Starting phenix.real_space_refine on Tue Aug 26 19:28:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z4g_39763/08_2025/8z4g_39763.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z4g_39763/08_2025/8z4g_39763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z4g_39763/08_2025/8z4g_39763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z4g_39763/08_2025/8z4g_39763.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z4g_39763/08_2025/8z4g_39763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z4g_39763/08_2025/8z4g_39763.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.037 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 70 5.16 5 C 24955 2.51 5 N 7350 2.21 5 O 8190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 315 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40565 Number of models: 1 Model: "" Number of chains: 1 Chain: "1" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1159 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain breaks: 2 Restraints were copied for chains: 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z Time building chain proxies: 3.85, per 1000 atoms: 0.09 Number of scatterers: 40565 At special positions: 0 Unit cell: (256.5, 256.5, 98.04, 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 70 16.00 O 8190 8.00 N 7350 7.00 C 24955 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 715.3 nanoseconds 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9730 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 37 sheets defined 32.9% alpha, 39.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain '1' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG 1 260 " --> pdb=" O SER 1 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS 1 261 " --> pdb=" O ALA 1 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU 1 262 " --> pdb=" O ALA 1 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL 1 280 " --> pdb=" O LYS 1 276 " (cutoff:3.500A) Proline residue: 1 283 - end of helix Processing helix chain '1' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY 1 432 " --> pdb=" O GLN 1 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR 1 433 " --> pdb=" O VAL 1 429 " (cutoff:3.500A) Processing helix chain '2' and resid 256 through 286 removed outlier: 4.050A pdb=" N ARG 2 260 " --> pdb=" O SER 2 256 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS 2 261 " --> pdb=" O ALA 2 257 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU 2 262 " --> pdb=" O ALA 2 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL 2 280 " --> pdb=" O LYS 2 276 " (cutoff:3.500A) Proline residue: 2 283 - end of helix Processing helix chain '2' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY 2 432 " --> pdb=" O GLN 2 428 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR 2 433 " --> pdb=" O VAL 2 429 " (cutoff:3.500A) Processing helix chain '3' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG 3 260 " --> pdb=" O SER 3 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS 3 261 " --> pdb=" O ALA 3 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU 3 262 " --> pdb=" O ALA 3 258 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL 3 280 " --> pdb=" O LYS 3 276 " (cutoff:3.500A) Proline residue: 3 283 - end of helix Processing helix chain '3' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY 3 432 " --> pdb=" O GLN 3 428 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR 3 433 " --> pdb=" O VAL 3 429 " (cutoff:3.500A) Processing helix chain '4' and resid 256 through 286 removed outlier: 4.050A pdb=" N ARG 4 260 " --> pdb=" O SER 4 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS 4 261 " --> pdb=" O ALA 4 257 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU 4 262 " --> pdb=" O ALA 4 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL 4 280 " --> pdb=" O LYS 4 276 " (cutoff:3.500A) Proline residue: 4 283 - end of helix Processing helix chain '4' and resid 419 through 435 removed outlier: 3.861A pdb=" N GLY 4 432 " --> pdb=" O GLN 4 428 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR 4 433 " --> pdb=" O VAL 4 429 " (cutoff:3.500A) Processing helix chain '5' and resid 256 through 286 removed outlier: 4.050A pdb=" N ARG 5 260 " --> pdb=" O SER 5 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS 5 261 " --> pdb=" O ALA 5 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU 5 262 " --> pdb=" O ALA 5 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL 5 280 " --> pdb=" O LYS 5 276 " (cutoff:3.500A) Proline residue: 5 283 - end of helix Processing helix chain '5' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY 5 432 " --> pdb=" O GLN 5 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR 5 433 " --> pdb=" O VAL 5 429 " (cutoff:3.500A) Processing helix chain '6' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG 6 260 " --> pdb=" O SER 6 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS 6 261 " --> pdb=" O ALA 6 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU 6 262 " --> pdb=" O ALA 6 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL 6 280 " --> pdb=" O LYS 6 276 " (cutoff:3.500A) Proline residue: 6 283 - end of helix Processing helix chain '6' and resid 419 through 435 removed outlier: 3.861A pdb=" N GLY 6 432 " --> pdb=" O GLN 6 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR 6 433 " --> pdb=" O VAL 6 429 " (cutoff:3.500A) Processing helix chain '7' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG 7 260 " --> pdb=" O SER 7 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS 7 261 " --> pdb=" O ALA 7 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU 7 262 " --> pdb=" O ALA 7 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL 7 280 " --> pdb=" O LYS 7 276 " (cutoff:3.500A) Proline residue: 7 283 - end of helix Processing helix chain '7' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY 7 432 " --> pdb=" O GLN 7 428 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR 7 433 " --> pdb=" O VAL 7 429 " (cutoff:3.500A) Processing helix chain '8' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG 8 260 " --> pdb=" O SER 8 256 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS 8 261 " --> pdb=" O ALA 8 257 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU 8 262 " --> pdb=" O ALA 8 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL 8 280 " --> pdb=" O LYS 8 276 " (cutoff:3.500A) Proline residue: 8 283 - end of helix Processing helix chain '8' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY 8 432 " --> pdb=" O GLN 8 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR 8 433 " --> pdb=" O VAL 8 429 " (cutoff:3.500A) Processing helix chain '9' and resid 256 through 286 removed outlier: 4.050A pdb=" N ARG 9 260 " --> pdb=" O SER 9 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS 9 261 " --> pdb=" O ALA 9 257 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU 9 262 " --> pdb=" O ALA 9 258 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL 9 280 " --> pdb=" O LYS 9 276 " (cutoff:3.500A) Proline residue: 9 283 - end of helix Processing helix chain '9' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY 9 432 " --> pdb=" O GLN 9 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR 9 433 " --> pdb=" O VAL 9 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY A 432 " --> pdb=" O GLN A 428 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG B 260 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY B 432 " --> pdb=" O GLN B 428 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 433 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 286 removed outlier: 4.050A pdb=" N ARG C 260 " --> pdb=" O SER C 256 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 280 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Proline residue: C 283 - end of helix Processing helix chain 'C' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY C 432 " --> pdb=" O GLN C 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 433 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG D 260 " --> pdb=" O SER D 256 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL D 280 " --> pdb=" O LYS D 276 " (cutoff:3.500A) Proline residue: D 283 - end of helix Processing helix chain 'D' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY D 432 " --> pdb=" O GLN D 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR D 433 " --> pdb=" O VAL D 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG E 260 " --> pdb=" O SER E 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL E 280 " --> pdb=" O LYS E 276 " (cutoff:3.500A) Proline residue: E 283 - end of helix Processing helix chain 'E' and resid 419 through 435 removed outlier: 3.863A pdb=" N GLY E 432 " --> pdb=" O GLN E 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 433 " --> pdb=" O VAL E 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG F 260 " --> pdb=" O SER F 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU F 262 " --> pdb=" O ALA F 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) Proline residue: F 283 - end of helix Processing helix chain 'F' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY F 432 " --> pdb=" O GLN F 428 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR F 433 " --> pdb=" O VAL F 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG G 260 " --> pdb=" O SER G 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS G 261 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU G 262 " --> pdb=" O ALA G 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL G 280 " --> pdb=" O LYS G 276 " (cutoff:3.500A) Proline residue: G 283 - end of helix Processing helix chain 'G' and resid 419 through 435 removed outlier: 3.861A pdb=" N GLY G 432 " --> pdb=" O GLN G 428 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR G 433 " --> pdb=" O VAL G 429 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 286 removed outlier: 4.050A pdb=" N ARG H 260 " --> pdb=" O SER H 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS H 261 " --> pdb=" O ALA H 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU H 262 " --> pdb=" O ALA H 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL H 280 " --> pdb=" O LYS H 276 " (cutoff:3.500A) Proline residue: H 283 - end of helix Processing helix chain 'H' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY H 432 " --> pdb=" O GLN H 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 433 " --> pdb=" O VAL H 429 