.606A pdb=" N GLY O 396 " --> pdb=" O VAL O 408 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER O 439 " --> pdb=" O THR O 397 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'O' and resid 434 through 435 removed outlier: 4.562A pdb=" N PHE O 471 " --> pdb=" O LEU O 435 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE O 470 " --> pdb=" O VAL O 463 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'O' and resid 551 through 555 Processing sheet with id=22, first strand: chain 'U' and resid 57 through 59 removed outlier: 6.566A pdb=" N THR U 57 " --> pdb=" O TYR U 73 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE U 75 " --> pdb=" O THR U 57 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY U 59 " --> pdb=" O ILE U 75 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LEU U 77 " --> pdb=" O GLY U 59 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR U 73 " --> pdb=" O LEU U 191 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU U 191 " --> pdb=" O TYR U 73 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE U 75 " --> pdb=" O VAL U 189 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL U 189 " --> pdb=" O ILE U 75 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU U 77 " --> pdb=" O THR U 187 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR U 187 " --> pdb=" O LEU U 77 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN U 79 " --> pdb=" O GLN U 185 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR U 181 " --> pdb=" O THR U 83 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN U 85 " --> pdb=" O GLY U 179 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N GLY U 179 " --> pdb=" O ASN U 85 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N LEU U 87 " --> pdb=" O VAL U 177 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N VAL U 177 " --> pdb=" O LEU U 87 " (cutoff:3.500A) removed outlier: 12.969A pdb=" N SER U 89 " --> pdb=" O GLY U 175 " (cutoff:3.500A) removed outlier: 12.828A pdb=" N GLY U 175 " --> pdb=" O SER U 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR U 253 " --> pdb=" O LEU U 224 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU U 224 " --> pdb=" O THR U 253 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'U' and resid 123 through 129 removed outlier: 6.664A pdb=" N THR U 167 " --> pdb=" O GLY U 124 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LEU U 126 " --> pdb=" O ILE U 165 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE U 165 " --> pdb=" O LEU U 126 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS U 128 " --> pdb=" O ASN U 163 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN U 163 " --> pdb=" O LYS U 128 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP U 100 " --> pdb=" O GLU U 168 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS U 170 " --> pdb=" O THR U 98 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR U 98 " --> pdb=" O LYS U 170 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR U 107 " --> pdb=" O THR U 118 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR U 118 " --> pdb=" O THR U 107 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'U' and resid 233 through 236 removed outlier: 6.703A pdb=" N ILE U 243 " --> pdb=" O ILE U 235 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=26, first strand: chain 'A' and resid 50 through 53 removed outlier: 6.344A pdb=" N PHE A 36 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N MET A 90 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 38 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 39 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 335 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N GLY A 367 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ILE A 458 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A 391 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'A' and resid 405 through 408 removed outlier: 3.658A pdb=" N GLY A 396 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 439 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'A' and resid 434 through 435 removed outlier: 4.488A pdb=" N PHE A 471 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE A 470 " --> pdb=" O VAL A 463 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'A' and resid 558 through 563 Processing sheet with id=30, first strand: chain 'A' and resid 573 through 580 removed outlier: 6.512A pdb=" N LYS A 573 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE C 561 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER A 575 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N MET C 563 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER A 577 " --> pdb=" O MET C 563 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL C 565 " --> pdb=" O SER A 577 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 579 " --> pdb=" O VAL C 565 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=32, first strand: chain 'C' and resid 51 through 53 removed outlier: 6.308A pdb=" N PHE C 36 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N MET C 90 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU C 38 " --> pdb=" O MET C 90 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY C 367 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ILE C 458 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU C 391 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.783A pdb=" N GLU C 43 " --> pdb=" O ARG C 64 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'C' and resid 404 through 407 removed outlier: 3.585A pdb=" N ARG C 404 " --> pdb=" O MET C 400 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'C' and resid 434 through 435 removed outlier: 4.224A pdb=" N PHE C 471 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C 470 " --> pdb=" O VAL C 463 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=37, first strand: chain 'D' and resid 50 through 53 removed outlier: 3.563A pdb=" N ILE D 39 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE D 335 " --> pdb=" O ILE D 365 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLY D 367 " --> pdb=" O ILE D 335 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'D' and resid 95 through 96 Processing sheet with id=39, first strand: chain 'D' and resid 99 through 102 Processing sheet with id=40, first strand: chain 'D' and resid 143 through 150 removed outlier: 3.681A pdb=" N ASN D 149 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU D 132 " --> pdb=" O ASN D 149 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU D 123 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU D 304 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'D' and resid 216 through 220 removed outlier: 3.781A pdb=" N PHE D 154 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'D' and resid 165 through 171 removed outlier: 4.055A pdb=" N ARG D 180 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS D 191 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL D 185 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'D' and resid 405 through 408 removed outlier: 3.605A pdb=" N GLY D 396 " --> pdb=" O VAL D 408 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER D 439 " --> pdb=" O THR D 397 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'D' and resid 434 through 435 removed outlier: 4.562A pdb=" N PHE D 471 " --> pdb=" O LEU D 435 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 470 " --> pdb=" O VAL D 463 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'D' and resid 551 through 555 Processing sheet with id=46, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.566A pdb=" N THR E 57 " --> pdb=" O TYR E 73 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE E 75 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY E 59 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LEU E 77 " --> pdb=" O GLY E 59 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR E 73 " --> pdb=" O LEU E 191 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU E 191 " --> pdb=" O TYR E 73 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE E 75 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL E 189 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU E 77 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR E 187 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN E 79 " --> pdb=" O GLN E 185 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR E 181 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN E 85 " --> pdb=" O GLY E 179 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N GLY E 179 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N LEU E 87 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N VAL E 177 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 12.969A pdb=" N SER E 89 " --> pdb=" O GLY E 175 " (cutoff:3.500A) removed outlier: 12.828A pdb=" N GLY E 175 " --> pdb=" O SER E 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR E 253 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU E 224 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'E' and resid 123 through 129 removed outlier: 6.664A pdb=" N THR E 167 " --> pdb=" O GLY E 124 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LEU E 126 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE E 165 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS E 128 " --> pdb=" O ASN E 163 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN E 163 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASP E 100 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS E 170 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR E 98 " --> pdb=" O LYS E 170 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N THR E 107 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR E 118 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'E' and resid 233 through 236 removed outlier: 6.702A pdb=" N ILE E 243 " --> pdb=" O ILE E 235 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=50, first strand: chain 'F' and resid 50 through 53 removed outlier: 6.344A pdb=" N PHE F 36 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N MET F 90 " --> pdb=" O PHE F 36 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU F 38 " --> pdb=" O MET F 90 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE F 39 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE F 335 " --> pdb=" O ILE F 365 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N GLY F 367 " --> pdb=" O ILE F 335 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ILE F 458 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU F 391 " --> pdb=" O ILE F 458 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'F' and resid 405 through 408 removed outlier: 3.659A pdb=" N GLY F 396 " --> pdb=" O VAL F 408 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER F 439 " --> pdb=" O THR F 397 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'F' and resid 434 through 435 removed outlier: 4.488A pdb=" N PHE F 471 " --> pdb=" O LEU F 435 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE F 470 " --> pdb=" O VAL F 463 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'F' and resid 558 through 563 Processing sheet with id=54, first strand: chain 'F' and resid 573 through 580 removed outlier: 6.511A pdb=" N LYS F 573 " --> pdb=" O ALA G 559 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE G 561 " --> pdb=" O LYS F 573 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER F 575 " --> pdb=" O ILE G 561 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET G 563 " --> pdb=" O SER F 575 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER F 577 " --> pdb=" O MET G 563 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL G 565 " --> pdb=" O SER F 577 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL F 579 " --> pdb=" O VAL G 565 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=56, first strand: chain 'G' and resid 51 through 53 removed outlier: 6.308A pdb=" N PHE G 36 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N MET G 90 " --> pdb=" O PHE G 36 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU G 38 " --> pdb=" O MET G 90 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY G 367 " --> pdb=" O PRO G 337 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ILE G 458 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU G 391 " --> pdb=" O ILE G 458 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'G' and resid 43 through 44 removed outlier: 3.783A pdb=" N GLU G 43 " --> pdb=" O ARG G 64 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'G' and resid 404 through 407 removed outlier: 3.585A pdb=" N ARG G 404 " --> pdb=" O MET G 400 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'G' and resid 434 through 435 removed outlier: 4.224A pdb=" N PHE G 471 " --> pdb=" O LEU G 435 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE G 470 " --> pdb=" O VAL G 463 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=61, first strand: chain 'H' and resid 50 through 53 removed outlier: 3.564A pdb=" N ILE H 39 " --> pdb=" O VAL H 336 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE H 335 " --> pdb=" O ILE H 365 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N GLY H 367 " --> pdb=" O ILE H 335 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'H' and resid 95 through 96 Processing sheet with id=63, first strand: chain 'H' and resid 99 through 102 Processing sheet with id=64, first strand: chain 'H' and resid 143 through 150 removed outlier: 3.681A pdb=" N ASN H 149 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU H 132 " --> pdb=" O ASN H 149 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU H 123 " --> pdb=" O GLU H 304 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU H 304 " --> pdb=" O LEU H 123 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'H' and resid 216 through 220 removed outlier: 3.781A pdb=" N PHE H 154 " --> pdb=" O VAL H 248 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'H' and resid 165 through 171 removed outlier: 4.055A pdb=" N ARG H 180 " --> pdb=" O GLU H 170 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS H 191 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL H 185 " --> pdb=" O GLU H 189 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU H 189 " --> pdb=" O VAL H 185 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'H' and resid 405 through 408 removed outlier: 3.605A pdb=" N GLY H 396 " --> pdb=" O VAL H 408 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER H 439 " --> pdb=" O THR H 397 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'H' and resid 434 through 435 removed outlier: 4.562A pdb=" N PHE H 471 " --> pdb=" O LEU H 435 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE H 470 " --> pdb=" O VAL H 463 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'H' and resid 551 through 555 Processing sheet with id=70, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.566A