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG I 260 " --> pdb=" O SER I 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU I 262 " --> pdb=" O ALA I 258 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL I 280 " --> pdb=" O LYS I 276 " (cutoff:3.500A) Proline residue: I 283 - end of helix Processing helix chain 'I' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY I 432 " --> pdb=" O GLN I 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR I 433 " --> pdb=" O VAL I 429 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 286 removed outlier: 4.050A pdb=" N ARG J 260 " --> pdb=" O SER J 256 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS J 261 " --> pdb=" O ALA J 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU J 262 " --> pdb=" O ALA J 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL J 280 " --> pdb=" O LYS J 276 " (cutoff:3.500A) Proline residue: J 283 - end of helix Processing helix chain 'J' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY J 432 " --> pdb=" O GLN J 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR J 433 " --> pdb=" O VAL J 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 286 removed outlier: 4.050A pdb=" N ARG K 260 " --> pdb=" O SER K 256 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS K 261 " --> pdb=" O ALA K 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU K 262 " --> pdb=" O ALA K 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL K 280 " --> pdb=" O LYS K 276 " (cutoff:3.500A) Proline residue: K 283 - end of helix Processing helix chain 'K' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY K 432 " --> pdb=" O GLN K 428 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR K 433 " --> pdb=" O VAL K 429 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG L 260 " --> pdb=" O SER L 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS L 261 " --> pdb=" O ALA L 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU L 262 " --> pdb=" O ALA L 258 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL L 280 " --> pdb=" O LYS L 276 " (cutoff:3.500A) Proline residue: L 283 - end of helix Processing helix chain 'L' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY L 432 " --> pdb=" O GLN L 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR L 433 " --> pdb=" O VAL L 429 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 286 removed outlier: 4.050A pdb=" N ARG M 260 " --> pdb=" O SER M 256 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS M 261 " --> pdb=" O ALA M 257 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU M 262 " --> pdb=" O ALA M 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL M 280 " --> pdb=" O LYS M 276 " (cutoff:3.500A) Proline residue: M 283 - end of helix Processing helix chain 'M' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY M 432 " --> pdb=" O GLN M 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR M 433 " --> pdb=" O VAL M 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG N 260 " --> pdb=" O SER N 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS N 261 " --> pdb=" O ALA N 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU N 262 " --> pdb=" O ALA N 258 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL N 280 " --> pdb=" O LYS N 276 " (cutoff:3.500A) Proline residue: N 283 - end of helix Processing helix chain 'N' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY N 432 " --> pdb=" O GLN N 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR N 433 " --> pdb=" O VAL N 429 " (cutoff:3.500A) Processing helix chain 'O' and resid 256 through 286 removed outlier: 4.050A pdb=" N ARG O 260 " --> pdb=" O SER O 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS O 261 " --> pdb=" O ALA O 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU O 262 " --> pdb=" O ALA O 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL O 280 " --> pdb=" O LYS O 276 " (cutoff:3.500A) Proline residue: O 283 - end of helix Processing helix chain 'O' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY O 432 " --> pdb=" O GLN O 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR O 433 " --> pdb=" O VAL O 429 " (cutoff:3.500A) Processing helix chain 'P' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG P 260 " --> pdb=" O SER P 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS P 261 " --> pdb=" O ALA P 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU P 262 " --> pdb=" O ALA P 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL P 280 " --> pdb=" O LYS P 276 " (cutoff:3.500A) Proline residue: P 283 - end of helix Processing helix chain 'P' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY P 432 " --> pdb=" O GLN P 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR P 433 " --> pdb=" O VAL P 429 " (cutoff:3.500A) Processing helix chain 'Q' and resid 256 through 286 removed outlier: 4.050A pdb=" N ARG Q 260 " --> pdb=" O SER Q 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU Q 262 " --> pdb=" O ALA Q 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL Q 280 " --> pdb=" O LYS Q 276 " (cutoff:3.500A) Proline residue: Q 283 - end of helix Processing helix chain 'Q' and resid 419 through 435 removed outlier: 3.863A pdb=" N GLY Q 432 " --> pdb=" O GLN Q 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR Q 433 " --> pdb=" O VAL Q 429 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG R 260 " --> pdb=" O SER R 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS R 261 " --> pdb=" O ALA R 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU R 262 " --> pdb=" O ALA R 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL R 280 " --> pdb=" O LYS R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY R 432 " --> pdb=" O GLN R 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR R 433 " --> pdb=" O VAL R 429 " (cutoff:3.500A) Processing helix chain 'S' and resid 256 through 286 removed outlier: 4.050A pdb=" N ARG S 260 " --> pdb=" O SER S 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS S 261 " --> pdb=" O ALA S 257 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU S 262 " --> pdb=" O ALA S 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL S 280 " --> pdb=" O LYS S 276 " (cutoff:3.500A) Proline residue: S 283 - end of helix Processing helix chain 'S' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY S 432 " --> pdb=" O GLN S 428 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR S 433 " --> pdb=" O VAL S 429 " (cutoff:3.500A) Processing helix chain 'T' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG T 260 " --> pdb=" O SER T 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS T 261 " --> pdb=" O ALA T 257 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU T 262 " --> pdb=" O ALA T 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL T 280 " --> pdb=" O LYS T 276 " (cutoff:3.500A) Proline residue: T 283 - end of helix Processing helix chain 'T' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY T 432 " --> pdb=" O GLN T 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR T 433 " --> pdb=" O VAL T 429 " (cutoff:3.500A) Processing helix chain 'U' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG U 260 " --> pdb=" O SER U 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS U 261 " --> pdb=" O ALA U 257 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU U 262 " --> pdb=" O ALA U 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL U 280 " --> pdb=" O LYS U 276 " (cutoff:3.500A) Proline residue: U 283 - end of helix Processing helix chain 'U' and resid 419 through 435 removed outlier: 3.861A pdb=" N GLY U 432 " --> pdb=" O GLN U 428 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR U 433 " --> pdb=" O VAL U 429 " (cutoff:3.500A) Processing helix chain 'V' and resid 256 through 286 removed outlier: 4.050A pdb=" N ARG V 260 " --> pdb=" O SER V 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS V 261 " --> pdb=" O ALA V 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU V 262 " --> pdb=" O ALA V 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL V 280 " --> pdb=" O LYS V 276 " (cutoff:3.500A) Proline residue: V 283 - end of helix Processing helix chain 'V' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY V 432 " --> pdb=" O GLN V 428 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR V 433 " --> pdb=" O VAL V 429 " (cutoff:3.500A) Processing helix chain 'W' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG W 260 " --> pdb=" O SER W 256 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS W 261 " --> pdb=" O ALA W 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU W 262 " --> pdb=" O ALA W 258 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL W 280 " --> pdb=" O LYS W 276 " (cutoff:3.500A) Proline residue: W 283 - end of helix Processing helix chain 'W' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY W 432 " --> pdb=" O GLN W 428 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR W 433 " --> pdb=" O VAL W 429 " (cutoff:3.500A) Processing helix chain 'X' and resid 256 through 286 removed outlier: 4.050A pdb=" N ARG X 260 " --> pdb=" O SER X 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS X 261 " --> pdb=" O ALA X 257 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU X 262 " --> pdb=" O ALA X 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL X 280 " --> pdb=" O LYS X 276 " (cutoff:3.500A) Proline residue: X 283 - end of helix Processing helix chain 'X' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY X 432 " --> pdb=" O GLN X 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR X 433 " --> pdb=" O VAL X 429 " (cutoff:3.500A) Processing helix chain 'Y' and resid 256 through 286 removed outlier: 4.050A pdb=" N ARG Y 260 " --> pdb=" O SER Y 256 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS Y 261 " --> pdb=" O ALA Y 257 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU Y 262 " --> pdb=" O ALA Y 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL Y 280 " --> pdb=" O LYS Y 276 " (cutoff:3.500A) Proline residue: Y 283 - end of helix Processing helix chain 'Y' and resid 419 through 435 removed outlier: 3.861A pdb=" N GLY Y 432 " --> pdb=" O GLN Y 428 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR Y 433 " --> pdb=" O VAL Y 429 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 286 removed outlier: 4.049A pdb=" N ARG Z 260 " --> pdb=" O SER Z 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS Z 261 " --> pdb=" O ALA Z 257 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU Z 262 " --> pdb=" O ALA Z 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL Z 280 " --> pdb=" O LYS Z 276 " (cutoff:3.500A) Proline residue: Z 283 - end of helix Processing helix chain 'Z' and resid 419 through 435 removed outlier: 3.862A pdb=" N GLY Z 432 " --> pdb=" O GLN Z 428 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR Z 433 " --> pdb=" O VAL Z 429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR 1 291 " --> pdb=" O VAL 1 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL 1 398 " --> pdb=" O THR 1 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN 1 293 " --> pdb=" O VAL 1 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL 1 396 " --> pdb=" O GLN 1 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP 1 295 " --> pdb=" O GLN 1 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN 1 394 " --> pdb=" O ASP 1 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN 1 297 " --> pdb=" O ALA 1 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR 1 390 " --> pdb=" O ASP 1 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU 1 443 " --> pdb=" O ALA 1 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN 1 394 " --> pdb=" O LEU 1 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN 1 445 " --> pdb=" O GLN 1 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL 1 396 " --> pdb=" O ASN 1 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU 1 447 " --> pdb=" O VAL 1 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL 1 398 " --> pdb=" O LEU 1 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL 1 449 " --> pdb=" O VAL 1 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE 1 400 " --> pdb=" O VAL 1 449 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 302 through 310 removed outlier: 3.524A pdb=" N ALA 2 302 " --> pdb=" O ARG 1 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 316 through 325 removed outlier: 5.545A pdb=" N THR 1 317 " --> pdb=" O GLU 1 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU 1 376 " --> pdb=" O THR 1 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER 1 319 " --> pdb=" O ASN 1 374 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS 1 369 " --> pdb=" O GLU Z 324 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG Z 318 " --> pdb=" O PHE 1 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR Z 317 " --> pdb=" O GLU Z 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU Z 376 " --> pdb=" O THR Z 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER Z 319 " --> pdb=" O ASN Z 374 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS Z 369 " --> pdb=" O GLU Y 324 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER Z 371 " --> pdb=" O ALA Y 322 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG Y 318 " --> pdb=" O PHE Z 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR Y 317 " --> pdb=" O GLU Y 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU Y 376 " --> pdb=" O THR Y 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER Y 319 " --> pdb=" O ASN Y 374 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS Y 369 " --> pdb=" O GLU X 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER Y 371 " --> pdb=" O ALA X 322 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU X 320 " --> pdb=" O ARG Y 373 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ARG X 318 " --> pdb=" O PHE Y 375 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR X 317 " --> pdb=" O GLU X 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU X 376 " --> pdb=" O THR X 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER X 319 " --> pdb=" O ASN X 374 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS X 369 " --> pdb=" O GLU W 324 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER X 371 " --> pdb=" O ALA W 322 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARG W 318 " --> pdb=" O PHE X 375 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR W 317 " --> pdb=" O GLU W 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU W 376 " --> pdb=" O THR W 317 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER W 319 " --> pdb=" O ASN W 374 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS W 369 " --> pdb=" O GLU V 324 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER W 371 " --> pdb=" O ALA V 322 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU V 320 " --> pdb=" O ARG W 373 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG V 318 " --> pdb=" O PHE W 375 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR V 317 " --> pdb=" O GLU V 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU V 376 " --> pdb=" O THR V 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER V 319 " --> pdb=" O ASN V 374 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS V 369 " --> pdb=" O GLU U 324 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER V 371 " --> pdb=" O ALA U 322 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU U 320 " --> pdb=" O ARG V 373 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ARG U 318 " --> pdb=" O PHE V 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR U 317 " --> pdb=" O GLU U 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU U 376 " --> pdb=" O THR U 317 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER U 319 " --> pdb=" O ASN U 374 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS U 369 " --> pdb=" O GLU T 324 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER U 371 " --> pdb=" O ALA T 322 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG T 318 " --> pdb=" O PHE U 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR T 317 " --> pdb=" O GLU T 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU T 376 " --> pdb=" O THR T 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER T 319 " --> pdb=" O ASN T 374 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS T 369 " --> pdb=" O GLU S 324 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER T 371 " --> pdb=" O ALA S 322 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU S 320 " --> pdb=" O ARG T 373 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG S 318 " --> pdb=" O PHE T 375 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR S 317 " --> pdb=" O GLU S 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU S 376 " --> pdb=" O THR S 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER S 319 " --> pdb=" O ASN S 374 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS S 369 " --> pdb=" O GLU R 324 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG R 318 " --> pdb=" O PHE S 375 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR R 317 " --> pdb=" O GLU R 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU R 376 " --> pdb=" O THR R 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER R 319 " --> pdb=" O ASN R 374 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LYS R 369 " --> pdb=" O GLU Q 324 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ARG Q 318 " --> pdb=" O PHE R 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR Q 317 " --> pdb=" O GLU Q 376 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU Q 376 " --> pdb=" O THR Q 317 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER Q 319 " --> pdb=" O ASN Q 374 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS Q 369 " --> pdb=" O GLU P 324 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ARG P 318 " --> pdb=" O PHE Q 375 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR P 317 " --> pdb=" O GLU P 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU P 376 " --> pdb=" O THR P 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER P 319 " --> pdb=" O ASN P 374 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS P 369 " --> pdb=" O GLU O 324 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG O 318 " --> pdb=" O PHE P 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR O 317 " --> pdb=" O GLU O 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU O 376 " --> pdb=" O THR O 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER O 319 " --> pdb=" O ASN O 374 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS O 369 " --> pdb=" O GLU N 324 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG N 318 " --> pdb=" O PHE O 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR N 317 " --> pdb=" O GLU N 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU N 376 " --> pdb=" O THR N 317 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER N 319 " --> pdb=" O ASN N 374 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS N 369 " --> pdb=" O GLU M 324 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARG M 318 " --> pdb=" O PHE N 375 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR M 317 " --> pdb=" O GLU M 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU M 376 " --> pdb=" O THR M 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER M 319 " --> pdb=" O ASN M 374 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS M 369 " --> pdb=" O GLU L 324 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ARG L 318 " --> pdb=" O PHE M 375 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR L 317 " --> pdb=" O GLU L 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU L 376 " --> pdb=" O THR L 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER L 319 " --> pdb=" O ASN L 374 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS L 369 " --> pdb=" O GLU K 324 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG K 318 " --> pdb=" O PHE L 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR K 317 " --> pdb=" O GLU K 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU K 376 " --> pdb=" O THR K 317 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER K 319 " --> pdb=" O ASN K 374 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LYS K 369 " --> pdb=" O GLU J 324 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG J 318 " --> pdb=" O PHE K 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR J 317 " --> pdb=" O GLU J 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU J 376 " --> pdb=" O THR J 317 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER J 319 " --> pdb=" O ASN J 374 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS J 369 " --> pdb=" O GLU I 324 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER J 371 " --> pdb=" O ALA I 322 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG I 318 " --> pdb=" O