pdb=" N THR J 57 " --> pdb=" O TYR J 73 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE J 75 " --> pdb=" O THR J 57 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY J 59 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LEU J 77 " --> pdb=" O GLY J 59 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TYR J 73 " --> pdb=" O LEU J 191 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU J 191 " --> pdb=" O TYR J 73 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE J 75 " --> pdb=" O VAL J 189 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL J 189 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU J 77 " --> pdb=" O THR J 187 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR J 187 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN J 79 " --> pdb=" O GLN J 185 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR J 181 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN J 85 " --> pdb=" O GLY J 179 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N GLY J 179 " --> pdb=" O ASN J 85 " (cutoff:3.500A) removed outlier: 9.429A pdb=" N LEU J 87 " --> pdb=" O VAL J 177 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N VAL J 177 " --> pdb=" O LEU J 87 " (cutoff:3.500A) removed outlier: 12.969A pdb=" N SER J 89 " --> pdb=" O GLY J 175 " (cutoff:3.500A) removed outlier: 12.828A pdb=" N GLY J 175 " --> pdb=" O SER J 89 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR J 253 " --> pdb=" O LEU J 224 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU J 224 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'J' and resid 123 through 129 removed outlier: 6.664A pdb=" N THR J 167 " --> pdb=" O GLY J 124 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LEU J 126 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE J 165 " --> pdb=" O LEU J 126 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS J 128 " --> pdb=" O ASN J 163 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN J 163 " --> pdb=" O LYS J 128 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASP J 100 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS J 170 " --> pdb=" O THR J 98 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR J 98 " --> pdb=" O LYS J 170 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR J 107 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR J 118 " --> pdb=" O THR J 107 " (cutoff:3.500A) Processing sheet with id=72, first strand: chain 'J' and resid 233 through 236 removed outlier: 6.703A pdb=" N ILE J 243 " --> pdb=" O ILE J 235 " (cutoff:3.500A) Processing sheet with id=73, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=74, first strand: chain 'K' and resid 50 through 53 removed outlier: 6.344A pdb=" N PHE K 36 " --> pdb=" O LEU K 88 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N MET K 90 " --> pdb=" O PHE K 36 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU K 38 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE K 39 " --> pdb=" O VAL K 336 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE K 335 " --> pdb=" O ILE K 365 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N GLY K 367 " --> pdb=" O ILE K 335 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ILE K 458 " --> pdb=" O VAL K 389 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU K 391 " --> pdb=" O ILE K 458 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain 'K' and resid 405 through 408 removed outlier: 3.659A pdb=" N GLY K 396 " --> pdb=" O VAL K 408 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER K 439 " --> pdb=" O THR K 397 " (cutoff:3.500A) Processing sheet with id=76, first strand: chain 'K' and resid 434 through 435 removed outlier: 4.488A pdb=" N PHE K 471 " --> pdb=" O LEU K 435 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE K 470 " --> pdb=" O VAL K 463 " (cutoff:3.500A) Processing sheet with id=77, first strand: chain 'K' and resid 558 through 563 Processing sheet with id=78, first strand: chain 'K' and resid 573 through 580 removed outlier: 6.511A pdb=" N LYS K 573 " --> pdb=" O ALA L 559 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE L 561 " --> pdb=" O LYS K 573 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER K 575 " --> pdb=" O ILE L 561 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET L 563 " --> pdb=" O SER K 575 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER K 577 " --> pdb=" O MET L 563 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL L 565 " --> pdb=" O SER K 577 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL K 579 " --> pdb=" O VAL L 565 " (cutoff:3.500A) Processing sheet with id=79, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=80, first strand: chain 'L' and resid 51 through 53 removed outlier: 6.307A pdb=" N PHE L 36 " --> pdb=" O LEU L 88 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N MET L 90 " --> pdb=" O PHE L 36 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU L 38 " --> pdb=" O MET L 90 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY L 367 " --> pdb=" O PRO L 337 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ILE L 458 " --> pdb=" O VAL L 389 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU L 391 " --> pdb=" O ILE L 458 " (cutoff:3.500A) Processing sheet with id=81, first strand: chain 'L' and resid 43 through 44 removed outlier: 3.783A pdb=" N GLU L 43 " --> pdb=" O ARG L 64 " (cutoff:3.500A) Processing sheet with id=82, first strand: chain 'L' and resid 404 through 407 removed outlier: 3.585A pdb=" N ARG L 404 " --> pdb=" O MET L 400 " (cutoff:3.500A) Processing sheet with id=83, first strand: chain 'L' and resid 434 through 435 removed outlier: 4.224A pdb=" N PHE L 471 " --> pdb=" O LEU L 435 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE L 470 " --> pdb=" O VAL L 463 " (cutoff:3.500A) Processing sheet with id=84, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=85, first strand: chain 'M' and resid 50 through 53 removed outlier: 3.564A pdb=" N ILE M 39 " --> pdb=" O VAL M 336 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE M 335 " --> pdb=" O ILE M 365 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLY M 367 " --> pdb=" O ILE M 335 " (cutoff:3.500A) Processing sheet with id=86, first strand: chain 'M' and resid 95 through 96 Processing sheet with id=87, first strand: chain 'M' and resid 99 through 102 Processing sheet with id=88, first strand: chain 'M' and resid 143 through 150 removed outlier: 3.681A pdb=" N ASN M 149 " --> pdb=" O LEU M 132 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU M 132 " --> pdb=" O ASN M 149 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU M 123 " --> pdb=" O GLU M 304 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU M 304 " --> pdb=" O LEU M 123 " (cutoff:3.500A) Processing sheet with id=89, first strand: chain 'M' and resid 216 through 220 removed outlier: 3.780A pdb=" N PHE M 154 " --> pdb=" O VAL M 248 " (cutoff:3.500A) Processing sheet with id=90, first strand: chain 'M' and resid 165 through 171 removed outlier: 4.055A pdb=" N ARG M 180 " --> pdb=" O GLU M 170 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS M 191 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL M 185 " --> pdb=" O GLU M 189 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU M 189 " --> pdb=" O VAL M 185 " (cutoff:3.500A) Processing sheet with id=91, first strand: chain 'M' and resid 405 through 408 removed outlier: 3.606A pdb=" N GLY M 396 " --> pdb=" O VAL M 408 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER M 439 " --> pdb=" O THR M 397 " (cutoff:3.500A) Processing sheet with id=92, first strand: chain 'M' and resid 434 through 435 removed outlier: 4.562A pdb=" N PHE M 471 " --> pdb=" O LEU M 435 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE M 470 " --> pdb=" O VAL M 463 " (cutoff:3.500A) Processing sheet with id=93, first strand: chain 'M' and resid 551 through 555 Processing sheet with id=94, first strand: chain 'N' and resid 57 through 59 removed outlier: 6.566A pdb=" N THR N 57 " --> pdb=" O TYR N 73 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE N 75 " --> pdb=" O THR N 57 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY N 59 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LEU N 77 " --> pdb=" O GLY N 59 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR N 73 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU N 191 " --> pdb=" O TYR N 73 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE N 75 " --> pdb=" O VAL N 189 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL N 189 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU N 77 " --> pdb=" O THR N 187 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR N 187 " --> pdb=" O LEU N 77 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN N 79 " --> pdb=" O GLN N 185 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR N 181 " --> pdb=" O THR N 83 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN N 85 " --> pdb=" O GLY N 179 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N GLY N 179 " --> pdb=" O ASN N 85 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N LEU N 87 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N VAL N 177 " --> pdb=" O LEU N 87 " (cutoff:3.500A) removed outlier: 12.969A pdb=" N SER N 89 " --> pdb=" O GLY N 175 " (cutoff:3.500A) removed outlier: 12.828A pdb=" N GLY N 175 " --> pdb=" O SER N 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR N 253 " --> pdb=" O LEU N 224 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU N 224 " --> pdb=" O THR N 253 " (cutoff:3.500A) Processing sheet with id=95, first strand: chain 'N' and resid 123 through 129 removed outlier: 6.664A pdb=" N THR N 167 " --> pdb=" O GLY N 124 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LEU N 126 " --> pdb=" O ILE N 165 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE N 165 " --> pdb=" O LEU N 126 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS N 128 " --> pdb=" O ASN N 163 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN N 163 " --> pdb=" O LYS N 128 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP N 100 " --> pdb=" O GLU N 168 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS N 170 " --> pdb=" O THR N 98 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR N 98 " --> pdb=" O LYS N 170 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR N 107 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR N 118 " --> pdb=" O THR N 107 " (cutoff:3.500A) Processing sheet with id=96, first strand: chain 'N' and resid 233 through 236 removed outlier: 6.703A pdb=" N ILE N 243 " --> pdb=" O ILE N 235 " (cutoff:3.500A) Processing sheet with id=97, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=98, first strand: chain 'P' and resid 50 through 53 removed outlier: 6.344A pdb=" N PHE P 36 " --> pdb=" O LEU P 88 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N MET P 90 " --> pdb=" O PHE P 36 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU P 38 " --> pdb=" O MET P 90 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE P 39 " --> pdb=" O VAL P 336 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE P 335 " --> pdb=" O ILE P 365 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N GLY P 367 " --> pdb=" O ILE P 335 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ILE P 458 " --> pdb=" O VAL P 389 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU P 391 " --> pdb=" O ILE P 458 " (cutoff:3.500A) Processing sheet with id=99, first strand: chain 'P' and resid 405 through 408 removed outlier: 3.658A pdb=" N GLY P 396 " --> pdb=" O VAL P 408 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER P 439 " --> pdb=" O THR P 397 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'P' and resid 434 through 435 removed outlier: 4.488A pdb=" N PHE P 471 " --> pdb=" O LEU P 435 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE P 470 " --> pdb=" O VAL P 463 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'P' and resid 558 through 563 Processing sheet with id=102, first strand: chain 'P' and resid 573 through 580 removed outlier: 6.512A pdb=" N LYS P 573 " --> pdb=" O ALA Q 559 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE Q 561 " --> pdb=" O LYS P 573 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER P 575 " --> pdb=" O ILE Q 561 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N MET Q 563 " --> pdb=" O SER P 575 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER P 577 " --> pdb=" O MET Q 563 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL Q 565 " --> pdb=" O SER P 577 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL P 579 " --> pdb=" O VAL Q 565 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=104, first strand: chain 'Q' and resid 51 through 53 removed outlier: 6.308A pdb=" N PHE Q 36 " --> pdb=" O LEU Q 88 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N MET Q 90 " --> pdb=" O PHE Q 36 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU Q 38 " --> pdb=" O MET Q 90 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY Q 367 " --> pdb=" O PRO Q 337 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ILE Q 458 " --> pdb=" O VAL Q 389 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU Q 391 " --> pdb=" O ILE Q 458 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'Q' and resid 43 through 44 removed outlier: 3.783A pdb=" N GLU Q 43 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'Q' and resid 404 through 407 removed outlier: 3.585A pdb=" N ARG Q 404 " --> pdb=" O MET Q 400 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'Q' and resid 434 through 435 removed outlier: 4.224A pdb=" N PHE Q 471 " --> pdb=" O LEU Q 435 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE Q 470 " --> pdb=" O VAL Q 463 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=109, first strand: chain 'R' and resid 50 through 53 removed outlier: 3.563A pdb=" N ILE R 39 " --> pdb=" O VAL R 336 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE R 335 " --> pdb=" O ILE R 365 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLY R 367 " --> pdb=" O ILE R 335 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'R' and resid 95 through 96 Processing sheet with id=111, first strand: chain 'R' and resid 99 through 102 Processing sheet with id=112, first strand: chain 'R' and resid 143 through 150 removed outlier: 3.681A pdb=" N ASN R 149 " --> pdb=" O LEU R 132 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU R 132 " --> pdb=" O ASN R 149 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU R 123 " --> pdb=" O GLU R 304 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU R 304 " --> pdb=" O LEU R 123 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'R' and resid 216 through 220 removed outlier: 3.781A pdb=" N PHE R 154 " --> pdb=" O VAL R 248 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'R' and resid 165 through 171 removed outlier: 4.055A pdb=" N ARG R 180 " --> pdb=" O GLU R 170 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS R 191 " --> pdb=" O LEU R 183 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL R 185 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU R 189 " --> pdb=" O VAL R 185 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain 'R' and resid 405 through 408 removed outlier: 3.605A pdb=" N GLY R 396 " --> pdb=" O VAL R 408 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER R 439 " --> pdb=" O THR R 397 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'R' and resid 434 through 435 removed outlier: 4.562A pdb=" N PHE R 471 " --> pdb=" O LEU R 435 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE R 470 " --> pdb=" O VAL R 463 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'R' and resid 551 through 555 Processing sheet with id=118, first strand: chain 'S' and resid 57 through 59 removed outlier: 6.566A pdb=" N THR S 57 " --> pdb=" O TYR S 73 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE S 75 " --> pdb=" O THR S 57 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY S 59 " --> pdb=" O ILE S 75 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LEU S 77 " --> pdb=" O GLY S 59 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR S 73 " --> pdb=" O LEU S 191 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU S 191 " --> pdb=" O TYR S 73 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE S 75 " --> pdb=" O VAL S 189 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL S 189 " --> pdb=" O ILE S 75 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU S 77 " --> pdb=" O THR S 187 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR S 187 " --> pdb=" O LEU S 77 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN S 79 " --> pdb=" O GLN S 185 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR S 181 " --> pdb=" O THR S 83 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN S 85 " --> pdb=" O GLY S 179 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N GLY S 179 " --> pdb=" O ASN S 85 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N LEU S 87 " --> pdb=" O VAL S 177 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N VAL S 177 " --> pdb=" O LEU S 87 " (cutoff:3.500A) removed outlier: 12.969A pdb=" N SER S 89 " --> pdb=" O GLY S 175 " (cutoff:3.500A) removed outlier: 12.828A pdb=" N GLY S 175 " --> pdb=" O SER S 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR S 253 " --> pdb=" O LEU S 224 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU S 224 " --> pdb=" O THR S 253 " (cutoff:3.500A) Processing sheet with id=119, first strand: chain 'S' and resid 123 through 129 removed outlier: 6.664A pdb=" N THR S 167 " --> pdb=" O GLY S 124 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LEU S 126 " --> pdb=" O ILE S 165 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE S 165 " --> pdb=" O LEU S 126 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS S 128 " --> pdb=" O ASN S 163 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN S 163 " --> pdb=" O LYS S 128 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASP S 100 " --> pdb=" O GLU S 168 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS S 170 " --> pdb=" O THR S 98 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR S 98 " --> pdb=" O LYS S 170 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N THR S 107 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR S 118 " --> pdb=" O THR S 107 " (cutoff:3.500A) Processing sheet with id=120, first strand: chain 'S' and resid 233 through 236 removed outlier: 6.702A pdb=" N ILE S 243 " --> pdb=" O ILE S 235 " (cutoff:3.500A) Processing sheet with id=121, first strand: chain 'T' and resid 4 through 6 Processing sheet with id=122, first strand: chain 'T' and resid 50 through 53 removed outlier: 6.344A pdb=" N PHE T 36 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N MET T 90 " --> pdb=" O PHE T 36 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU T 38 " --> pdb=" O MET T 90 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE T 39 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE T 335 " --> pdb=" O ILE T 365 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N GLY T 367 " --> pdb=" O ILE T 335 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ILE T 458 " --> pdb=" O VAL T 389 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU T 391 " --> pdb=" O ILE T 458 " (cutoff:3.500A) Processing sheet with id=123, first strand: chain 'T' and resid 405 through 408 removed outlier: 3.659A pdb=" N GLY T 396 " --> pdb=" O VAL T 408 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER T 439 " --> pdb=" O THR T 397 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain 'T' and resid 434 through 435 removed outlier: 4.488A pdb=" N PHE T 471 " --> pdb=" O LEU T 435 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE T 470 " --> pdb=" O VAL T 463 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain 'T' and resid 558 through 563 Processing sheet with id=126, first strand: chain 'T' and resid 573 through 580 removed outlier: 6.511A pdb=" N LYS T 573 " --> pdb=" O ALA V 559 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE V 561 " --> pdb=" O LYS T 573 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER T 575 " --> pdb=" O ILE V 561 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET V 563 " --> pdb=" O SER T 575 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER T 577 " --> pdb=" O MET V 563 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL V 565 " --> pdb=" O SER T 577 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL T 579 " --> pdb=" O VAL V 565 " (cutoff:3.500A) Processing sheet with id=127, first strand: chain 'V' and resid 3 through 6 Processing sheet with id=128, first strand: chain 'V' and resid 51 through 53 removed outlier: 6.308A pdb=" N PHE V 36 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N MET V 90 " --> pdb=" O PHE V 36 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU V 38 " --> pdb=" O MET V 90 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY V 367 " --> pdb=" O PRO V 337 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ILE V 458 " --> pdb=" O VAL V 389 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU V 391 " --> pdb=" O ILE V 458 " (cutoff:3.500A) Processing sheet with id=129, first strand: chain 'V' and resid 43 through 44 removed outlier: 3.783A pdb=" N GLU V 43 " --> pdb=" O ARG V 64 " (cutoff:3.500A) Processing sheet with id=130, first strand: chain 'V' and resid 404 through 407 removed outlier: 3.585A pdb=" N ARG V 404 " --> pdb=" O MET V 400 " (cutoff:3.500A) Processing sheet with id=131, first strand: chain 'V' and resid 434 through 435 removed outlier: 4.224A pdb=" N PHE V 471 " --> pdb=" O LEU V 435 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE V 470 " --> pdb=" O VAL V 463 " (cutoff:3.500A) Processing sheet with id=132, first strand: chain 'W' and resid 3 through 6 Processing sheet with id=133, first strand: chain 'W' and resid 50 through 53 removed outlier: 3.564A pdb=" N ILE W 39 " --> pdb=" O VAL W 336 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE W 335 " --> pdb=" O ILE W 365 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N GLY W 367 " --> pdb=" O ILE W 335 " (cutoff:3.500A) Processing sheet with id=134, first strand: chain 'W' and resid 95 through 96 Processing sheet with id=135, first strand: chain 'W' and resid 99 through 102 Processing sheet with id=136, first strand: chain 'W' and resid 143 through 150 removed outlier: 3.681A pdb=" N ASN W 149 " --> pdb=" O LEU W 132 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU W 132 " --> pdb=" O ASN W 149 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU W 123 " --> pdb=" O GLU W 304 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU W 304 " --> pdb=" O LEU W 123 " (cutoff:3.500A) Processing sheet with id=137, first strand: chain 'W' and resid 216 through 220 removed outlier: 3.781A pdb=" N PHE W 154 " --> pdb=" O VAL W 248 " (cutoff:3.500A) Processing sheet with id=138, first strand: chain 'W' and resid 165 through 171 removed outlier: 4.055A pdb=" N ARG W 180 " --> pdb=" O GLU W 170 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS W 191 " --> pdb=" O LEU W 183 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL W 185 " --> pdb=" O GLU W 189 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU W 189 " --> pdb=" O VAL W 185 " (cutoff:3.500A) Processing sheet with id=139, first strand: chain 'W' and resid 405 through 408 removed outlier: 3.605A pdb=" N GLY W 396 " --> pdb=" O VAL W 408 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER W 439 " --> pdb=" O THR W 397 " (cutoff:3.500A) Processing sheet with id=140, first strand: chain 'W' and resid 434 through 435 removed outlier: 4.562A pdb=" N PHE W 471 " --> pdb=" O LEU W 435 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE W 470 " --> pdb=" O VAL W 463 " (cutoff:3.500A) Processing sheet with id=141, first strand: chain 'W' and resid 551 through 555 Processing sheet with id=142, first strand: chain 'X' and resid 57 through 59 removed outlier: 6.566A pdb=" N THR X 57 " --> pdb=" O TYR X 73 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE X 75 " --> pdb=" O THR X 57 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY X 59 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LEU X 77 " --> pdb=" O GLY X 59 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TYR X 73 " --> pdb=" O LEU X 191 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU X 191 " --> pdb=" O TYR X 73 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE X 75 " --> pdb=" O VAL X 189 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL X 189 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU X 77 " --> pdb=" O THR X 187 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR X 187 " --> pdb=" O LEU X 77 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN X 79 " --> pdb=" O GLN X 185 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR X 181 " --> pdb=" O THR X 83 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN X 85 " --> pdb=" O GLY X 179 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N GLY X 179 " --> pdb=" O ASN X 85 " (cutoff:3.500A) removed outlier: 9.429A pdb=" N LEU X 87 " --> pdb=" O VAL X 177 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N VAL X 177 " --> pdb=" O LEU X 87 " (cutoff:3.500A) removed outlier: 12.969A pdb=" N SER X 89 " --> pdb=" O GLY X 175 " (cutoff:3.500A) removed outlier: 12.828A pdb=" N GLY X 175 " --> pdb=" O SER X 89 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR X 253 " --> pdb=" O LEU X 224 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU X 224 " --> pdb=" O THR X 253 " (cutoff:3.500A) Processing sheet with id=143, first strand: chain 'X' and resid 123 through 129 removed outlier: 6.664A pdb=" N THR X 167 " --> pdb=" O GLY X 124 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LEU X 126 " --> pdb=" O ILE X 165 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE X 165 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS X 128 " --> pdb=" O ASN X 163 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN X 163 " --> pdb=" O LYS X 128 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASP X 100 " --> pdb=" O GLU X 168 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS X 170 " --> pdb=" O THR X 98 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR X 98 " --> pdb=" O LYS X 170 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR X 107 " --> pdb=" O THR X 118 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR X 118 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing sheet with id=144, first strand: chain 'X' and resid 233 through 236 removed outlier: 6.703A pdb=" N ILE X 243 " --> pdb=" O ILE X 235 " (cutoff:3.500A) 3084 hydrogen bonds defined for protein. 8532 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: 32.37 Time building geometry restraints manager: 14.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 24608 1.34 - 1.46: 12614 1.46 - 1.58: 36788 1.58 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 74298 Sorted by residual: bond pdb=" N ALA W 2 " pdb=" CA ALA W 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N ALA G 2 " pdb=" CA ALA G 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N ALA V 2 " pdb=" CA ALA V 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N ALA M 2 " pdb=" CA ALA M 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N ALA O 2 " pdb=" CA ALA O 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 ... (remaining 74293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 90075 1.12 - 2.24: 8746 2.24 - 3.35: 1091 3.35 - 4.47: 372 4.47 - 5.59: 90 Bond angle restraints: 100374 Sorted by residual: angle pdb=" CA GLU X 218 " pdb=" CB GLU X 218 " pdb=" CG GLU X 218 " ideal model delta sigma weight residual 114.10 119.29 -5.19 2.00e+00 2.50e-01 6.73e+00 angle pdb=" CA GLU J 218 " pdb=" CB GLU J 218 " pdb=" CG GLU J 218 " ideal model delta sigma weight residual 114.10 119.29 -5.19 2.00e+00 2.50e-01 6.73e+00 angle pdb=" CA GLU N 218 " pdb=" CB GLU N 218 " pdb=" CG GLU N 218 " ideal model delta sigma weight residual 114.10 119.28 -5.18 2.00e+00 2.50e-01 6.70e+00 angle pdb=" CA GLU U 218 " pdb=" CB GLU U 218 " pdb=" CG GLU U 218 " ideal model delta sigma weight residual 114.10 119.28 -5.18 2.00e+00 2.50e-01 6.70e+00 angle pdb=" CA GLU E 218 " pdb=" CB GLU E 218 " pdb=" CG GLU E 218 " ideal model delta sigma weight residual 114.10 119.25 -5.15 2.00e+00 2.50e-01 6.64e+00 ... (remaining 100369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 41558 17.68 - 35.35: 2788 35.35 - 53.03: 456 53.03 - 70.71: 180 70.71 - 88.38: 60 Dihedral angle restraints: 45042 sinusoidal: 18114 harmonic: 26928 Sorted by residual: dihedral pdb=" CA ARG N 110 " pdb=" C ARG N 110 " pdb=" N GLU N 111 " pdb=" CA GLU N 111 " ideal model delta harmonic sigma weight residual 180.00 151.50 28.50 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ARG U 110 " pdb=" C ARG U 110 " pdb=" N GLU U 111 " pdb=" CA GLU U 111 " ideal model delta harmonic sigma weight residual 180.00 151.50 28.50 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ARG X 110 " pdb=" C ARG X 110 " pdb=" N GLU X 111 " pdb=" CA GLU X 111 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 45039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 6328 0.032 - 0.063: 3113 0.063 - 0.095: 879 0.095 - 0.127: 762 0.127 - 0.159: 138 Chirality restraints: 11220 Sorted by residual: chirality pdb=" CA ILE T 553 " pdb=" N ILE T 553 " pdb=" C ILE T 553 " pdb=" CB ILE T 553 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA ILE F 553 " pdb=" N ILE F 553 " pdb=" C ILE F 553 " pdb=" CB ILE F 553 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA ILE P 553 " pdb=" N ILE P 553 " pdb=" C ILE P 553 " pdb=" CB ILE P 553 