PHE J 375 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR I 317 " --> pdb=" O GLU I 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU I 376 " --> pdb=" O THR I 317 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER I 319 " --> pdb=" O ASN I 374 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS I 369 " --> pdb=" O GLU H 324 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER I 371 " --> pdb=" O ALA H 322 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG H 318 " --> pdb=" O PHE I 375 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR H 317 " --> pdb=" O GLU H 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU H 376 " --> pdb=" O THR H 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER H 319 " --> pdb=" O ASN H 374 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS H 369 " --> pdb=" O GLU G 324 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER H 371 " --> pdb=" O ALA G 322 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG G 318 " --> pdb=" O PHE H 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR G 317 " --> pdb=" O GLU G 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU G 376 " --> pdb=" O THR G 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER G 319 " --> pdb=" O ASN G 374 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS G 369 " --> pdb=" O GLU F 324 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER G 371 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU F 320 " --> pdb=" O ARG G 373 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ARG F 318 " --> pdb=" O PHE G 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR F 317 " --> pdb=" O GLU F 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU F 376 " --> pdb=" O THR F 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER F 319 " --> pdb=" O ASN F 374 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS F 369 " --> pdb=" O GLU E 324 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER F 371 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU E 320 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ARG E 318 " --> pdb=" O PHE F 375 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR E 317 " --> pdb=" O GLU E 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU E 376 " --> pdb=" O THR E 317 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER E 319 " --> pdb=" O ASN E 374 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS E 369 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER E 371 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 320 " --> pdb=" O ARG E 373 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ARG D 318 " --> pdb=" O PHE E 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR D 317 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU D 376 " --> pdb=" O THR D 317 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER D 319 " --> pdb=" O ASN D 374 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS D 369 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ARG C 318 " --> pdb=" O PHE D 375 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR C 317 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU C 376 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER C 319 " --> pdb=" O ASN C 374 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS C 369 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER C 371 " --> pdb=" O ALA B 322 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 320 " --> pdb=" O ARG C 373 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG B 318 " --> pdb=" O PHE C 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR B 317 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU B 376 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER B 319 " --> pdb=" O ASN B 374 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS B 369 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ARG A 318 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR A 317 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU A 376 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 319 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS A 369 " --> pdb=" O GLU 9 324 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 371 " --> pdb=" O ALA 9 322 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ARG 9 318 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR 9 317 " --> pdb=" O GLU 9 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU 9 376 " --> pdb=" O THR 9 317 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER 9 319 " --> pdb=" O ASN 9 374 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS 9 369 " --> pdb=" O GLU 8 324 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ARG 8 318 " --> pdb=" O PHE 9 375 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR 8 317 " --> pdb=" O GLU 8 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU 8 376 " --> pdb=" O THR 8 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER 8 319 " --> pdb=" O ASN 8 374 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS 8 369 " --> pdb=" O GLU 7 324 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG 7 318 " --> pdb=" O PHE 8 375 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR 7 317 " --> pdb=" O GLU 7 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU 7 376 " --> pdb=" O THR 7 317 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER 7 319 " --> pdb=" O ASN 7 374 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS 7 369 " --> pdb=" O GLU 6 324 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG 6 318 " --> pdb=" O PHE 7 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR 6 317 " --> pdb=" O GLU 6 376 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU 6 376 " --> pdb=" O THR 6 317 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER 6 319 " --> pdb=" O ASN 6 374 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS 6 369 " --> pdb=" O GLU 5 324 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ARG 5 318 " --> pdb=" O PHE 6 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR 5 317 " --> pdb=" O GLU 5 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU 5 376 " --> pdb=" O THR 5 317 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER 5 319 " --> pdb=" O ASN 5 374 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS 5 369 " --> pdb=" O GLU 4 324 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG 4 318 " --> pdb=" O PHE 5 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR 4 317 " --> pdb=" O GLU 4 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU 4 376 " --> pdb=" O THR 4 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER 4 319 " --> pdb=" O ASN 4 374 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS 4 369 " --> pdb=" O GLU 3 324 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG 3 318 " --> pdb=" O PHE 4 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR 3 317 " --> pdb=" O GLU 3 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU 3 376 " --> pdb=" O THR 3 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER 3 319 " --> pdb=" O ASN 3 374 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS 3 369 " --> pdb=" O GLU 2 324 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ARG 2 318 " --> pdb=" O PHE 3 375 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR 2 317 " --> pdb=" O GLU 2 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU 2 376 " --> pdb=" O THR 2 317 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER 2 319 " --> pdb=" O ASN 2 374 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS 2 369 " --> pdb=" O GLU 1 324 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER 2 371 " --> pdb=" O ALA 1 322 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU 1 320 " --> pdb=" O ARG 2 373 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ARG 1 318 " --> pdb=" O PHE 2 375 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR 2 291 " --> pdb=" O VAL 2 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL 2 398 " --> pdb=" O THR 2 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN 2 293 " --> pdb=" O VAL 2 396 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL 2 396 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP 2 295 " --> pdb=" O GLN 2 394 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN 2 394 " --> pdb=" O ASP 2 295 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN 2 297 " --> pdb=" O ALA 2 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR 2 390 " --> pdb=" O ASP 2 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU 2 443 " --> pdb=" O ALA 2 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN 2 394 " --> pdb=" O LEU 2 443 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASN 2 445 " --> pdb=" O GLN 2 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL 2 396 " --> pdb=" O ASN 2 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU 2 447 " --> pdb=" O VAL 2 396 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL 2 398 " --> pdb=" O LEU 2 447 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL 2 449 " --> pdb=" O VAL 2 398 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE 2 400 " --> pdb=" O VAL 2 449 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR 3 291 " --> pdb=" O VAL 3 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL 3 398 " --> pdb=" O THR 3 291 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN 3 293 " --> pdb=" O VAL 3 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL 3 396 " --> pdb=" O GLN 3 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP 3 295 " --> pdb=" O GLN 3 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN 3 394 " --> pdb=" O ASP 3 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN 3 297 " --> pdb=" O ALA 3 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR 3 390 " --> pdb=" O ASP 3 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU 3 443 " --> pdb=" O ALA 3 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN 3 394 " --> pdb=" O LEU 3 443 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASN 3 445 " --> pdb=" O GLN 3 394 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL 3 396 " --> pdb=" O ASN 3 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU 3 447 " --> pdb=" O VAL 3 396 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL 3 398 " --> pdb=" O LEU 3 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL 3 449 " --> pdb=" O VAL 3 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE 3 