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 11217 not shown) Planarity restraints: 13236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG O 560 " 0.253 9.50e-02 1.11e+02 1.14e-01 1.03e+01 pdb=" NE ARG O 560 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG O 560 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG O 560 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG O 560 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 560 " 0.253 9.50e-02 1.11e+02 1.14e-01 1.03e+01 pdb=" NE ARG M 560 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG M 560 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG M 560 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG M 560 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 560 " 0.253 9.50e-02 1.11e+02 1.14e-01 1.03e+01 pdb=" NE ARG R 560 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG R 560 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG R 560 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG R 560 " 0.000 2.00e-02 2.50e+03 ... (remaining 13233 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 156 2.51 - 3.11: 54230 3.11 - 3.70: 104415 3.70 - 4.30: 154676 4.30 - 4.90: 260938 Nonbonded interactions: 574415 Sorted by model distance: nonbonded pdb=" CE2 PHE S 180 " pdb=" NH1 ARG X 213 " model vdw 1.911 3.420 nonbonded pdb=" CE2 PHE E 180 " pdb=" NH1 ARG J 213 " model vdw 1.911 3.420 nonbonded pdb=" NH1 ARG U 213 " pdb=" CE2 PHE X 180 " model vdw 1.912 3.420 nonbonded pdb=" CE2 PHE J 180 " pdb=" NH1 ARG N 213 " model vdw 1.912 3.420 nonbonded pdb=" CE2 PHE U 180 " pdb=" NH1 ARG E 213 " model vdw 1.912 3.420 ... (remaining 574410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 2 through 93 or resid 318 through 503 or resid 510 through \ 536 or (resid 537 and (name N or name CA or name C or name O )) or resid 538 th \ rough 539 or (resid 540 and (name N or name CA or name C or name O )) or resid 5 \ 45 through 587)) selection = chain 'F' selection = (chain 'G' and (resid 2 through 93 or resid 318 through 503 or resid 510 through \ 536 or (resid 537 and (name N or name CA or name C or name O )) or resid 538 th \ rough 539 or (resid 540 and (name N or name CA or name C or name O )) or resid 5 \ 45 through 587)) selection = (chain 'I' and (resid 2 through 93 or resid 318 through 503 or resid 510 through \ 536 or (resid 537 and (name N or name CA or name C or name O )) or resid 538 th \ rough 539 or (resid 540 and (name N or name CA or name C or name O )) or resid 5 \ 45 through 587)) selection = chain 'K' selection = (chain 'L' and (resid 2 through 93 or resid 318 through 503 or resid 510 through \ 536 or (resid 537 and (name N or name CA or name C or name O )) or resid 538 th \ rough 539 or (resid 540 and (name N or name CA or name C or name O )) or resid 5 \ 45 through 587)) selection = chain 'P' selection = (chain 'Q' and (resid 2 through 93 or resid 318 through 503 or resid 510 through \ 536 or (resid 537 and (name N or name CA or name C or name O )) or resid 538 th \ rough 539 or (resid 540 and (name N or name CA or name C or name O )) or resid 5 \ 45 through 587)) selection = chain 'T' selection = (chain 'V' and (resid 2 through 93 or resid 318 through 503 or resid 510 through \ 536 or (resid 537 and (name N or name CA or name C or name O )) or resid 538 th \ rough 539 or (resid 540 and (name N or name CA or name C or name O )) or resid 5 \ 45 through 587)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'M' selection = chain 'O' selection = chain 'R' selection = chain 'W' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'N' selection = chain 'S' selection = chain 'U' selection = chain 'X' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 2.190 Check model and map are aligned: 0.460 Set scattering table: 0.530 Process input model: 114.210 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.320 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:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 74298 Z= 0.235 Angle : 0.723 5.589 100374 Z= 0.417 Chirality : 0.047 0.159 11220 Planarity : 0.009 0.114 13236 Dihedral : 13.443 88.384 27714 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.08), residues: 9246 helix: -0.95 (0.09), residues: 2718 sheet: 0.58 (0.11), residues: 1920 loop : -0.71 (0.08), residues: 4608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP B 76 HIS 0.007 0.002 HIS R 15 PHE 0.017 0.003 PHE L 471 TYR 0.037 0.006 TYR C 56 ARG 0.027 0.003 ARG R 560 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18492 Ramachandran restraints generated. 9246 Oldfield, 0 Emsley, 9246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18492 Ramachandran restraints generated. 9246 Oldfield, 0 Emsley, 9246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1632 residues out of total 7998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1632 time to evaluate : 6.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 ILE cc_start: 0.8365 (mt) cc_final: 0.7994 (tp) REVERT: B 57 SER cc_start: 0.8311 (t) cc_final: 0.7939 (p) REVERT: B 61 ARG cc_start: 0.7013 (ttm170) cc_final: 0.6655 (tpp-160) REVERT: B 319 THR cc_start: 0.6168 (t) cc_final: 0.5889 (m) REVERT: B 353 LYS cc_start: 0.6839 (tppt) cc_final: 0.6623 (mmmt) REVERT: B 360 GLU cc_start: 0.5949 (mt-10) cc_final: 0.5691 (mt-10) REVERT: B 384 LEU cc_start: 0.6872 (tp) cc_final: 0.6654 (tt) REVERT: B 491 MET cc_start: 0.8414 (ttm) cc_final: 0.8070 (ttm) REVERT: B 563 MET cc_start: 0.6573 (mpp) cc_final: 0.6075 (mmm) REVERT: I 425 GLU cc_start: 0.7989 (tt0) cc_final: 0.7605 (tt0) REVERT: I 436 ARG cc_start: 0.6653 (ttt90) cc_final: 0.6216 (mmm-85) REVERT: I 551 GLN cc_start: 0.7276 (mt0) cc_final: 0.7066 (tt0) REVERT: O 90 MET cc_start: 0.8428 (ttp) cc_final: 0.8118 (ttp) REVERT: O 110 LYS cc_start: 0.6179 (mttt) cc_final: 0.5865 (mttp) REVERT: O 112 TYR cc_start: 0.7359 (m-80) cc_final: 0.6594 (m-10) REVERT: O 201 ASP cc_start: 0.5808 (p0) cc_final: 0.5555 (p0) REVERT: O 252 PHE cc_start: 0.6140 (t80) cc_final: 0.5565 (t80) REVERT: O 400 MET cc_start: 0.8287 (mmm) cc_final: 0.8014 (mmm) REVERT: O 401 ASP cc_start: 0.7413 (m-30) cc_final: 0.6990 (m-30) REVERT: O 441 ASP cc_start: 0.8321 (m-30) cc_final: 0.7964 (m-30) REVERT: O 442 GLN cc_start: 0.7381 (mm110) cc_final: 0.7173 (mm-40) REVERT: O 538 ARG cc_start: 0.6937 (ttm-80) cc_final: 0.6393 (ttp-170) REVERT: O 581 LYS cc_start: 0.8339 (mttt) cc_final: 0.8051 (mttm) REVERT: U 29 ASP cc_start: 0.7538 (t70) cc_final: 0.6883 (m-30) REVERT: U 41 GLU cc_start: 0.6878 (tp30) cc_final: 0.6619 (tp30) REVERT: U 50 LYS cc_start: 0.5696 (pttt) cc_final: 0.5438 (tptt) REVERT: U 123 ILE cc_start: 0.7165 (mt) cc_final: 0.6866 (tt) REVERT: U 141 GLN cc_start: 0.6327 (mt0) cc_final: 0.5870 (mm-40) REVERT: U 237 GLU cc_start: 0.6080 (tt0) cc_final: 0.5656 (tt0) REVERT: U 260 TYR cc_start: 0.6683 (t80) cc_final: 0.6472 (t80) REVERT: U 269 LEU cc_start: 0.6095 (mt) cc_final: 0.5872 (mt) REVERT: A 12 THR cc_start: 0.6479 (p) cc_final: 0.6111 (p) REVERT: A 39 ILE cc_start: 0.8397 (mt) cc_final: 0.7967 (tp) REVERT: A 57 SER cc_start: 0.8238 (t) cc_final: 0.7826 (p) REVERT: A 61 ARG cc_start: 0.7029 (ttm170) cc_final: 0.6774 (ttm-80) REVERT: A 360 GLU cc_start: 0.6330 (mt-10) cc_final: 0.6061 (mt-10) REVERT: A 491 MET cc_start: 0.8434 (ttm) cc_final: 0.8160 (ttp) REVERT: A 524 ILE cc_start: 0.7551 (tp) cc_final: 0.7318 (mt) REVERT: A 549 ASP cc_start: 0.7142 (m-30) cc_final: 0.6899 (m-30) REVERT: A 562 SER cc_start: 0.7732 (m) cc_final: 0.7437 (t) REVERT: A 563 MET cc_start: 0.6390 (mpp) cc_final: 0.6145 (mmm) REVERT: C 436 ARG cc_start: 0.6548 (ttt90) cc_final: 0.6324 (mtp180) REVERT: C 510 ASP cc_start: 0.8121 (m-30) cc_final: 0.7903 (m-30) REVERT: D 73 GLU cc_start: 0.7286 (tt0) cc_final: 0.6854 (tt0) REVERT: D 110 LYS cc_start: 0.6206 (mttt) cc_final: 0.5892 (mttt) REVERT: D 138 PHE cc_start: 0.6480 (t80) cc_final: 0.6241 (t80) REVERT: D 201 ASP cc_start: 0.5700 (p0) cc_final: 0.5463 (p0) REVERT: D 226 LYS cc_start: 0.4754 (mttt) cc_final: 0.4481 (mttt) REVERT: D 400 MET cc_start: 0.8425 (mmm) cc_final: 0.8073 (mmm) REVERT: D 401 ASP cc_start: 0.7613 (m-30) cc_final: 0.7118 (m-30) REVERT: D 442 GLN cc_start: 0.7468 (mm110) cc_final: 0.7241 (mm-40) REVERT: D 538 ARG cc_start: 0.7134 (ttm-80) cc_final: 0.6535 (ttp80) REVERT: E 29 ASP cc_start: 0.7418 (t70) cc_final: 0.6573 (m-30) REVERT: E 41 GLU cc_start: 0.6673 (tp30) cc_final: 0.6443 (tp30) REVERT: E 50 LYS cc_start: 0.5357 (pttt) cc_final: 0.5156 (tptt) REVERT: E 123 ILE cc_start: 0.7235 (mt) cc_final: 0.6959 (tt) REVERT: E 141 GLN cc_start: 0.6718 (mt0) cc_final: 0.6107 (mm-40) REVERT: E 170 LYS cc_start: 0.7088 (mtpp) cc_final: 0.6520 (mmtt) REVERT: E 171 ASN cc_start: 0.4763 (p0) cc_final: 0.3436 (t0) REVERT: E 260 TYR cc_start: 0.6609 (t80) cc_final: 0.6369 (t80) REVERT: F 39 ILE cc_start: 0.8235 (mt) cc_final: 0.7764 (tp) REVERT: F 57 SER cc_start: 0.8493 (t) cc_final: 0.8204 (p) REVERT: F 61 ARG cc_start: 0.6902 (ttm170) cc_final: 0.6572 (tpp-160) REVERT: F 353 LYS cc_start: 0.6761 (tppt) cc_final: 0.6519 (mmmt) REVERT: F 360 GLU cc_start: 0.6105 (mt-10) cc_final: 0.5820 (mt-10) REVERT: F 362 MET cc_start: 0.7788 (mtp) cc_final: 0.7104 (mtt) REVERT: F 491 MET cc_start: 0.8410 (ttm) cc_final: 0.8189 (ttp) REVERT: F 549 ASP cc_start: 0.6749 (m-30) cc_final: 0.6537 (m-30) REVERT: F 562 SER cc_start: 0.7997 (m) cc_final: 0.7568 (t) REVERT: F 563 MET cc_start: 0.6866 (mpp) cc_final: 0.6298 (mmm) REVERT: G 436 ARG cc_start: 0.6968 (ttt90) cc_final: 0.6621 (mmm-85) REVERT: H 46 GLU cc_start: 0.7234 (tt0) cc_final: 0.6879 (tt0) REVERT: H 73 GLU cc_start: 0.7196 (tt0) cc_final: 0.6957 (tt0) REVERT: H 400 MET cc_start: 0.8331 (mmm) cc_final: 0.8098 (mmm) REVERT: H 401 ASP cc_start: 0.7723 (m-30) cc_final: 0.7343 (m-30) REVERT: H 412 MET cc_start: 0.8046 (mmm) cc_final: 0.7826 (mmt) REVERT: H 441 ASP cc_start: 0.8242 (m-30) cc_final: 0.8006 (m-30) REVERT: H 442 GLN cc_start: 0.7343 (mm110) cc_final: 0.7106 (mm110) REVERT: H 538 ARG cc_start: 0.6963 (ttm-80) cc_final: 0.6290 (ttp80) REVERT: J 29 ASP cc_start: 0.7680 (t70) cc_final: 0.7027 (m-30) REVERT: J 41 GLU cc_start: 0.6762 (tp30) cc_final: 0.6539 (tp30) REVERT: J 50 LYS cc_start: 0.5590 (pttt) cc_final: 0.5269 (tptt) REVERT: J 69 TYR cc_start: 0.8131 (m-80) cc_final: 0.7887 (m-10) REVERT: J 123 ILE cc_start: 0.7173 (mt) cc_final: 0.6903 (tt) REVERT: J 141 GLN cc_start: 0.6437 (mt0) cc_final: 0.5738 (mm-40) REVERT: J 168 GLU cc_start: 0.7470 (pt0) cc_final: 0.7204 (pt0) REVERT: J 171 ASN cc_start: 0.4898 (p0) cc_final: 0.3689 (t0) REVERT: J 237 GLU cc_start: 0.6104 (tt0) cc_final: 0.5903 (tt0) REVERT: J 260 TYR cc_start: 0.6504 (t80) cc_final: 0.6221 (t80) REVERT: J 269 LEU cc_start: 0.6244 (mt) cc_final: 0.6017 (mt) REVERT: K 39 ILE cc_start: 0.8365 (mt) cc_final: 0.7994 (tp) REVERT: K 57 SER cc_start: 0.8305 (t) cc_final: 0.7935 (p) REVERT: K 61 ARG cc_start: 0.7012 (ttm170) cc_final: 0.6654 (tpp-160) REVERT: K 319 THR cc_start: 0.6167 (t) cc_final: 0.5889 (m) REVERT: K 353 LYS cc_start: 0.6841 (tppt) cc_final: 0.6624 (mmmt) REVERT: K 360 GLU cc_start: 0.5951 (mt-10) cc_final: 0.5692 (mt-10) REVERT: K 384 LEU cc_start: 0.6875 (tp) cc_final: 0.6660 (tt) REVERT: K 491 MET cc_start: 0.8412 (ttm) cc_final: 0.8070 (ttm) REVERT: K 563 MET cc_start: 0.6577 (mpp) cc_final: 0.6082 (mmm) REVERT: L 425 GLU cc_start: 0.7992 (tt0) cc_final: 0.7607 (tt0) REVERT: L 436 ARG cc_start: 0.6655 (ttt90) cc_final: 0.6215 (mmm-85) REVERT: L 551 GLN cc_start: 0.7281 (mt0) cc_final: 0.7069 (tt0) REVERT: M 90 MET cc_start: 0.8433 (ttp) cc_final: 0.8121 (ttp) REVERT: M 110 LYS cc_start: 0.6176 (mttt) cc_final: 0.5860 (mttp) REVERT: M 112 TYR cc_start: 0.7356 (m-80) cc_final: 0.6589 (m-10) REVERT: M 201 ASP cc_start: 0.5812 (p0) cc_final: 0.5559 (p0) REVERT: M 252 PHE cc_start: 0.6139 (t80) cc_final: 0.5562 (t80) REVERT: M 400 MET cc_start: 0.8289 (mmm) cc_final: 0.8015 (mmm) REVERT: M 401 ASP cc_start: 0.7411 (m-30) cc_final: 0.6992 (m-30) REVERT: M 441 ASP cc_start: 0.8322 (m-30) cc_final: 0.7965 (m-30) REVERT: M 442 GLN cc_start: 0.7382 (mm110) cc_final: 0.7177 (mm-40) REVERT: M 538 ARG cc_start: 0.6936 (ttm-80) cc_final: 0.6392 (ttp-170) REVERT: M 581 LYS cc_start: 0.8340 (mttt) cc_final: 0.8053 (mttm) REVERT: N 29 ASP cc_start: 0.7538 (t70) cc_final: 0.6884 (m-30) REVERT: N 41 GLU cc_start: 0.6875 (tp30) cc_final: 0.6617 (tp30) REVERT: N 50 LYS cc_start: 0.5695 (pttt) cc_final: 0.5435 (tptt) REVERT: N 123 ILE cc_start: 0.7164 (mt) cc_final: 0.6862 (tt) REVERT: N 141 GLN cc_start: 0.6324 (mt0) cc_final: 0.5869 (mm-40) REVERT: N 237 GLU cc_start: 0.6079 (tt0) cc_final: 0.5657 (tt0) REVERT: N 260 TYR cc_start: 0.6686 (t80) cc_final: 0.6476 (t80) REVERT: N 269 LEU cc_start: 0.6079 (mt) cc_final: 0.5866 (mt) REVERT: P 12 THR cc_start: 0.6479 (p) cc_final: 0.6109 (p) REVERT: P 39 ILE cc_start: 0.8395 (mt) cc_final: 0.7966 (tp) REVERT: P 57 SER cc_start: 0.8239 (t) cc_final: 0.7827 (p) REVERT: P 61 ARG cc_start: 0.7030 (ttm170) cc_final: 0.6774 (ttm-80) REVERT: P 360 GLU cc_start: 0.6329 (mt-10) cc_final: 0.6061 (mt-10) REVERT: P 491 MET cc_start: 0.8434 (ttm) cc_final: 0.8156 (ttp) REVERT: P 524 ILE cc_start: 0.7556 (tp) cc_final: 0.7322 (mt) REVERT: P 549 ASP cc_start: 0.7142 (m-30) cc_final: 0.6901 (m-30) REVERT: P 562 SER cc_start: 0.7738 (m) cc_final: 0.7444 (t) REVERT: P 563 MET cc_start: 0.6394 (mpp) cc_final: 0.6150 (mmm) REVERT: Q 436 ARG cc_start: 0.6546 (ttt90) cc_final: 0.6321 (mtp180) REVERT: Q 510 ASP cc_start: 0.8116 (m-30) cc_final: 0.7899 (m-30) REVERT: R 73 GLU cc_start: 0.7288 (tt0) cc_final: 0.6857 (tt0) REVERT: R 110 LYS cc_start: 0.6209 (mttt) cc_final: 0.5894 (mttt) REVERT: R 138 PHE cc_start: 0.6483 (t80) cc_final: 0.6244 (t80) REVERT: R 201 ASP cc_start: 0.5698 (p0) cc_final: 0.5461 (p0) REVERT: R 226 LYS cc_start: 0.4757 (mttt) cc_final: 0.4480 (mttt) REVERT: R 400 MET cc_start: 0.8427 (mmm) cc_final: 0.8077 (mmm) REVERT: R 401 ASP cc_start: 0.7617 (m-30) cc_final: 0.7121 (m-30) REVERT: R 442 GLN cc_start: 0.7467 (mm110) cc_final: 0.7240 (mm-40) REVERT: R 538 ARG cc_start: 0.7133 (ttm-80) cc_final: 0.6535 (ttp80) REVERT: S 29 ASP cc_start: 0.7420 (t70) cc_final: 0.6573 (m-30) REVERT: S 41 GLU cc_start: 0.6675 (tp30) cc_final: 0.6442 (tp30) REVERT: S 50 LYS cc_start: 0.5359 (pttt) cc_final: 0.5157 (tptt) REVERT: S 123 ILE cc_start: 0.7236 (mt) cc_final: 0.6956 (tt) REVERT: S 141 GLN cc_start: 0.6717 (mt0) cc_final: 0.6107 (mm-40) REVERT: S 170 LYS cc_start: 0.7086 (mtpp) cc_final: 0.6518 (mmtt) REVERT: S 171 ASN cc_start: 0.4759 (p0) cc_final: 0.3434 (t0) REVERT: S 260 TYR cc_start: 0.6610 (t80) cc_final: 0.6369 (t80) REVERT: T 39 ILE cc_start: 0.8239 (mt) cc_final: 0.7766 (tp) REVERT: T 57 SER cc_start: 0.8493 (t) cc_final: 0.8206 (p) REVERT: T 61 ARG cc_start: 0.6904 (ttm170) cc_final: 0.6573 (tpp-160) REVERT: T 353 LYS cc_start: 0.6763 (tppt) cc_final: 0.6519 (mmmt) REVERT: T 360 GLU cc_start: 0.6101 (mt-10) cc_final: 0.5814 (mt-10) REVERT: T 362 MET cc_start: 0.7784 (mtp) cc_final: 0.7100 (mtt) REVERT: T 491 MET cc_start: 0.8413 (ttm) cc_final: 0.8192 (ttp) REVERT: T 549 ASP cc_start: 0.6749 (m-30) cc_final: 0.6539 (m-30) REVERT: T 562 SER cc_start: 0.7998 (m) cc_final: 0.7569 (t) REVERT: T 563 MET cc_start: 0.6868 (mpp) cc_final: 0.6298 (mmm) REVERT: V 436 ARG cc_start: 0.6973 (ttt90) cc_final: 0.6622 (mmm-85) REVERT: W 46 GLU cc_start: 0.7231 (tt0) cc_final: 0.6877 (tt0) REVERT: W 73 GLU cc_start: 0.7199 (tt0) cc_final: 0.6958 (tt0) REVERT: W 400 MET cc_start: 0.8332 (mmm) cc_final: 0.8096 (mmm) REVERT: W 401 ASP cc_start: 0.7726 (m-30) cc_final: 0.7347 (m-30) REVERT: W 412 MET cc_start: 0.8043 (mmm) cc_final: 0.7824 (mmt) REVERT: W 441 ASP cc_start: 0.8240 (m-30) cc_final: 0.8004 (m-30) REVERT: W 442 GLN cc_start: 0.7344 (mm110) cc_final: 0.7107 (mm110) REVERT: W 538 ARG cc_start: 0.6969 (ttm-80) cc_final: 0.6293 (ttp80) REVERT: X 29 ASP cc_start: 0.7681 (t70) cc_final: 0.7029 (m-30) REVERT: X 41 GLU cc_start: 0.6760 (tp30) cc_final: 0.6538 (tp30) REVERT: X 50 LYS cc_start: 0.5592 (pttt) cc_final: 0.5268 (tptt) REVERT: X 69 TYR cc_start: 0.8131 (m-80) cc_final: 0.7886 (m-10) REVERT: X 123 ILE cc_start: 0.7174 (mt) cc_final: 0.6907 (tt) REVERT: X 141 GLN cc_start: 0.6438 (mt0) cc_final: 0.5739 (mm-40) REVERT: X 168 GLU cc_start: 0.7462 (pt0) cc_final: 0.7194 (pt0) REVERT: X 171 ASN cc_start: 0.4895 (p0) cc_final: 0.3686 (t0) REVERT: X 237 GLU cc_start: 0.6105 (tt0) cc_final: 0.5904 (tt0) REVERT: X 260 TYR cc_start: 0.6504 (t80) cc_final: 0.6222 (t80) REVERT: X 268 LYS cc_start: 0.4526 (ptmt) cc_final: 0.4269 (ptmt) outliers start: 0 outliers final: 0 residues processed: 1632 average time/residue: 0.7240 time to fit residues: 1931.6891 Evaluate side-chains 921 residues out of total 7998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 921 time to evaluate : 6.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 780 optimal weight: 8.9990 chunk 700 optimal weight: 10.0000 chunk 388 optimal weight: 20.0000 chunk 239 optimal weight: 9.9990 chunk 472 optimal weight: 9.9990 chunk 374 optimal weight: 0.2980 chunk 724 optimal weight: 7.9990 chunk 280 optimal weight: 2.9990 chunk 440 optimal weight: 8.9990 chunk 539 optimal weight: 5.9990 chunk 839 optimal weight: 10.0000 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 GLN B 530 GLN U 67 ASN U 185 GLN A 376 GLN A 530 GLN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 GLN D 551 GLN E 67 ASN E 185 GLN E 220 GLN F 376 GLN F 530 GLN H 258 GLN J 185 GLN K 376 GLN K 530 GLN N 67 ASN N 185 GLN P 376 GLN P 530 GLN ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 507 GLN R 551 GLN S 67 ASN S 185 GLN S 220 GLN T 376 GLN T 530 GLN X 185 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 74298 Z= 0.342 Angle : 0.645 9.598 100374 Z= 0.356 Chirality : 0.049 0.184 11220 Planarity : 0.005 0.042 13236 Dihedral : 6.318 81.441 10086 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.58 % Allowed : 6.44 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.08), residues: 9246 helix: 0.64 (0.10), residues: 2760 sheet: 0.18 (0.11), residues: 1974 loop : -0.58 (0.09), residues: 4512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 76 HIS 0.006 0.002 HIS O 15 PHE 0.024 0.002 PHE X 134 TYR 0.020 0.002 TYR C 566 ARG 0.009 0.001 ARG J 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18492 Ramachandran restraints generated. 9246 Oldfield, 0 Emsley, 9246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18492 Ramachandran restraints generated. 9246 Oldfield, 0 Emsley, 9246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1129 residues out of total 7998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1003 time to evaluate : 6.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 SER cc_start: 0.8220 (t) cc_final: 0.7902 (p) REVERT: B 61 ARG cc_start: 0.7047 (ttm170) cc_final: 0.6784 (tpp-160) REVERT: B 353 LYS cc_start: 0.6756 (tppt) cc_final: 0.6440 (tttt) REVERT: B 374 LYS cc_start: 0.6960 (mttt) cc_final: 0.6702 (mtmm) REVERT: B 384 LEU cc_start: 0.7132 (tp) cc_final: 0.6928 (tt) REVERT: B 491 MET cc_start: 0.8491 (ttm) cc_final: 0.8037 (ttm) REVERT: B 563 MET cc_start: 0.6314 (mpp) cc_final: 0.6075 (mmm) REVERT: I 425 GLU cc_start: 0.8145 (tt0) cc_final: 0.7787 (tt0) REVERT: I 436 ARG cc_start: 0.6833 (ttt90) cc_final: 0.6222 (mmm-85) REVERT: I 551 GLN cc_start: 0.7445 (mt0) cc_final: 0.7099 (tt0) REVERT: O 90 MET cc_start: 0.8231 (ttp) cc_final: 0.7974 (ttp) REVERT: O 138 PHE cc_start: 0.6417 (t80) cc_final: 0.6013 (t80) REVERT: O 442 GLN cc_start: 0.7441 (mm110) cc_final: 0.7230 (mm-40) REVERT: O 518 ILE cc_start: 0.8619 (mt) cc_final: 0.8332 (mm) REVERT: O 538 ARG cc_start: 0.7168 (ttm-80) cc_final: 0.6904 (ttp80) REVERT: O 581 LYS cc_start: 0.8295 (mttt) cc_final: 0.8014 (mttm) REVERT: U 29 ASP cc_start: 0.7644 (t70) cc_final: 0.6732 (m-30) REVERT: U 41 GLU cc_start: 0.7081 (tp30) cc_final: 0.6236 (tp30) REVERT: U 50 LYS cc_start: 0.5596 (pttt) cc_final: 0.5351 (tptt) REVERT: U 127 ILE cc_start: 0.8491 (mt) cc_final: 0.8245 (mm) REVERT: U 141 GLN cc_start: 0.6386 (mt0) cc_final: 0.5952 (mm-40) REVERT: U 237 GLU cc_start: 0.6154 (tt0) cc_final: 0.5903 (tt0) REVERT: U 260 TYR cc_start: 0.6702 (t80) cc_final: 0.6338 (t80) REVERT: A 57 SER cc_start: 0.8340 (t) cc_final: 0.8018 (p) REVERT: A 61 ARG cc_start: 0.7216 (ttm170) cc_final: 0.6792 (ttm-80) REVERT: A 491 MET cc_start: 0.8485 (ttm) cc_final: 0.8086 (ttp) REVERT: A 499 PHE cc_start: 0.6642 (m-80) cc_final: 0.6122 (m-80) REVERT: A 563 MET cc_start: 0.6334 (mpp) cc_final: 0.5914 (mmm) REVERT: C 405 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7527 (mtpt) REVERT: C 436 ARG cc_start: 0.6611 (ttt90) cc_final: 0.6218 (mmm-85) REVERT: C 510 ASP cc_start: 0.8131 (m-30) cc_final: 0.7756 (m-30) REVERT: D 73 GLU cc_start: 0.7316 (tt0) cc_final: 0.7056 (tt0) REVERT: D 110 LYS cc_start: 0.6261 (mttt) cc_final: 0.6007 (mttt) REVERT: D 138 PHE cc_start: 0.6451 (t80) cc_final: 0.6094 (t80) REVERT: D 401 ASP cc_start: 0.7634 (m-30) cc_final: 0.7194 (m-30) REVERT: D 442 GLN cc_start: 0.7754 (mm110) cc_final: 0.7494 (mm-40) REVERT: D 531 SER cc_start: 0.7887 (t) cc_final: 0.7641 (p) REVERT: D 538 ARG cc_start: 0.7245 (ttm-80) cc_final: 0.7028 (ttm110) REVERT: E 29 ASP cc_start: 0.7527 (t70) cc_final: 0.6680 (m-30) REVERT: E 41 GLU cc_start: 0.6612 (tp30) cc_final: 0.6136 (tp30) REVERT: E 50 LYS cc_start: 0.5423 (pttt) cc_final: 0.5211 (tptt) REVERT: E 123 ILE cc_start: 0.7023 (mt) cc_final: 0.6765 (tt) REVERT: E 140 LEU cc_start: 0.8171 (tp) cc_final: 0.7918 (tt) REVERT: E 141 GLN cc_start: 0.6700 (mt0) cc_final: 0.5993 (mm-40) REVERT: E 169 LYS cc_start: 0.7261 (ptmt) cc_final: 0.7036 (ptmm) REVERT: E 170 LYS cc_start: 0.7371 (mtpp) cc_final: 0.7091 (mtmm) REVERT: F 57 SER cc_start: 0.8278 (t) cc_final: 0.7981 (p) REVERT: F 61 ARG cc_start: 0.7094 (ttm170) cc_final: 0.6792 (ttm170) REVERT: F 353 LYS cc_start: 0.6794 (tppt) cc_final: 0.6521 (mmmt) REVERT: F 400 MET cc_start: 0.8429 (mmt) cc_final: 0.7756 (mmt) REVERT: F 563 MET cc_start: 0.6558 (mpp) cc_final: 0.6282 (mmm) REVERT: G 405 LYS cc_start: 0.7770 (mtpt) cc_final: 0.7540 (mtpt) REVERT: G 412 MET cc_start: 0.8762 (mmm) cc_final: 0.8343 (mmt) REVERT: G 436 ARG cc_start: 0.6785 (ttt90) cc_final: 0.6259 (mmm-85) REVERT: H 46 GLU cc_start: 0.7378 (tt0) cc_final: 0.7074 (tt0) REVERT: H 401 ASP cc_start: 0.7636 (m-30) cc_final: 0.7151 (m-30) REVERT: H 581 LYS cc_start: 0.8307 (mttt) cc_final: 0.8055 (mttm) REVERT: J 29 ASP cc_start: 0.7776 (t70) cc_final: 0.7356 (t70) REVERT: J 41 GLU cc_start: 0.6889 (tp30) cc_final: 0.6608 (tp30) REVERT: J 50 LYS cc_start: 0.5746 (pttt) cc_final: 0.5335 (tptt) REVERT: J 89 SER cc_start: 0.6990 (m) cc_final: 0.5996 (t) REVERT: J 123 ILE cc_start: 0.7122 (mt) cc_final: 0.6889 (tt) REVERT: J 125 GLU cc_start: 0.6450 (tt0) cc_final: 0.6247 (tt0) REVERT: J 127 ILE cc_start: 0.8499 (mt) cc_final: 0.8299 (mm) REVERT: J 141 GLN cc_start: 0.6472 (mt0) cc_final: 0.5775 (mm-40) REVERT: J 269 LEU cc_start: 0.6675 (mt) cc_final: 0.6209 (mt) REVERT: K 57 SER cc_start: 0.8216 (t) cc_final: 0.7901 (p) REVERT: K 61 ARG cc_start: 0.7048 (ttm170) cc_final: 0.6784 (tpp-160) REVERT: K 353 LYS cc_start: 0.6757 (tppt) cc_final: 0.6441 (tttt) REVERT: K 374 LYS cc_start: 0.6963 (mttt) cc_final: 0.6705 (mtmm) REVERT: K 384 LEU cc_start: 0.7134 (tp) cc_final: 0.6929 (tt) REVERT: K 491 MET cc_start: 0.8491 (ttm) cc_final: 0.8037 (ttm) REVERT: K 563 MET cc_start: 0.6384 (mpp) cc_final: 0.6058 (mmm) REVERT: L 425 GLU cc_start: 0.8143 (tt0) cc_final: 0.7783 (tt0) REVERT: L 436 ARG cc_start: 0.6831 (ttt90) cc_final: 0.6221 (mmm-85) REVERT: L 551 GLN cc_start: 0.7447 (mt0) cc_final: 0.7101 (tt0) REVERT: M 90 MET cc_start: 0.8228 (ttp) cc_final: 0.7971 (ttp) REVERT: M 138 PHE cc_start: 0.6424 (t80) cc_final: 0.6018 (t80) REVERT: M 442 GLN cc_start: 0.7442 (mm110) cc_final: 0.7233 (mm-40) REVERT: M 518 ILE cc_start: 0.8622 (mt) cc_final: 0.8334 (mm) REVERT: M 538 ARG cc_start: 0.7166 (ttm-80) cc_final: 0.6904 (ttp80) REVERT: M 581 LYS cc_start: 0.8293 (mttt) cc_final: 0.8014 (mttm) REVERT: N 29 ASP cc_start: 0.7638 (t70) cc_final: 0.6728 (m-30) REVERT: N 41 GLU cc_start: 0.7077 (tp30) cc_final: 0.6230 (tp30) REVERT: N 50 LYS cc_start: 0.5589 (pttt) cc_final: 0.5346 (tptt) REVERT: N 127 ILE cc_start: 0.8490 (mt) cc_final: 0.8244 (mm) REVERT: N 141 GLN cc_start: 0.6381 (mt0) cc_final: 0.5950 (mm-40) REVERT: N 237 GLU cc_start: 0.6155 (tt0) cc_final: 0.5901 (tt0) REVERT: N 260 TYR cc_start: 0.6706 (t80) cc_final: 0.6342 (t80) REVERT: P 57 SER cc_start: 0.8338 (t) cc_final: 0.8017 (p) REVERT: P 61 ARG cc_start: 0.7220 (ttm170) cc_final: 0.6794 (ttm-80) REVERT: P 491 MET cc_start: 0.8487 (ttm) cc_final: 0.8087 (ttp) REVERT: P 499 PHE cc_start: 0.6644 (m-80) cc_final: 0.6121 (m-80) REVERT: P 563 MET cc_start: 0.6331 (mpp) cc_final: 0.5914 (mmm) REVERT: Q 405 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7527 (mtpt) REVERT: Q 436 ARG cc_start: 0.6612 (ttt90) cc_final: 0.6218 (mmm-85) REVERT: Q 510 ASP cc_start: 0.8130 (m-30) cc_final: 0.7751 (m-30) REVERT: R 73 GLU cc_start: 0.7316 (tt0) cc_final: 0.7046 (tt0) REVERT: R 110 LYS cc_start: 0.6256 (mttt) cc_final: 0.6003 (mttt) REVERT: R 138 PHE cc_start: 0.6455 (t80) cc_final: 0.6101 (t80) REVERT: R 401 ASP cc_start: 0.7636 (m-30) cc_final: 0.7183 (m-30) REVERT: R 442 GLN cc_start: 0.7757 (mm110) cc_final: 0.7495 (mm-40) REVERT: R 531 SER cc_start: 0.7882 (t) cc_final: 0.7641 (p) REVERT: R 538 ARG cc_start: 0.7244 (ttm-80) cc_final: 0.7026 (ttm110) REVERT: S 29 ASP cc_start: 0.7525 (t70) cc_final: 0.6677 (m-30) REVERT: S 41 GLU cc_start: 0.6613 (tp30) cc_final: 0.6131 (tp30) REVERT: S 50 LYS cc_start: 0.5425 (pttt) cc_final: 0.5213 (tptt) REVERT: S 123 ILE cc_start: 0.7031 (mt) cc_final: 0.6769 (tt) REVERT: S 140 LEU cc_start: 0.8172 (tp) cc_final: 0.7919 (tt) REVERT: S 141 GLN cc_start: 0.6700 (mt0) cc_final: 0.5992 (mm-40) REVERT: S 169 LYS cc_start: 0.7263 (ptmt) cc_final: 0.7036 (ptmm) REVERT: S 170 LYS cc_start: 0.7370 (mtpp) cc_final: 0.7089 (mtmm) REVERT: T 57 SER cc_start: 0.8280 (t) cc_final: 0.7981 (p) REVERT: T 61 ARG cc_start: 0.7094 (ttm170) cc_final: 0.6796 (ttm170) REVERT: T 353 LYS cc_start: 0.6795 (tppt) cc_final: 0.6522 (mmmt) REVERT: T 400 MET cc_start: 0.8423 (mmt) cc_final: 0.7752 (mmt) REVERT: T 563 MET cc_start: 0.6553 (mpp) cc_final: 0.6276 (mmm) REVERT: V 405 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7543 (mtpt) REVERT: V 412 MET cc_start: 0.8764 (mmm) cc_final: 0.8346 (mmt) REVERT: V 436 ARG cc_start: 0.6787 (ttt90) cc_final: 0.6260 (mmm-85) REVERT: W 46 GLU cc_start: 0.7381 (tt0) cc_final: 0.7075 (tt0) REVERT: W 401 ASP cc_start: 0.7638 (m-30) cc_final: 0.7148 (m-30) REVERT: W 581 LYS cc_start: 0.8311 (mttt) cc_final: 0.8058 (mttm) REVERT: X 29 ASP cc_start: 0.7779 (t70) cc_final: 0.7361 (t70) REVERT: X 41 GLU cc_start: 0.6888 (tp30) cc_final: 0.6609 (tp30) REVERT: X 50 LYS cc_start: 0.5745 (pttt) cc_final: 0.5333 (tptt) REVERT: X 89 SER cc_start: 0.6990 (m) cc_final: 0.5997 (t) REVERT: X 123 ILE cc_start: 0.7128 (mt) cc_final: 0.6891 (tt) REVERT: X 125 GLU cc_start: 0.6446 (tt0) cc_final: 0.6243 (tt0) REVERT: X 127 ILE cc_start: 0.8502 (mt) cc_final: 0.8300 (mm) REVERT: X 141 GLN cc_start: 0.6490 (mt0) cc_final: 0.5787 (mm-40) REVERT: X 268 LYS cc_start: 0.4984 (ptmt) cc_final: 0.4499 (ptpp) REVERT: X 269 LEU cc_start: 0.7286 (mm) cc_final: 0.6790 (mt) outliers start: 126 outliers final: 102 residues processed: 1088 average time/residue: 0.6996 time to fit residues: 1270.3332 Evaluate side-chains 941 residues out of total 7998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 839 time to evaluate : 6.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 148 ASP Chi-restraints excluded: chain O residue 233 LEU Chi-restraints excluded: chain O residue 432 PHE Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 116 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 432 PHE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 515 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 469 THR Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 515 THR Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain K residue 515 THR Chi-restraints excluded: chain K residue 561 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 148 ASP Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 432 PHE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 92 ILE Chi-restraints excluded: chain P residue 515 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 469 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 313 ASN Chi-restraints excluded: chain R residue 432 PHE Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 100 ASP Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 344 VAL Chi-restraints excluded: chain T residue 352 VAL Chi-restraints excluded: chain T residue 426 ILE Chi-restraints excluded: chain T residue 515 THR Chi-restraints excluded: chain V residue 20 VAL Chi-restraints excluded: chain V residue 64 ARG Chi-restraints excluded: chain V residue 469 THR Chi-restraints excluded: chain W residue 195 LEU Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 432 PHE Chi-restraints excluded: chain W residue 515 THR Chi-restraints excluded: chain X residue 4 THR Chi-restraints excluded: chain X residue 19 ASN Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain X residue 263 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 466 optimal weight: 7.9990 chunk 260 optimal weight: 8.9990 chunk 698 optimal weight: 4.9990 chunk 571 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 840 optimal weight: 9.9990 chunk 908 optimal weight: 9.9990 chunk 748 optimal weight: 20.0000 chunk 833 optimal weight: 0.8980 chunk 286 optimal weight: 20.0000 chunk 674 optimal weight: 0.0030 overall best weight: 3.