400 " --> pdb=" O VAL 3 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '4' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR 4 291 " --> pdb=" O VAL 4 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL 4 398 " --> pdb=" O THR 4 291 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLN 4 293 " --> pdb=" O VAL 4 396 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL 4 396 " --> pdb=" O GLN 4 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP 4 295 " --> pdb=" O GLN 4 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN 4 394 " --> pdb=" O ASP 4 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN 4 297 " --> pdb=" O ALA 4 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR 4 390 " --> pdb=" O ASP 4 299 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N LEU 4 443 " --> pdb=" O ALA 4 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN 4 394 " --> pdb=" O LEU 4 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN 4 445 " --> pdb=" O GLN 4 394 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL 4 396 " --> pdb=" O ASN 4 445 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU 4 447 " --> pdb=" O VAL 4 396 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL 4 398 " --> pdb=" O LEU 4 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL 4 449 " --> pdb=" O VAL 4 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE 4 400 " --> pdb=" O VAL 4 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '5' and resid 290 through 299 removed outlier: 6.920A pdb=" N THR 5 291 " --> pdb=" O VAL 5 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL 5 398 " --> pdb=" O THR 5 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN 5 293 " --> pdb=" O VAL 5 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL 5 396 " --> pdb=" O GLN 5 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP 5 295 " --> pdb=" O GLN 5 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN 5 394 " --> pdb=" O ASP 5 295 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN 5 297 " --> pdb=" O ALA 5 392 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR 5 390 " --> pdb=" O ASP 5 299 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N LEU 5 443 " --> pdb=" O ALA 5 392 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN 5 394 " --> pdb=" O LEU 5 443 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASN 5 445 " --> pdb=" O GLN 5 394 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL 5 396 " --> pdb=" O ASN 5 445 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU 5 447 " --> pdb=" O VAL 5 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL 5 398 " --> pdb=" O LEU 5 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL 5 449 " --> pdb=" O VAL 5 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE 5 400 " --> pdb=" O VAL 5 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '6' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR 6 291 " --> pdb=" O VAL 6 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL 6 398 " --> pdb=" O THR 6 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN 6 293 " --> pdb=" O VAL 6 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL 6 396 " --> pdb=" O GLN 6 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP 6 295 " --> pdb=" O GLN 6 394 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN 6 394 " --> pdb=" O ASP 6 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN 6 297 " --> pdb=" O ALA 6 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR 6 390 " --> pdb=" O ASP 6 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU 6 443 " --> pdb=" O ALA 6 392 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN 6 394 " --> pdb=" O LEU 6 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN 6 445 " --> pdb=" O GLN 6 394 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL 6 396 " --> pdb=" O ASN 6 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU 6 447 " --> pdb=" O VAL 6 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL 6 398 " --> pdb=" O LEU 6 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL 6 449 " --> pdb=" O VAL 6 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE 6 400 " --> pdb=" O VAL 6 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '7' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR 7 291 " --> pdb=" O VAL 7 398 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL 7 398 " --> pdb=" O THR 7 291 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN 7 293 " --> pdb=" O VAL 7 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL 7 396 " --> pdb=" O GLN 7 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP 7 295 " --> pdb=" O GLN 7 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN 7 394 " --> pdb=" O ASP 7 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN 7 297 " --> pdb=" O ALA 7 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR 7 390 " --> pdb=" O ASP 7 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU 7 443 " --> pdb=" O ALA 7 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN 7 394 " --> pdb=" O LEU 7 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN 7 445 " --> pdb=" O GLN 7 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL 7 396 " --> pdb=" O ASN 7 445 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU 7 447 " --> pdb=" O VAL 7 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL 7 398 " --> pdb=" O LEU 7 447 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL 7 449 " --> pdb=" O VAL 7 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE 7 400 " --> pdb=" O VAL 7 449 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '8' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR 8 291 " --> pdb=" O VAL 8 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL 8 398 " --> pdb=" O THR 8 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN 8 293 " --> pdb=" O VAL 8 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL 8 396 " --> pdb=" O GLN 8 293 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP 8 295 " --> pdb=" O GLN 8 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN 8 394 " --> pdb=" O ASP 8 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN 8 297 " --> pdb=" O ALA 8 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR 8 390 " --> pdb=" O ASP 8 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU 8 443 " --> pdb=" O ALA 8 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN 8 394 " --> pdb=" O LEU 8 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN 8 445 " --> pdb=" O GLN 8 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL 8 396 " --> pdb=" O ASN 8 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU 8 447 " --> pdb=" O VAL 8 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL 8 398 " --> pdb=" O LEU 8 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL 8 449 " --> pdb=" O VAL 8 398 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE 8 400 " --> pdb=" O VAL 8 449 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '9' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR 9 291 " --> pdb=" O VAL 9 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL 9 398 " --> pdb=" O THR 9 291 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN 9 293 " --> pdb=" O VAL 9 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL 9 396 " --> pdb=" O GLN 9 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP 9 295 " --> pdb=" O GLN 9 394 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN 9 394 " --> pdb=" O ASP 9 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN 9 297 " --> pdb=" O ALA 9 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR 9 390 " --> pdb=" O ASP 9 299 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N LEU 9 443 " --> pdb=" O ALA 9 392 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN 9 394 " --> pdb=" O LEU 9 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN 9 445 " --> pdb=" O GLN 9 394 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL 9 396 " --> pdb=" O ASN 9 445 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU 9 447 " --> pdb=" O VAL 9 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL 9 398 " --> pdb=" O LEU 9 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL 9 449 " --> pdb=" O VAL 9 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE 9 400 " --> pdb=" O VAL 9 449 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 290 through 299 removed outlier: 6.920A pdb=" N THR A 291 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL A 398 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN A 293 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL A 396 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP A 295 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN A 394 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN A 297 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 390 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU A 443 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN A 394 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN A 445 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL A 396 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU A 447 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL A 398 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL A 449 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE A 400 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR B 291 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL B 398 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLN B 293 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL B 396 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP B 295 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN B 394 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN B 297 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 390 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N LEU B 443 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN B 394 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN B 445 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL B 396 " --> pdb=" O ASN B 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU B 447 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL B 398 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL B 449 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE B 400 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR C 291 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL C 398 