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 329 HIS I 407 HIS I 468 ASN C 407 HIS ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 GLN E 163 ASN G 407 HIS J 163 ASN L 329 HIS L 407 HIS L 468 ASN Q 407 HIS ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 258 GLN S 163 ASN V 407 HIS X 163 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 74298 Z= 0.241 Angle : 0.550 11.348 100374 Z= 0.301 Chirality : 0.045 0.171 11220 Planarity : 0.004 0.037 13236 Dihedral : 5.736 80.499 10086 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.13 % Allowed : 8.55 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.08), residues: 9246 helix: 1.01 (0.10), residues: 2802 sheet: 0.16 (0.11), residues: 2010 loop : -0.62 (0.09), residues: 4434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 76 HIS 0.006 0.001 HIS P 329 PHE 0.020 0.002 PHE S 134 TYR 0.018 0.002 TYR J 137 ARG 0.006 0.001 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18492 Ramachandran restraints generated. 9246 Oldfield, 0 Emsley, 9246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18492 Ramachandran restraints generated. 9246 Oldfield, 0 Emsley, 9246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 7998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 894 time to evaluate : 6.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 SER cc_start: 0.8303 (t) cc_final: 0.8044 (p) REVERT: B 61 ARG cc_start: 0.7010 (ttm170) cc_final: 0.6667 (tpp-160) REVERT: B 353 LYS cc_start: 0.6495 (tppt) cc_final: 0.6254 (tttt) REVERT: B 374 LYS cc_start: 0.7046 (mttt) cc_final: 0.6779 (mtmm) REVERT: B 491 MET cc_start: 0.8422 (ttm) cc_final: 0.8038 (ttm) REVERT: B 563 MET cc_start: 0.6450 (mpp) cc_final: 0.6158 (mmm) REVERT: I 405 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7621 (mtpt) REVERT: I 425 GLU cc_start: 0.8138 (tt0) cc_final: 0.7779 (tt0) REVERT: I 436 ARG cc_start: 0.6766 (ttt90) cc_final: 0.6221 (mmm-85) REVERT: I 516 ARG cc_start: 0.7344 (mtp85) cc_final: 0.7115 (mtp85) REVERT: I 551 GLN cc_start: 0.7579 (mt0) cc_final: 0.7093 (tt0) REVERT: O 90 MET cc_start: 0.8238 (ttp) cc_final: 0.7925 (ttp) REVERT: O 138 PHE cc_start: 0.6394 (t80) cc_final: 0.6117 (t80) REVERT: O 468 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6953 (m-40) REVERT: O 538 ARG cc_start: 0.7151 (ttm-80) cc_final: 0.6876 (ttp-110) REVERT: O 581 LYS cc_start: 0.8367 (mttt) cc_final: 0.8115 (mttm) REVERT: U 29 ASP cc_start: 0.7543 (t70) cc_final: 0.6659 (m-30) REVERT: U 41 GLU cc_start: 0.6818 (tp30) cc_final: 0.6396 (tp30) REVERT: U 50 LYS cc_start: 0.5549 (pttt) cc_final: 0.5320 (tptt) REVERT: U 89 SER cc_start: 0.7113 (m) cc_final: 0.6121 (t) REVERT: U 141 GLN cc_start: 0.6324 (mt0) cc_final: 0.5785 (mm-40) REVERT: U 260 TYR cc_start: 0.6779 (t80) cc_final: 0.6350 (t80) REVERT: U 268 LYS cc_start: 0.4981 (ptmt) cc_final: 0.4547 (ptpp) REVERT: A 57 SER cc_start: 0.8330 (t) cc_final: 0.8044 (p) REVERT: A 61 ARG cc_start: 0.7245 (ttm170) cc_final: 0.6822 (ttm-80) REVERT: A 491 MET cc_start: 0.8458 (ttm) cc_final: 0.8035 (ttp) REVERT: A 499 PHE cc_start: 0.6451 (m-80) cc_final: 0.5928 (m-80) REVERT: A 563 MET cc_start: 0.6294 (mpp) cc_final: 0.5890 (mmm) REVERT: C 436 ARG cc_start: 0.6589 (ttt90) cc_final: 0.6111 (mmm-85) REVERT: D 73 GLU cc_start: 0.7395 (tt0) cc_final: 0.7163 (tt0) REVERT: D 110 LYS cc_start: 0.6348 (mttt) cc_final: 0.6112 (mttt) REVERT: D 138 PHE cc_start: 0.6480 (t80) cc_final: 0.6190 (t80) REVERT: D 442 GLN cc_start: 0.7793 (mm110) cc_final: 0.7481 (mm-40) REVERT: D 538 ARG cc_start: 0.7265 (ttm-80) cc_final: 0.6575 (ttp80) REVERT: E 29 ASP cc_start: 0.7518 (t70) cc_final: 0.6692 (m-30) REVERT: E 41 GLU cc_start: 0.6395 (tp30) cc_final: 0.6189 (tp30) REVERT: E 50 LYS cc_start: 0.5399 (pttt) cc_final: 0.5183 (tptt) REVERT: E 141 GLN cc_start: 0.6549 (mt0) cc_final: 0.5949 (mm-40) REVERT: E 170 LYS cc_start: 0.7392 (mtpp) cc_final: 0.7173 (mtmm) REVERT: E 260 TYR cc_start: 0.6691 (t80) cc_final: 0.6322 (t80) REVERT: E 268 LYS cc_start: 0.4853 (ptmt) cc_final: 0.4469 (pttt) REVERT: F 57 SER cc_start: 0.8239 (t) cc_final: 0.8009 (p) REVERT: F 61 ARG cc_start: 0.6990 (ttm170) cc_final: 0.6739 (ttm170) REVERT: F 353 LYS cc_start: 0.6869 (tppt) cc_final: 0.6581 (tttt) REVERT: F 562 SER cc_start: 0.7950 (m) cc_final: 0.7270 (t) REVERT: F 563 MET cc_start: 0.6503 (mpp) cc_final: 0.6109 (mmm) REVERT: G 405 LYS cc_start: 0.7908 (mtpt) cc_final: 0.7553 (mtpt) REVERT: G 436 ARG cc_start: 0.6776 (ttt90) cc_final: 0.6275 (mmm-85) REVERT: H 33 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6492 (mt-10) REVERT: H 46 GLU cc_start: 0.7567 (tt0) cc_final: 0.7264 (tt0) REVERT: H 227 ASN cc_start: 0.6713 (m-40) cc_final: 0.6267 (t0) REVERT: H 400 MET cc_start: 0.8211 (mmt) cc_final: 0.8010 (mmm) REVERT: H 581 LYS cc_start: 0.8193 (mttt) cc_final: 0.6559 (pptt) REVERT: J 29 ASP cc_start: 0.7738 (t70) cc_final: 0.7368 (t70) REVERT: J 41 GLU cc_start: 0.6814 (tp30) cc_final: 0.6538 (tp30) REVERT: J 50 LYS cc_start: 0.5689 (pttt) cc_final: 0.5348 (tptt) REVERT: J 89 SER cc_start: 0.7009 (m) cc_final: 0.6059 (t) REVERT: J 141 GLN cc_start: 0.6396 (mt0) cc_final: 0.6001 (mm-40) REVERT: J 217 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6693 (mm-30) REVERT: J 231 ASP cc_start: 0.7299 (t0) cc_final: 0.7029 (t0) REVERT: J 269 LEU cc_start: 0.6604 (mt) cc_final: 0.6282 (mt) REVERT: K 57 SER cc_start: 0.8302 (t) cc_final: 0.8044 (p) REVERT: K 61 ARG cc_start: 0.7009 (ttm170) cc_final: 0.6668 (tpp-160) REVERT: K 353 LYS cc_start: 0.6499 (tppt) cc_final: 0.6257 (tttt) REVERT: K 374 LYS cc_start: 0.7049 (mttt) cc_final: 0.6780 (mtmm) REVERT: K 491 MET cc_start: 0.8423 (ttm) cc_final: 0.8039 (ttm) REVERT: K 563 MET cc_start: 0.6437 (mpp) cc_final: 0.6146 (mmm) REVERT: L 405 LYS cc_start: 0.7873 (mtpt) cc_final: 0.7620 (mtpt) REVERT: L 425 GLU cc_start: 0.8138 (tt0) cc_final: 0.7779 (tt0) REVERT: L 436 ARG cc_start: 0.6764 (ttt90) cc_final: 0.6219 (mmm-85) REVERT: L 516 ARG cc_start: 0.7345 (mtp85) cc_final: 0.7118 (mtp85) REVERT: L 551 GLN cc_start: 0.7579 (mt0) cc_final: 0.7096 (tt0) REVERT: M 90 MET cc_start: 0.8235 (ttp) cc_final: 0.7920 (ttp) REVERT: M 138 PHE cc_start: 0.6396 (t80) cc_final: 0.6123 (t80) REVERT: M 468 ASN cc_start: 0.7302 (OUTLIER) cc_final: 0.6953 (m-40) REVERT: M 538 ARG cc_start: 0.7149 (ttm-80) cc_final: 0.6875 (ttp-110) REVERT: M 581 LYS cc_start: 0.8365 (mttt) cc_final: 0.8116 (mttm) REVERT: N 29 ASP cc_start: 0.7539 (t70) cc_final: 0.6658 (m-30) REVERT: N 41 GLU cc_start: 0.6817 (tp30) cc_final: 0.6397 (tp30) REVERT: N 50 LYS cc_start: 0.5542 (pttt) cc_final: 0.5316 (tptt) REVERT: N 89 SER cc_start: 0.7110 (m) cc_final: 0.6116 (t) REVERT: N 141 GLN cc_start: 0.6323 (mt0) cc_final: 0.5781 (mm-40) REVERT: N 260 TYR cc_start: 0.6780 (t80) cc_final: 0.6353 (t80) REVERT: N 268 LYS cc_start: 0.4983 (ptmt) cc_final: 0.4546 (ptpp) REVERT: P 57 SER cc_start: 0.8330 (t) cc_final: 0.8043 (p) REVERT: P 61 ARG cc_start: 0.7250 (ttm170) cc_final: 0.6825 (ttm-80) REVERT: P 491 MET cc_start: 0.8461 (ttm) cc_final: 0.8040 (ttp) REVERT: P 499 PHE cc_start: 0.6454 (m-80) cc_final: 0.5932 (m-80) REVERT: P 563 MET cc_start: 0.6297 (mpp) cc_final: 0.5890 (mmm) REVERT: Q 436 ARG cc_start: 0.6590 (ttt90) cc_final: 0.6110 (mmm-85) REVERT: R 73 GLU cc_start: 0.7398 (tt0) cc_final: 0.7164 (tt0) REVERT: R 110 LYS cc_start: 0.6341 (mttt) cc_final: 0.6106 (mttt) REVERT: R 138 PHE cc_start: 0.6480 (t80) cc_final: 0.6186 (t80) REVERT: R 442 GLN cc_start: 0.7794 (mm110) cc_final: 0.7481 (mm-40) REVERT: R 538 ARG cc_start: 0.7263 (ttm-80) cc_final: 0.6574 (ttp80) REVERT: S 29 ASP cc_start: 0.7516 (t70) cc_final: 0.6689 (m-30) REVERT: S 41 GLU cc_start: 0.6395 (tp30) cc_final: 0.6193 (tp30) REVERT: S 50 LYS cc_start: 0.5400 (pttt) cc_final: 0.5184 (tptt) REVERT: S 141 GLN cc_start: 0.6550 (mt0) cc_final: 0.5950 (mm-40) REVERT: S 170 LYS cc_start: 0.7395 (mtpp) cc_final: 0.7177 (mtmm) REVERT: S 260 TYR cc_start: 0.6730 (t80) cc_final: 0.6366 (t80) REVERT: S 268 LYS cc_start: 0.4856 (ptmt) cc_final: 0.4472 (pttt) REVERT: T 57 SER cc_start: 0.8240 (t) cc_final: 0.8010 (p) REVERT: T 61 ARG cc_start: 0.6987 (ttm170) cc_final: 0.6740 (ttm170) REVERT: T 353 LYS cc_start: 0.6868 (tppt) cc_final: 0.6582 (tttt) REVERT: T 562 SER cc_start: 0.7948 (m) cc_final: 0.7271 (t) REVERT: T 563 MET cc_start: 0.6495 (mpp) cc_final: 0.6101 (mmm) REVERT: V 405 LYS cc_start: 0.7904 (mtpt) cc_final: 0.7551 (mtpt) REVERT: V 436 ARG cc_start: 0.6775 (ttt90) cc_final: 0.6275 (mmm-85) REVERT: W 33 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6489 (mt-10) REVERT: W 46 GLU cc_start: 0.7565 (tt0) cc_final: 0.7261 (tt0) REVERT: W 227 ASN cc_start: 0.6717 (m-40) cc_final: 0.6271 (t0) REVERT: W 400 MET cc_start: 0.8210 (mmt) cc_final: 0.8008 (mmm) REVERT: W 581 LYS cc_start: 0.8198 (mttt) cc_final: 0.6564 (pptt) REVERT: X 29 ASP cc_start: 0.7743 (t70) cc_final: 0.7374 (t70) REVERT: X 41 GLU cc_start: 0.6812 (tp30) cc_final: 0.6538 (tp30) REVERT: X 50 LYS cc_start: 0.5690 (pttt) cc_final: 0.5348 (tptt) REVERT: X 89 SER cc_start: 0.7012 (m) cc_final: 0.6062 (t) REVERT: X 127 ILE cc_start: 0.8478 (mt) cc_final: 0.8277 (mm) REVERT: X 141 GLN cc_start: 0.6394 (mt0) cc_final: 0.6003 (mm-40) REVERT: X 217 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6692 (mm-30) REVERT: X 231 ASP cc_start: 0.7301 (t0) cc_final: 0.7030 (t0) REVERT: X 268 LYS cc_start: 0.4760 (ptmt) cc_final: 0.4330 (ptpp) outliers start: 170 outliers final: 132 residues processed: 1004 average time/residue: 0.6598 time to fit residues: 1114.4424 Evaluate side-chains 943 residues out of total 7998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 807 time to evaluate : 6.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 407 HIS Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain O residue 33 GLU Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 76 TRP Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain O residue 233 LEU Chi-restraints excluded: chain O residue 375 GLU Chi-restraints excluded: chain O residue 432 PHE Chi-restraints excluded: chain O residue 468 ASN Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 58 VAL Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 116 VAL Chi-restraints excluded: chain U residue 235 ILE Chi-restraints excluded: chain U residue 238 ASP Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain D residue 76 TRP Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 432 PHE Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 515 THR Chi-restraints excluded: chain F residue 561 ILE Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 407 HIS Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain H residue 76 TRP Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 217 GLU Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain K residue 561 ILE Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 407 HIS Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain M residue 33 GLU Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 76 TRP Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 375 GLU Chi-restraints excluded: chain M residue 432 PHE Chi-restraints excluded: chain M residue 468 ASN Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 235 ILE Chi-restraints excluded: chain N residue 238 ASP Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 64 ARG Chi-restraints excluded: chain P residue 92 ILE Chi-restraints excluded: chain Q residue 469 THR Chi-restraints excluded: chain R residue 76 TRP Chi-restraints excluded: chain R residue 148 ASP Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 313 ASN Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 432 PHE Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 64 ARG Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain T residue 352 VAL Chi-restraints excluded: chain T residue 426 ILE Chi-restraints excluded: chain T residue 515 THR Chi-restraints excluded: chain T residue 561 ILE Chi-restraints excluded: chain V residue 64 ARG Chi-restraints excluded: chain V residue 407 HIS Chi-restraints excluded: chain V residue 447 ILE Chi-restraints excluded: chain W residue 76 TRP Chi-restraints excluded: chain W residue 137 ILE Chi-restraints excluded: chain W residue 148 ASP Chi-restraints excluded: chain W residue 195 LEU Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 432 PHE Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 189 VAL Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain X residue 263 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 830 optimal weight: 8.9990 chunk 632 optimal weight: 0.6980 chunk 436 optimal weight: 1.9990 chunk 93 optimal weight: 30.0000 chunk 401 optimal weight: 30.0000 chunk 564 optimal weight: 10.0000 chunk 843 optimal weight: 8.9990 chunk 893 optimal weight: 4.9990 chunk 440 optimal weight: 10.0000 chunk 799 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 ASN I 468 ASN U 163 ASN C 407 HIS C 543 GLN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 453 ASN G 543 GLN K 453 ASN L 468 ASN N 163 ASN Q 407 HIS Q 543 GLN ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 453 ASN V 543 GLN W 258 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 74298 Z= 0.325 Angle : 0.595 11.073 100374 Z= 0.322 Chirality : 0.046 0.229 11220 Planarity : 0.004 0.036 13236 Dihedral : 5.804 76.436 10086 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.11 % Allowed : 9.87 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.08), residues: 9246 helix: 1.02 (0.10), residues: 2772 sheet: 0.05 (0.11), residues: 2088 loop : -0.76 (0.08), residues: 4386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 76 HIS 0.016 0.002 HIS I 407 PHE 0.020 0.002 PHE G 470 TYR 0.015 0.002 TYR G 566 ARG 0.005 0.001 ARG P 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18492 Ramachandran restraints generated. 9246 Oldfield, 0 Emsley, 9246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18492 Ramachandran restraints generated. 9246 Oldfield, 0 Emsley, 9246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 7998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 857 time to evaluate : 6.