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN C 293 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL C 396 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP C 295 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN C 394 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN C 297 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR C 390 " --> pdb=" O ASP C 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU C 443 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN C 394 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASN C 445 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL C 396 " --> pdb=" O ASN C 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU C 447 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL C 398 " --> pdb=" O LEU C 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL C 449 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE C 400 " --> pdb=" O VAL C 449 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR D 291 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL D 398 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN D 293 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL D 396 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP D 295 " --> pdb=" O GLN D 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN D 394 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN D 297 " --> pdb=" O ALA D 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 390 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N LEU D 443 " --> pdb=" O ALA D 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN D 394 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASN D 445 " --> pdb=" O GLN D 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL D 396 " --> pdb=" O ASN D 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU D 447 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL D 398 " --> pdb=" O LEU D 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL D 449 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE D 400 " --> pdb=" O VAL D 449 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR E 291 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL E 398 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN E 293 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL E 396 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP E 295 " --> pdb=" O GLN E 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN E 394 " --> pdb=" O ASP E 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN E 297 " --> pdb=" O ALA E 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR E 390 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU E 443 " --> pdb=" O ALA E 392 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN E 394 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN E 445 " --> pdb=" O GLN E 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL E 396 " --> pdb=" O ASN E 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU E 447 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL E 398 " --> pdb=" O LEU E 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL E 449 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE E 400 " --> pdb=" O VAL E 449 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 290 through 299 removed outlier: 6.920A pdb=" N THR F 291 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL F 398 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN F 293 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL F 396 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP F 295 " --> pdb=" O GLN F 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN F 394 " --> pdb=" O ASP F 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN F 297 " --> pdb=" O ALA F 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR F 390 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU F 443 " --> pdb=" O ALA F 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN F 394 " --> pdb=" O LEU F 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN F 445 " --> pdb=" O GLN F 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL F 396 " --> pdb=" O ASN F 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU F 447 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL F 398 " --> pdb=" O LEU F 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL F 449 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE F 400 " --> pdb=" O VAL F 449 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR G 291 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL G 398 " --> pdb=" O THR G 291 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN G 293 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL G 396 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP G 295 " --> pdb=" O GLN G 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN G 394 " --> pdb=" O ASP G 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN G 297 " --> pdb=" O ALA G 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR G 390 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU G 443 " --> pdb=" O ALA G 392 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN G 394 " --> pdb=" O LEU G 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN G 445 " --> pdb=" O GLN G 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL G 396 " --> pdb=" O ASN G 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU G 447 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL G 398 " --> pdb=" O LEU G 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL G 449 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE G 400 " --> pdb=" O VAL G 449 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR H 291 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL H 398 " --> pdb=" O THR H 291 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLN H 293 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL H 396 " --> pdb=" O GLN H 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP H 295 " --> pdb=" O GLN H 394 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN H 394 " --> pdb=" O ASP H 295 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN H 297 " --> pdb=" O ALA H 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR H 390 " --> pdb=" O ASP H 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU H 443 " --> pdb=" O ALA H 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN H 394 " --> pdb=" O LEU H 443 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASN H 445 " --> pdb=" O GLN H 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL H 396 " --> pdb=" O ASN H 445 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU H 447 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL H 398 " --> pdb=" O LEU H 447 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL H 449 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE H 400 " --> pdb=" O VAL H 449 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR I 291 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL I 398 " --> pdb=" O THR I 291 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN I 293 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL I 396 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP I 295 " --> pdb=" O GLN I 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN I 394 " --> pdb=" O ASP I 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN I 297 " --> pdb=" O ALA I 392 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR I 390 " --> pdb=" O ASP I 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU I 443 " --> pdb=" O ALA I 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN I 394 " --> pdb=" O LEU I 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN I 445 " --> pdb=" O GLN I 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL I 396 " --> pdb=" O ASN I 445 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU I 447 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL I 398 " --> pdb=" O LEU I 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL I 449 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE I 400 " --> pdb=" O VAL I 449 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR J 291 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL J 398 " --> pdb=" O THR J 291 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN J 293 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL J 396 " --> pdb=" O GLN J 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP J 295 " --> pdb=" O GLN J 394 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN J 394 " --> pdb=" O ASP J 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN J 297 " --> pdb=" O ALA J 392 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR J 390 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU J 443 " --> pdb=" O ALA J 392 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN J 394 " --> pdb=" O LEU J 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN J 445 " --> pdb=" O GLN J 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL J 396 " --> pdb=" O ASN J 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU J 447 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL J 398 " --> pdb=" O LEU J 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL J 449 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE J 400 " --> pdb=" O VAL J 449 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 290 through 299 removed outlier: 6.920A pdb=" N THR K 291 " --> pdb=" O VAL K 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL K 398 " --> pdb=" O THR K 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN K 293 " --> pdb=" O VAL K 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL K 396 " --> pdb=" O GLN K 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP K 295 " --> pdb=" O GLN K 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN K 394 " --> pdb=" O ASP K 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN K 297 " --> pdb=" O ALA K 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR K 390 " --> pdb=" O ASP K 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU K 443 " --> pdb=" O ALA K 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN K 394 " --> pdb=" O LEU K 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN K 445 " --> pdb=" O GLN K 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL K 396 " --> pdb=" O ASN K 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU K 447 " --> pdb=" O VAL K 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL K 398 " --> pdb=" O LEU K 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL K 449 " --> pdb=" O VAL K 398 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE K 400 " --> pdb=" O VAL K 449 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 290 through 299 removed outlier: 6.920A pdb=" N THR L 291 " --> pdb=" O VAL L 398 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL L 398 " --> pdb=" O THR L 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN L 293 " --> pdb=" O VAL L 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL L 396 " --> pdb=" O GLN L 293 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP L 295 " --> pdb=" O GLN L 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN L 394 " --> pdb=" O ASP L 295 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLN L 297 " --> pdb=" O ALA L 392 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR L 390 " --> pdb=" O ASP L 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU L 443 " --> pdb=" O ALA L 392 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN L 394 " --> pdb=" O LEU L 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN L 445 " --> pdb=" O GLN L 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL L 396 " --> pdb=" O ASN L 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU L 447 " --> pdb=" O VAL L 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL L 398 " --> pdb=" O LEU L 447 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL L 449 " --> pdb=" O VAL L 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE L 400 " --> pdb=" O VAL L 449 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR M 291 " --> pdb=" O VAL M 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL M 398 " --> pdb=" O THR M 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN M 293 " --> pdb=" O VAL M 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL M 396 " --> pdb=" O GLN M 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP M 295 " --> pdb=" O GLN M 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN M 394 " --> pdb=" O ASP M 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN M 297 " --> pdb=" O ALA M 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR M 390 " --> pdb=" O ASP M 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU M 443 " --> pdb=" O ALA M 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN M 394 " --> pdb=" O LEU M 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN M 445 " --> pdb=" O GLN M 394 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL M 396 " --> pdb=" O ASN M 445 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU M 447 " --> pdb=" O VAL M 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL M 398 " --> pdb=" O LEU M 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL M 449 " --> pdb=" O VAL M 398 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE M 400 " --> pdb=" O VAL M 449 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 290 through 299 removed outlier: 6.920A pdb=" N THR N 291 " --> pdb=" O VAL N 398 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL N 398 " --> pdb=" O THR N 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN N 293 " --> pdb=" O VAL N 396 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL N 396 " --> pdb=" O GLN N 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP N 295 " --> pdb=" O GLN N 394 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN N 394 " --> pdb=" O ASP N 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN N 297 " --> pdb=" O ALA N 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR N 390 " --> pdb=" O ASP N 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU N 443 " --> pdb=" O ALA N 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN N 394 " --> pdb=" O LEU N 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN N 445 " --> pdb=" O GLN N 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL N 396 " --> pdb=" O ASN N 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU N 447 " --> pdb=" O VAL N 396 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL N 398 " --> pdb=" O LEU N 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL N 449 " --> pdb=" O VAL N 398 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE N 400 " --> pdb=" O VAL N 449 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR O 291 " --> pdb=" O VAL O 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL O 398 " --> pdb=" O THR O 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN O 293 " --> pdb=" O VAL O 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL O 396 " --> pdb=" O GLN O 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP O 295 " --> pdb=" O GLN O 394 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN O 394 " --> pdb=" O ASP O 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN O 297 " --> pdb=" O ALA O 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR O 390 " --> pdb=" O ASP O 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU O 443 " --> pdb=" O ALA O 392 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN O 394 " --> pdb=" O LEU O 443 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASN O 445 " --> pdb=" O GLN O 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL O 396 " --> pdb=" O ASN O 445 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU O 447 " --> pdb=" O VAL O 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL O 398 " --> pdb=" O LEU O 447 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL O 449 " --> pdb=" O VAL O 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE O 400 " --> pdb=" O VAL O 449 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR P 291 " --> pdb=" O VAL P 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL P 398 " --> pdb=" O THR P 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN P 293 " --> pdb=" O VAL P 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL P 396 " --> pdb=" O GLN P 293 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP P 295 " --> pdb=" O GLN P 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN P 394 " --> pdb=" O ASP P 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN P 297 " --> pdb=" O ALA P 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR P 390 " --> pdb=" O ASP P 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU P 443 " --> pdb=" O ALA P 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN P 394 " --> pdb=" O LEU P 443 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASN P 445 " --> pdb=" O GLN P 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL P 396 " --> pdb=" O ASN P 445 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU P 447 " --> pdb=" O VAL P 396 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL P 398 " --> pdb=" O LEU P 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL P 449 " --> pdb=" O VAL P 398 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE P 400 " --> pdb=" O VAL P 449 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 290 through 299 removed outlier: 6.920A pdb=" N THR Q 291 " --> pdb=" O VAL Q 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL Q 398 " --> pdb=" O THR Q 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN Q 293 " --> pdb=" O VAL Q 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL Q 396 " --> pdb=" O GLN Q 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP Q 295 " --> pdb=" O GLN Q 394 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN Q 394 " --> pdb=" O ASP Q 295 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN Q 297 " --> pdb=" O ALA Q 392 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR Q 390 " --> pdb=" O ASP Q 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU Q 443 " --> pdb=" O ALA Q 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN Q 394 " --> pdb=" O LEU Q 443 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASN Q 445 " --> pdb=" O GLN Q 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL Q 396 " --> pdb=" O ASN Q 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU Q 447 " --> pdb=" O VAL Q 396 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL Q 398 " --> pdb=" O LEU Q 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL Q 449 " --> pdb=" O VAL Q 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE Q 400 " --> pdb=" O VAL Q 449 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 290 through 299 removed outlier: 6.920A pdb=" N THR R 291 " --> pdb=" O VAL R 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL R 398 " --> pdb=" O THR R 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN R 293 " --> pdb=" O VAL R 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL R 396 " --> pdb=" O GLN R 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP R 295 " --> pdb=" O GLN R 394 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN R 394 " --> pdb=" O ASP R 295 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN R 297 " --> pdb=" O ALA R 392 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR R 390 " --> pdb=" O ASP R 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU R 443 " --> pdb=" O ALA R 392 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN R 394 " --> pdb=" O LEU R 443 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASN R 445 " --> pdb=" O GLN R 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL R 396 " --> pdb=" O ASN R 445 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU R 447 " --> pdb=" O VAL R 396 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL R 398 " --> pdb=" O LEU R 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL R 449 " --> pdb=" O VAL R 398 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE R 400 " --> pdb=" O VAL R 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 290 through 299 removed outlier: 6.920A pdb=" N THR S 291 " --> pdb=" O VAL S 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL S 398 " --> pdb=" O THR S 291 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN S 293 " --> pdb=" O VAL S 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL S 396 " --> pdb=" O GLN S 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP S 295 " --> pdb=" O GLN S 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN S 394 " --> pdb=" O ASP S 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN S 297 " --> pdb=" O ALA S 392 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR S 390 " --> pdb=" O ASP S 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU S 443 " --> pdb=" O ALA S 392 