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 SER cc_start: 0.8300 (t) cc_final: 0.8051 (p) REVERT: B 61 ARG cc_start: 0.7011 (ttm170) cc_final: 0.6647 (tpp-160) REVERT: B 353 LYS cc_start: 0.6600 (tppt) cc_final: 0.6359 (tttt) REVERT: B 374 LYS cc_start: 0.7073 (mttt) cc_final: 0.6776 (mtmm) REVERT: B 491 MET cc_start: 0.8519 (ttm) cc_final: 0.8173 (ttm) REVERT: B 533 LEU cc_start: 0.1757 (OUTLIER) cc_final: 0.1485 (tp) REVERT: B 563 MET cc_start: 0.6427 (mpp) cc_final: 0.6067 (mmm) REVERT: I 425 GLU cc_start: 0.8140 (tt0) cc_final: 0.7769 (tt0) REVERT: I 436 ARG cc_start: 0.6745 (ttt90) cc_final: 0.6141 (mmm-85) REVERT: I 551 GLN cc_start: 0.7708 (mt0) cc_final: 0.7044 (tt0) REVERT: O 90 MET cc_start: 0.8321 (ttp) cc_final: 0.8062 (ttp) REVERT: O 135 ARG cc_start: 0.6460 (tpt-90) cc_final: 0.6203 (tpp80) REVERT: O 233 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7250 (tt) REVERT: O 252 PHE cc_start: 0.6155 (t80) cc_final: 0.5905 (t80) REVERT: O 468 ASN cc_start: 0.7219 (OUTLIER) cc_final: 0.6806 (m-40) REVERT: O 581 LYS cc_start: 0.8295 (mttt) cc_final: 0.8005 (mttm) REVERT: U 23 GLU cc_start: 0.5900 (mt-10) cc_final: 0.5693 (pt0) REVERT: U 29 ASP cc_start: 0.7561 (t70) cc_final: 0.6830 (m-30) REVERT: U 41 GLU cc_start: 0.6606 (tp30) cc_final: 0.6275 (tp30) REVERT: U 45 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7694 (mt-10) REVERT: U 50 LYS cc_start: 0.5442 (pttt) cc_final: 0.5241 (tptt) REVERT: U 89 SER cc_start: 0.7134 (m) cc_final: 0.6240 (t) REVERT: U 141 GLN cc_start: 0.6057 (mt0) cc_final: 0.5534 (mm-40) REVERT: U 217 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6925 (mm-30) REVERT: U 260 TYR cc_start: 0.6722 (t80) cc_final: 0.6323 (t80) REVERT: A 57 SER cc_start: 0.8353 (t) cc_final: 0.8010 (p) REVERT: A 61 ARG cc_start: 0.7280 (ttm170) cc_final: 0.6801 (ttm-80) REVERT: A 491 MET cc_start: 0.8523 (ttm) cc_final: 0.8085 (ttp) REVERT: A 499 PHE cc_start: 0.6555 (m-80) cc_final: 0.6068 (m-80) REVERT: A 562 SER cc_start: 0.7644 (m) cc_final: 0.7305 (t) REVERT: A 563 MET cc_start: 0.6491 (mpp) cc_final: 0.5975 (mmm) REVERT: C 436 ARG cc_start: 0.6572 (ttt90) cc_final: 0.6009 (mmm-85) REVERT: D 22 THR cc_start: 0.9046 (m) cc_final: 0.8775 (m) REVERT: D 33 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6834 (mt-10) REVERT: D 90 MET cc_start: 0.8242 (ttp) cc_final: 0.7865 (ttm) REVERT: D 110 LYS cc_start: 0.6227 (mttt) cc_final: 0.5911 (mttt) REVERT: D 138 PHE cc_start: 0.6499 (t80) cc_final: 0.6231 (t80) REVERT: D 170 GLU cc_start: 0.3867 (mt-10) cc_final: 0.3451 (mm-30) REVERT: D 226 LYS cc_start: 0.5570 (mttt) cc_final: 0.5280 (mtmt) REVERT: D 401 ASP cc_start: 0.7557 (m-30) cc_final: 0.7162 (m-30) REVERT: D 538 ARG cc_start: 0.7438 (ttm-80) cc_final: 0.7150 (ttm110) REVERT: D 569 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7075 (mmm160) REVERT: E 29 ASP cc_start: 0.7556 (t70) cc_final: 0.6723 (m-30) REVERT: E 50 LYS cc_start: 0.5439 (pttt) cc_final: 0.5230 (tptt) REVERT: E 89 SER cc_start: 0.7249 (m) cc_final: 0.6301 (t) REVERT: E 141 GLN cc_start: 0.6480 (mt0) cc_final: 0.5916 (mm-40) REVERT: E 170 LYS cc_start: 0.7448 (mtpp) cc_final: 0.7214 (mtmm) REVERT: E 260 TYR cc_start: 0.6702 (t80) cc_final: 0.6323 (t80) REVERT: E 268 LYS cc_start: 0.4738 (ptmt) cc_final: 0.4303 (pttt) REVERT: F 57 SER cc_start: 0.8454 (t) cc_final: 0.8215 (p) REVERT: F 61 ARG cc_start: 0.7116 (ttm170) cc_final: 0.6804 (ttm170) REVERT: F 353 LYS cc_start: 0.7025 (tppt) cc_final: 0.6640 (tttt) REVERT: F 533 LEU cc_start: 0.2088 (OUTLIER) cc_final: 0.1733 (tp) REVERT: F 563 MET cc_start: 0.6552 (mpp) cc_final: 0.5971 (mmm) REVERT: G 436 ARG cc_start: 0.6703 (ttt90) cc_final: 0.6183 (mmm-85) REVERT: G 516 ARG cc_start: 0.7480 (mtp85) cc_final: 0.7200 (mtp85) REVERT: H 46 GLU cc_start: 0.7559 (tt0) cc_final: 0.7254 (tt0) REVERT: H 135 ARG cc_start: 0.6597 (tpt-90) cc_final: 0.6318 (tpp80) REVERT: H 227 ASN cc_start: 0.6741 (m-40) cc_final: 0.6064 (t0) REVERT: H 569 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8102 (mmm-85) REVERT: J 29 ASP cc_start: 0.7693 (t70) cc_final: 0.6771 (m-30) REVERT: J 41 GLU cc_start: 0.6820 (tp30) cc_final: 0.6443 (tp30) REVERT: J 50 LYS cc_start: 0.5698 (pttt) cc_final: 0.5341 (tptt) REVERT: J 89 SER cc_start: 0.7120 (m) cc_final: 0.6157 (t) REVERT: J 141 GLN cc_start: 0.6337 (mt0) cc_final: 0.5969 (mm-40) REVERT: J 217 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6848 (mm-30) REVERT: J 269 LEU cc_start: 0.6686 (mt) cc_final: 0.6340 (mt) REVERT: K 57 SER cc_start: 0.8300 (t) cc_final: 0.8052 (p) REVERT: K 61 ARG cc_start: 0.6981 (ttm170) cc_final: 0.6622 (tpp-160) REVERT: K 353 LYS cc_start: 0.6603 (tppt) cc_final: 0.6362 (tttt) REVERT: K 374 LYS cc_start: 0.7077 (mttt) cc_final: 0.6779 (mtmm) REVERT: K 491 MET cc_start: 0.8519 (ttm) cc_final: 0.8175 (ttm) REVERT: K 533 LEU cc_start: 0.1763 (OUTLIER) cc_final: 0.1489 (tp) REVERT: K 563 MET cc_start: 0.6444 (mpp) cc_final: 0.6067 (mmm) REVERT: L 425 GLU cc_start: 0.8140 (tt0) cc_final: 0.7767 (tt0) REVERT: L 436 ARG cc_start: 0.6746 (ttt90) cc_final: 0.6140 (mmm-85) REVERT: L 551 GLN cc_start: 0.7704 (mt0) cc_final: 0.7048 (tt0) REVERT: M 90 MET cc_start: 0.8316 (ttp) cc_final: 0.8055 (ttp) REVERT: M 135 ARG cc_start: 0.6464 (tpt-90) cc_final: 0.6206 (tpp80) REVERT: M 233 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7255 (tt) REVERT: M 252 PHE cc_start: 0.6155 (t80) cc_final: 0.5906 (t80) REVERT: M 468 ASN cc_start: 0.7217 (OUTLIER) cc_final: 0.6804 (m-40) REVERT: M 581 LYS cc_start: 0.8295 (mttt) cc_final: 0.8006 (mttm) REVERT: N 23 GLU cc_start: 0.5901 (mt-10) cc_final: 0.5691 (pt0) REVERT: N 29 ASP cc_start: 0.7560 (t70) cc_final: 0.6829 (m-30) REVERT: N 41 GLU cc_start: 0.6604 (tp30) cc_final: 0.6272 (tp30) REVERT: N 45 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7694 (mt-10) REVERT: N 50 LYS cc_start: 0.5443 (pttt) cc_final: 0.5241 (tptt) REVERT: N 89 SER cc_start: 0.7134 (m) cc_final: 0.6239 (t) REVERT: N 141 GLN cc_start: 0.6056 (mt0) cc_final: 0.5529 (mm-40) REVERT: N 217 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6928 (mm-30) REVERT: N 260 TYR cc_start: 0.6721 (t80) cc_final: 0.6323 (t80) REVERT: P 57 SER cc_start: 0.8353 (t) cc_final: 0.8010 (p) REVERT: P 61 ARG cc_start: 0.7283 (ttm170) cc_final: 0.6802 (ttm-80) REVERT: P 491 MET cc_start: 0.8528 (ttm) cc_final: 0.8089 (ttp) REVERT: P 499 PHE cc_start: 0.6545 (m-80) cc_final: 0.6061 (m-80) REVERT: P 562 SER cc_start: 0.7643 (m) cc_final: 0.7306 (t) REVERT: P 563 MET cc_start: 0.6492 (mpp) cc_final: 0.5975 (mmm) REVERT: Q 436 ARG cc_start: 0.6577 (ttt90) cc_final: 0.6011 (mmm-85) REVERT: R 22 THR cc_start: 0.9049 (m) cc_final: 0.8777 (m) REVERT: R 33 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6835 (mt-10) REVERT: R 90 MET cc_start: 0.8239 (ttp) cc_final: 0.7861 (ttm) REVERT: R 110 LYS cc_start: 0.6221 (mttt) cc_final: 0.5906 (mttt) REVERT: R 135 ARG cc_start: 0.6473 (tpt-90) cc_final: 0.6248 (tpp80) REVERT: R 138 PHE cc_start: 0.6501 (t80) cc_final: 0.6230 (t80) REVERT: R 170 GLU cc_start: 0.3871 (mt-10) cc_final: 0.3453 (mm-30) REVERT: R 226 LYS cc_start: 0.5565 (mttt) cc_final: 0.5278 (mtmt) REVERT: R 401 ASP cc_start: 0.7561 (m-30) cc_final: 0.7166 (m-30) REVERT: R 538 ARG cc_start: 0.7437 (ttm-80) cc_final: 0.7151 (ttm110) REVERT: R 569 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7074 (mmm160) REVERT: S 29 ASP cc_start: 0.7553 (t70) cc_final: 0.6719 (m-30) REVERT: S 50 LYS cc_start: 0.5437 (pttt) cc_final: 0.5230 (tptt) REVERT: S 89 SER cc_start: 0.7249 (m) cc_final: 0.6302 (t) REVERT: S 141 GLN cc_start: 0.6483 (mt0) cc_final: 0.5917 (mm-40) REVERT: S 170 LYS cc_start: 0.7451 (mtpp) cc_final: 0.7219 (mtmm) REVERT: S 260 TYR cc_start: 0.6706 (t80) cc_final: 0.6328 (t80) REVERT: S 268 LYS cc_start: 0.4741 (ptmt) cc_final: 0.4305 (pttt) REVERT: T 57 SER cc_start: 0.8457 (t) cc_final: 0.8218 (p) REVERT: T 61 ARG cc_start: 0.7116 (ttm170) cc_final: 0.6807 (ttm170) REVERT: T 353 LYS cc_start: 0.7024 (tppt) cc_final: 0.6639 (tttt) REVERT: T 533 LEU cc_start: 0.2086 (OUTLIER) cc_final: 0.1732 (tp) REVERT: T 563 MET cc_start: 0.6545 (mpp) cc_final: 0.5969 (mmm) REVERT: V 436 ARG cc_start: 0.6702 (ttt90) cc_final: 0.6182 (mmm-85) REVERT: V 516 ARG cc_start: 0.7481 (mtp85) cc_final: 0.7201 (mtp85) REVERT: W 46 GLU cc_start: 0.7562 (tt0) cc_final: 0.7255 (tt0) REVERT: W 135 ARG cc_start: 0.6600 (tpt-90) cc_final: 0.6322 (tpp80) REVERT: W 227 ASN cc_start: 0.6741 (m-40) cc_final: 0.6061 (t0) REVERT: W 569 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8106 (mmm-85) REVERT: X 29 ASP cc_start: 0.7696 (t70) cc_final: 0.6773 (m-30) REVERT: X 41 GLU cc_start: 0.6824 (tp30) cc_final: 0.6445 (tp30) REVERT: X 50 LYS cc_start: 0.5697 (pttt) cc_final: 0.5340 (tptt) REVERT: X 89 SER cc_start: 0.7121 (m) cc_final: 0.6158 (t) REVERT: X 141 GLN cc_start: 0.6337 (mt0) cc_final: 0.5969 (mm-40) REVERT: X 217 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6845 (mm-30) REVERT: X 268 LYS cc_start: 0.4689 (ptmt) cc_final: 0.4251 (ptpp) REVERT: X 269 LEU cc_start: 0.7120 (mm) cc_final: 0.6895 (mm) outliers start: 248 outliers final: 192 residues processed: 1025 average time/residue: 0.6594 time to fit residues: 1131.1087 Evaluate side-chains 1014 residues out of total 7998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 806 time to evaluate : 5.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 352 VAL Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain I residue 584 THR Chi-restraints excluded: chain O residue 33 GLU Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 76 TRP Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 148 ASP Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain O residue 233 LEU Chi-restraints excluded: chain O residue 375 GLU Chi-restraints excluded: chain O residue 432 PHE Chi-restraints excluded: chain O residue 438 SER Chi-restraints excluded: chain O residue 468 ASN Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 58 VAL Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 116 VAL Chi-restraints excluded: chain U residue 123 ILE Chi-restraints excluded: chain U residue 182 VAL Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 217 GLU Chi-restraints excluded: chain U residue 235 ILE Chi-restraints excluded: chain U residue 238 ASP Chi-restraints excluded: chain U residue 269 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 407 HIS Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 76 TRP Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 432 PHE Chi-restraints excluded: chain D residue 569 ARG Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 515 THR Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain F residue 561 ILE Chi-restraints excluded: chain G residue 41 GLN Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 469 THR Chi-restraints excluded: chain H residue 76 TRP Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 515 THR Chi-restraints excluded: chain H residue 569 ARG Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 217 GLU Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain K residue 533 LEU Chi-restraints excluded: chain K residue 561 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain L residue 584 THR Chi-restraints excluded: chain M residue 33 GLU Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 76 TRP Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 148 ASP Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 375 GLU Chi-restraints excluded: chain M residue 432 PHE Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain M residue 468 ASN Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 217 GLU Chi-restraints excluded: chain N residue 235 ILE Chi-restraints excluded: chain N residue 238 ASP Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 64 ARG Chi-restraints excluded: chain P residue 92 ILE Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 384 LEU Chi-restraints excluded: chain P residue 515 THR Chi-restraints excluded: chain Q residue 352 VAL Chi-restraints excluded: chain Q residue 407 HIS Chi-restraints excluded: chain Q residue 447 ILE Chi-restraints excluded: chain Q residue 469 THR Chi-restraints excluded: chain Q residue 584 THR Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 76 TRP Chi-restraints excluded: chain R residue 148 ASP Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 313 ASN Chi-restraints excluded: chain R residue 432 PHE Chi-restraints excluded: chain R residue 569 ARG Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain T residue 344 VAL Chi-restraints excluded: chain T residue 352 VAL Chi-restraints excluded: chain T residue 426 ILE Chi-restraints excluded: chain T residue 515 THR Chi-restraints excluded: chain T residue 533 LEU Chi-restraints excluded: chain T residue 561 ILE Chi-restraints excluded: chain V residue 41 GLN Chi-restraints excluded: chain V residue 64 ARG Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 352 VAL Chi-restraints excluded: chain V residue 447 ILE Chi-restraints excluded: chain V residue 469 THR Chi-restraints excluded: chain W residue 76 TRP Chi-restraints excluded: chain W residue 137 ILE Chi-restraints excluded: chain W residue 148 ASP Chi-restraints excluded: chain W residue 195 LEU Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 264 ILE Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 432 PHE Chi-restraints excluded: chain W residue 515 THR Chi-restraints excluded: chain W residue 569 ARG Chi-restraints excluded: chain X residue 4 THR Chi-restraints excluded: chain X residue 19 ASN Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 100 ASP Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 189 VAL Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain X residue 263 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 743 optimal weight: 9.9990 chunk 506 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 665 optimal weight: 7.9990 chunk 368 optimal weight: 7.9990 chunk 762 optimal weight: 9.9990 chunk 617 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 456 optimal weight: 10.0000 chunk 801 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 329 HIS I 407 HIS I 468 ASN A 453 ASN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 GLN H 519 ASN L 329 HIS L 407 HIS L 468 ASN P 453 ASN ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 519 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 74298 Z= 0.326 Angle : 0.591 11.718 100374 Z= 0.319 Chirality : 0.047 0.270 11220 Planarity : 0.004 0.038 13236 Dihedral : 5.754 74.564 10086 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.34 % Allowed : 11.32 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.08), residues: 9246 helix: 0.92 (0.10), residues: 2808 sheet: -0.01 (0.11), residues: 2058 loop : -0.92 (0.08), residues: 4380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 76 HIS 0.019 0.002 HIS C 407 PHE 0.031 0.002 PHE E 43 TYR 0.021 0.002 TYR X 137 ARG 0.005 0.001 ARG K 464 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18492 Ramachandran restraints generated. 9246 Oldfield, 0 Emsley, 9246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18492 Ramachandran restraints generated. 9246 Oldfield, 0 Emsley, 9246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 7998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 823 time to evaluate : 7.