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN S 394 " --> pdb=" O LEU S 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN S 445 " --> pdb=" O GLN S 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL S 396 " --> pdb=" O ASN S 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU S 447 " --> pdb=" O VAL S 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL S 398 " --> pdb=" O LEU S 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL S 449 " --> pdb=" O VAL S 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE S 400 " --> pdb=" O VAL S 449 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR T 291 " --> pdb=" O VAL T 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL T 398 " --> pdb=" O THR T 291 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN T 293 " --> pdb=" O VAL T 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL T 396 " --> pdb=" O GLN T 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP T 295 " --> pdb=" O GLN T 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN T 394 " --> pdb=" O ASP T 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN T 297 " --> pdb=" O ALA T 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR T 390 " --> pdb=" O ASP T 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU T 443 " --> pdb=" O ALA T 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN T 394 " --> pdb=" O LEU T 443 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASN T 445 " --> pdb=" O GLN T 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL T 396 " --> pdb=" O ASN T 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU T 447 " --> pdb=" O VAL T 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL T 398 " --> pdb=" O LEU T 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL T 449 " --> pdb=" O VAL T 398 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE T 400 " --> pdb=" O VAL T 449 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR U 291 " --> pdb=" O VAL U 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL U 398 " --> pdb=" O THR U 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN U 293 " --> pdb=" O VAL U 396 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL U 396 " --> pdb=" O GLN U 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP U 295 " --> pdb=" O GLN U 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN U 394 " --> pdb=" O ASP U 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN U 297 " --> pdb=" O ALA U 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR U 390 " --> pdb=" O ASP U 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU U 443 " --> pdb=" O ALA U 392 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN U 394 " --> pdb=" O LEU U 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN U 445 " --> pdb=" O GLN U 394 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL U 396 " --> pdb=" O ASN U 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU U 447 " --> pdb=" O VAL U 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL U 398 " --> pdb=" O LEU U 447 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL U 449 " --> pdb=" O VAL U 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE U 400 " --> pdb=" O VAL U 449 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'V' and resid 290 through 299 removed outlier: 6.920A pdb=" N THR V 291 " --> pdb=" O VAL V 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL V 398 " --> pdb=" O THR V 291 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN V 293 " --> pdb=" O VAL V 396 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL V 396 " --> pdb=" O GLN V 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP V 295 " --> pdb=" O GLN V 394 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN V 394 " --> pdb=" O ASP V 295 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN V 297 " --> pdb=" O ALA V 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR V 390 " --> pdb=" O ASP V 299 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N LEU V 443 " --> pdb=" O ALA V 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN V 394 " --> pdb=" O LEU V 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN V 445 " --> pdb=" O GLN V 394 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL V 396 " --> pdb=" O ASN V 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU V 447 " --> pdb=" O VAL V 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL V 398 " --> pdb=" O LEU V 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL V 449 " --> pdb=" O VAL V 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE V 400 " --> pdb=" O VAL V 449 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'W' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR W 291 " --> pdb=" O VAL W 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL W 398 " --> pdb=" O THR W 291 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN W 293 " --> pdb=" O VAL W 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL W 396 " --> pdb=" O GLN W 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP W 295 " --> pdb=" O GLN W 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN W 394 " --> pdb=" O ASP W 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN W 297 " --> pdb=" O ALA W 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR W 390 " --> pdb=" O ASP W 299 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N LEU W 443 " --> pdb=" O ALA W 392 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN W 394 " --> pdb=" O LEU W 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN W 445 " --> pdb=" O GLN W 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL W 396 " --> pdb=" O ASN W 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU W 447 " --> pdb=" O VAL W 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL W 398 " --> pdb=" O LEU W 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL W 449 " --> pdb=" O VAL W 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE W 400 " --> pdb=" O VAL W 449 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 290 through 299 removed outlier: 6.921A pdb=" N THR X 291 " --> pdb=" O VAL X 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL X 398 " --> pdb=" O THR X 291 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN X 293 " --> pdb=" O VAL X 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL X 396 " --> pdb=" O GLN X 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP X 295 " --> pdb=" O GLN X 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN X 394 " --> pdb=" O ASP X 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN X 297 " --> pdb=" O ALA X 392 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR X 390 " --> pdb=" O ASP X 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU X 443 " --> pdb=" O ALA X 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN X 394 " --> pdb=" O LEU X 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN X 445 " --> pdb=" O GLN X 394 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL X 396 " --> pdb=" O ASN X 445 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU X 447 " --> pdb=" O VAL X 396 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL X 398 " --> pdb=" O LEU X 447 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL X 449 " --> pdb=" O VAL X 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE X 400 " --> pdb=" O VAL X 449 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 290 through 299 removed outlier: 6.920A pdb=" N THR Y 291 " --> pdb=" O VAL Y 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL Y 398 " --> pdb=" O THR Y 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN Y 293 " --> pdb=" O VAL Y 396 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL Y 396 " --> pdb=" O GLN Y 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP Y 295 " --> pdb=" O GLN Y 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN Y 394 " --> pdb=" O ASP Y 295 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN Y 297 " --> pdb=" O ALA Y 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR Y 390 " --> pdb=" O ASP Y 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU Y 443 " --> pdb=" O ALA Y 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN Y 394 " --> pdb=" O LEU Y 443 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ASN Y 445 " --> pdb=" O GLN Y 394 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL Y 396 " --> pdb=" O ASN Y 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU Y 447 " --> pdb=" O VAL Y 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL Y 398 " --> pdb=" O LEU Y 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL Y 449 " --> pdb=" O VAL Y 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE Y 400 " --> pdb=" O VAL Y 449 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 290 through 299 removed outlier: 6.920A pdb=" N THR Z 291 " --> pdb=" O VAL Z 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL Z 398 " --> pdb=" O THR Z 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN Z 293 " --> pdb=" O VAL Z 396 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL Z 396 " --> pdb=" O GLN Z 293 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP Z 295 " --> pdb=" O GLN Z 394 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN Z 394 " --> pdb=" O ASP Z 295 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN Z 297 " --> pdb=" O ALA Z 392 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR Z 390 " --> pdb=" O ASP Z 299 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU Z 443 " --> pdb=" O ALA Z 392 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN Z 394 " --> pdb=" O LEU Z 443 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN Z 445 " --> pdb=" O GLN Z 394 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL Z 396 " --> pdb=" O ASN Z 445 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU Z 447 " --> pdb=" O VAL Z 396 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL Z 398 " --> pdb=" O LEU Z 447 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL Z 449 " --> pdb=" O VAL Z 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE Z 400 " --> pdb=" O VAL Z 449 " (cutoff:3.500A) 2074 hydrogen bonds defined for protein. 5910 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: 10.17 Time building geometry restraints manager: 4.37 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: 14242 1.34 - 1.45: 3349 1.45 - 1.57: 23219 1.57 - 1.69: 0 1.69 - 1.80: 140 Bond restraints: 40950 Sorted by residual