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 SER cc_start: 0.8370 (t) cc_final: 0.8027 (p) REVERT: B 61 ARG cc_start: 0.7023 (ttm170) cc_final: 0.6665 (tpp-160) REVERT: B 353 LYS cc_start: 0.6594 (tppt) cc_final: 0.6377 (tttt) REVERT: B 374 LYS cc_start: 0.7057 (mttt) cc_final: 0.6758 (mtmm) REVERT: B 428 GLU cc_start: 0.7279 (mt-10) cc_final: 0.7005 (mt-10) REVERT: B 464 ARG cc_start: 0.7411 (mtm-85) cc_final: 0.7148 (mtm-85) REVERT: B 491 MET cc_start: 0.8534 (ttm) cc_final: 0.8170 (ttm) REVERT: B 533 LEU cc_start: 0.1852 (OUTLIER) cc_final: 0.1586 (tp) REVERT: B 563 MET cc_start: 0.6407 (mpp) cc_final: 0.6057 (mmm) REVERT: I 436 ARG cc_start: 0.6723 (ttt90) cc_final: 0.6091 (mmm-85) REVERT: I 551 GLN cc_start: 0.7738 (mt0) cc_final: 0.7081 (tt0) REVERT: O 18 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8382 (mm) REVERT: O 43 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7293 (mt-10) REVERT: O 46 GLU cc_start: 0.7541 (tt0) cc_final: 0.7271 (tt0) REVERT: O 90 MET cc_start: 0.8332 (ttp) cc_final: 0.8102 (ttp) REVERT: O 138 PHE cc_start: 0.6649 (t80) cc_final: 0.6190 (t80) REVERT: O 252 PHE cc_start: 0.6261 (t80) cc_final: 0.6049 (t80) REVERT: O 468 ASN cc_start: 0.7210 (OUTLIER) cc_final: 0.6754 (m-40) REVERT: O 581 LYS cc_start: 0.8284 (mttt) cc_final: 0.8030 (mttm) REVERT: U 29 ASP cc_start: 0.7479 (t70) cc_final: 0.7169 (t0) REVERT: U 41 GLU cc_start: 0.6585 (tp30) cc_final: 0.6171 (tp30) REVERT: U 45 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7672 (mt-10) REVERT: U 50 LYS cc_start: 0.5428 (pttt) cc_final: 0.5175 (tptt) REVERT: U 89 SER cc_start: 0.7175 (m) cc_final: 0.6296 (t) REVERT: U 141 GLN cc_start: 0.5821 (mt0) cc_final: 0.5406 (mm-40) REVERT: U 207 MET cc_start: 0.6855 (tmm) cc_final: 0.6638 (tmm) REVERT: U 217 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6959 (mm-30) REVERT: U 260 TYR cc_start: 0.6756 (t80) cc_final: 0.6316 (t80) REVERT: A 57 SER cc_start: 0.8410 (t) cc_final: 0.7982 (p) REVERT: A 61 ARG cc_start: 0.7325 (ttm170) cc_final: 0.6838 (ttm-80) REVERT: A 384 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6980 (tt) REVERT: A 491 MET cc_start: 0.8501 (ttm) cc_final: 0.8033 (ttp) REVERT: A 499 PHE cc_start: 0.6588 (m-80) cc_final: 0.6113 (m-80) REVERT: A 563 MET cc_start: 0.6409 (mpp) cc_final: 0.5881 (mmm) REVERT: C 436 ARG cc_start: 0.6576 (ttt90) cc_final: 0.5994 (mmm-85) REVERT: C 516 ARG cc_start: 0.7479 (mtp85) cc_final: 0.7210 (mtp85) REVERT: D 22 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8745 (m) REVERT: D 33 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6811 (mt-10) REVERT: D 90 MET cc_start: 0.8273 (ttp) cc_final: 0.8024 (ttm) REVERT: D 110 LYS cc_start: 0.6231 (mttt) cc_final: 0.5941 (mttt) REVERT: D 170 GLU cc_start: 0.3913 (mt-10) cc_final: 0.3463 (mm-30) REVERT: D 226 LYS cc_start: 0.5370 (mttt) cc_final: 0.5015 (mtmt) REVERT: D 538 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.7217 (ttm110) REVERT: D 569 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7099 (mmm160) REVERT: E 29 ASP cc_start: 0.7580 (t70) cc_final: 0.7130 (t0) REVERT: E 41 GLU cc_start: 0.6257 (tp30) cc_final: 0.6019 (tp30) REVERT: E 50 LYS cc_start: 0.5548 (pttt) cc_final: 0.5303 (tptt) REVERT: E 89 SER cc_start: 0.7263 (m) cc_final: 0.6362 (t) REVERT: E 141 GLN cc_start: 0.6453 (mt0) cc_final: 0.5892 (mm-40) REVERT: E 170 LYS cc_start: 0.7420 (mtpp) cc_final: 0.7181 (mtmm) REVERT: E 217 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6663 (mm-30) REVERT: E 260 TYR cc_start: 0.6621 (t80) cc_final: 0.6242 (t80) REVERT: E 268 LYS cc_start: 0.4462 (ptmt) cc_final: 0.4030 (pttt) REVERT: F 57 SER cc_start: 0.8423 (t) cc_final: 0.8191 (p) REVERT: F 61 ARG cc_start: 0.7094 (ttm170) cc_final: 0.6773 (ttm170) REVERT: F 353 LYS cc_start: 0.7044 (tppt) cc_final: 0.6671 (tttt) REVERT: F 533 LEU cc_start: 0.1923 (OUTLIER) cc_final: 0.1547 (tp) REVERT: F 563 MET cc_start: 0.6499 (mpp) cc_final: 0.5930 (mmm) REVERT: G 436 ARG cc_start: 0.6591 (ttt90) cc_final: 0.6202 (mmm-85) REVERT: G 516 ARG cc_start: 0.7450 (mtp85) cc_final: 0.7153 (mtp85) REVERT: H 135 ARG cc_start: 0.6610 (tpt-90) cc_final: 0.6389 (tpp80) REVERT: H 322 ASP cc_start: 0.7488 (p0) cc_final: 0.7265 (p0) REVERT: H 366 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8352 (m) REVERT: H 569 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8107 (mmm-85) REVERT: J 29 ASP cc_start: 0.7696 (t70) cc_final: 0.6827 (m-30) REVERT: J 41 GLU cc_start: 0.6799 (tp30) cc_final: 0.6445 (tp30) REVERT: J 50 LYS cc_start: 0.5797 (pttt) cc_final: 0.5430 (tptt) REVERT: J 89 SER cc_start: 0.7110 (m) cc_final: 0.6180 (t) REVERT: J 141 GLN cc_start: 0.6120 (mt0) cc_final: 0.5799 (mm-40) REVERT: J 217 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6925 (mm-30) REVERT: J 269 LEU cc_start: 0.6684 (mt) cc_final: 0.6391 (mt) REVERT: K 57 SER cc_start: 0.8369 (t) cc_final: 0.8028 (p) REVERT: K 61 ARG cc_start: 0.7023 (ttm170) cc_final: 0.6664 (tpp-160) REVERT: K 353 LYS cc_start: 0.6596 (tppt) cc_final: 0.6380 (tttt) REVERT: K 374 LYS cc_start: 0.7058 (mttt) cc_final: 0.6759 (mtmm) REVERT: K 428 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7006 (mt-10) REVERT: K 464 ARG cc_start: 0.7414 (mtm-85) cc_final: 0.7151 (mtm-85) REVERT: K 491 MET cc_start: 0.8535 (ttm) cc_final: 0.8172 (ttm) REVERT: K 533 LEU cc_start: 0.1860 (OUTLIER) cc_final: 0.1591 (tp) REVERT: K 563 MET cc_start: 0.6422 (mpp) cc_final: 0.6059 (mmm) REVERT: L 436 ARG cc_start: 0.6720 (ttt90) cc_final: 0.6088 (mmm-85) REVERT: L 551 GLN cc_start: 0.7734 (mt0) cc_final: 0.7083 (tt0) REVERT: M 18 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8380 (mm) REVERT: M 43 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7287 (mt-10) REVERT: M 46 GLU cc_start: 0.7538 (tt0) cc_final: 0.7268 (tt0) REVERT: M 90 MET cc_start: 0.8328 (ttp) cc_final: 0.8098 (ttp) REVERT: M 138 PHE cc_start: 0.6653 (t80) cc_final: 0.6194 (t80) REVERT: M 252 PHE cc_start: 0.6259 (t80) cc_final: 0.6050 (t80) REVERT: M 468 ASN cc_start: 0.7209 (OUTLIER) cc_final: 0.6754 (m-40) REVERT: M 581 LYS cc_start: 0.8283 (mttt) cc_final: 0.8030 (mttm) REVERT: N 29 ASP cc_start: 0.7480 (t70) cc_final: 0.7170 (t0) REVERT: N 41 GLU cc_start: 0.6583 (tp30) cc_final: 0.6171 (tp30) REVERT: N 45 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7643 (mt-10) REVERT: N 50 LYS cc_start: 0.5426 (pttt) cc_final: 0.5175 (tptt) REVERT: N 89 SER cc_start: 0.7174 (m) cc_final: 0.6293 (t) REVERT: N 141 GLN cc_start: 0.5821 (mt0) cc_final: 0.5405 (mm-40) REVERT: N 207 MET cc_start: 0.6856 (tmm) cc_final: 0.6642 (tmm) REVERT: N 217 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6959 (mm-30) REVERT: N 260 TYR cc_start: 0.6755 (t80) cc_final: 0.6316 (t80) REVERT: P 57 SER cc_start: 0.8409 (t) cc_final: 0.7980 (p) REVERT: P 61 ARG cc_start: 0.7326 (ttm170) cc_final: 0.6835 (ttm-80) REVERT: P 384 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6979 (tt) REVERT: P 491 MET cc_start: 0.8505 (ttm) cc_final: 0.8037 (ttp) REVERT: P 499 PHE cc_start: 0.6587 (m-80) cc_final: 0.6112 (m-80) REVERT: P 563 MET cc_start: 0.6410 (mpp) cc_final: 0.5882 (mmm) REVERT: Q 436 ARG cc_start: 0.6579 (ttt90) cc_final: 0.5992 (mmm-85) REVERT: Q 516 ARG cc_start: 0.7434 (mtp85) cc_final: 0.7163 (mtp85) REVERT: R 22 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8747 (m) REVERT: R 33 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6812 (mt-10) REVERT: R 90 MET cc_start: 0.8270 (ttp) cc_final: 0.8021 (ttm) REVERT: R 110 LYS cc_start: 0.6226 (mttt) cc_final: 0.5940 (mttt) REVERT: R 135 ARG cc_start: 0.6510 (tpt-90) cc_final: 0.6261 (tpp80) REVERT: R 170 GLU cc_start: 0.3912 (mt-10) cc_final: 0.3463 (mm-30) REVERT: R 226 LYS cc_start: 0.5362 (mttt) cc_final: 0.5008 (mtmt) REVERT: R 538 ARG cc_start: 0.7505 (ttm-80) cc_final: 0.7217 (ttm110) REVERT: R 569 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7098 (mmm160) REVERT: S 29 ASP cc_start: 0.7574 (t70) cc_final: 0.7128 (t0) REVERT: S 41 GLU cc_start: 0.6256 (tp30) cc_final: 0.6016 (tp30) REVERT: S 50 LYS cc_start: 0.5544 (pttt) cc_final: 0.5301 (tptt) REVERT: S 89 SER cc_start: 0.7261 (m) cc_final: 0.6362 (t) REVERT: S 141 GLN cc_start: 0.6456 (mt0) cc_final: 0.5892 (mm-40) REVERT: S 170 LYS cc_start: 0.7422 (mtpp) cc_final: 0.7183 (mtmm) REVERT: S 217 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6660 (mm-30) REVERT: S 260 TYR cc_start: 0.6581 (t80) cc_final: 0.6248 (t80) REVERT: S 268 LYS cc_start: 0.4461 (ptmt) cc_final: 0.4029 (pttt) REVERT: T 57 SER cc_start: 0.8416 (t) cc_final: 0.8183 (p) REVERT: T 61 ARG cc_start: 0.7094 (ttm170) cc_final: 0.6778 (ttm170) REVERT: T 353 LYS cc_start: 0.7044 (tppt) cc_final: 0.6671 (tttt) REVERT: T 533 LEU cc_start: 0.1922 (OUTLIER) cc_final: 0.1546 (tp) REVERT: T 563 MET cc_start: 0.6493 (mpp) cc_final: 0.5936 (mmm) REVERT: V 436 ARG cc_start: 0.6592 (ttt90) cc_final: 0.6202 (mmm-85) REVERT: V 516 ARG cc_start: 0.7450 (mtp85) cc_final: 0.7155 (mtp85) REVERT: W 135 ARG cc_start: 0.6613 (tpt-90) cc_final: 0.6389 (tpp80) REVERT: W 227 ASN cc_start: 0.6465 (m-40) cc_final: 0.5911 (t0) REVERT: W 322 ASP cc_start: 0.7488 (p0) cc_final: 0.7268 (p0) REVERT: W 366 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8356 (m) REVERT: W 569 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8113 (mmm-85) REVERT: X 29 ASP cc_start: 0.7698 (t70) cc_final: 0.6829 (m-30) REVERT: X 41 GLU cc_start: 0.6799 (tp30) cc_final: 0.6447 (tp30) REVERT: X 50 LYS cc_start: 0.5797 (pttt) cc_final: 0.5428 (tptt) REVERT: X 89 SER cc_start: 0.7111 (m) cc_final: 0.6180 (t) REVERT: X 141 GLN cc_start: 0.6118 (mt0) cc_final: 0.5798 (mm-40) REVERT: X 217 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6925 (mm-30) REVERT: X 268 LYS cc_start: 0.4736 (ptmt) cc_final: 0.4168 (ptpp) REVERT: X 269 LEU cc_start: 0.7157 (mm) cc_final: 0.6928 (mm) outliers start: 267 outliers final: 211 residues processed: 1011 average time/residue: 0.6563 time to fit residues: 1119.7306 Evaluate side-chains 1034 residues out of total 7998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 799 time to evaluate : 5.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 352 VAL Chi-restraints excluded: chain I residue 407 HIS Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain I residue 584 THR Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 76 TRP Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 148 ASP Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain O residue 375 GLU Chi-restraints excluded: chain O residue 432 PHE Chi-restraints excluded: chain O residue 438 SER Chi-restraints excluded: chain O residue 468 ASN Chi-restraints excluded: chain O residue 531 SER Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 58 VAL Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 109 ILE Chi-restraints excluded: chain U residue 116 VAL Chi-restraints excluded: chain U residue 123 ILE Chi-restraints excluded: chain U residue 182 VAL Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 217 GLU Chi-restraints excluded: chain U residue 235 ILE Chi-restraints excluded: chain U residue 238 ASP Chi-restraints excluded: chain U residue 269 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 76 TRP Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 432 PHE Chi-restraints excluded: chain D residue 569 ARG Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 515 THR Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain F residue 561 ILE Chi-restraints excluded: chain G residue 41 GLN Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 469 THR Chi-restraints excluded: chain G residue 495 GLU Chi-restraints excluded: chain G residue 520 THR Chi-restraints excluded: chain G residue 584 THR Chi-restraints excluded: chain H residue 76 TRP Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 515 THR Chi-restraints excluded: chain H residue 569 ARG Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 217 GLU Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain K residue 515 THR Chi-restraints excluded: chain K residue 533 LEU Chi-restraints excluded: chain K residue 561 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 407 HIS Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain L residue 584 THR Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 76 TRP Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 148 ASP Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 375 GLU Chi-restraints excluded: chain M residue 432 PHE Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain M residue 468 ASN Chi-restraints excluded: chain M residue 531 SER Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 217 GLU Chi-restraints excluded: chain N residue 235 ILE Chi-restraints excluded: chain N residue 238 ASP Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 92 ILE Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 384 LEU Chi-restraints excluded: chain P residue 515 THR Chi-restraints excluded: chain Q residue 352 VAL Chi-restraints excluded: chain Q residue 447 ILE Chi-restraints excluded: chain Q residue 469 THR Chi-restraints excluded: chain Q residue 520 THR Chi-restraints excluded: chain Q residue 584 THR Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 76 TRP Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 148 ASP Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 313 ASN Chi-restraints excluded: chain R residue 432 PHE Chi-restraints excluded: chain R residue 569 ARG Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 74 LEU Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain S residue 217 GLU Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain T residue 344 VAL Chi-restraints excluded: chain T residue 352 VAL Chi-restraints excluded: chain T residue 426 ILE Chi-restraints excluded: chain T residue 515 THR Chi-restraints excluded: chain T residue 533 LEU Chi-restraints excluded: chain T residue 561 ILE Chi-restraints excluded: chain V residue 41 GLN Chi-restraints excluded: chain V residue 64 ARG Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 352 VAL Chi-restraints excluded: chain V residue 447 ILE Chi-restraints excluded: chain V residue 469 THR Chi-restraints excluded: chain V residue 495 GLU Chi-restraints excluded: chain V residue 520 THR Chi-restraints excluded: chain V residue 584 THR Chi-restraints excluded: chain W residue 76 TRP Chi-restraints excluded: chain W residue 92 ILE Chi-restraints excluded: chain W residue 137 ILE Chi-restraints excluded: chain W residue 148 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 264 ILE Chi-restraints excluded: chain W residue 366 VAL Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 432 PHE Chi-restraints excluded: chain W residue 515 THR Chi-restraints excluded: chain W residue 569 ARG Chi-restraints excluded: chain X residue 4 THR Chi-restraints excluded: chain X residue 19 ASN Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 189 VAL Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain X residue 263 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 300 optimal weight: 9.9990 chunk 804 optimal weight: 9.9990 chunk 176 optimal weight: 0.0060 chunk 524 optimal weight: 8.9990 chunk 220 optimal weight: 0.4980 chunk 894 optimal weight: 7.9990 chunk 742 optimal weight: 8.9990 chunk 413 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 295 optimal weight: 8.9990 chunk 469 optimal weight: 4.9990 overall best weight: 4.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: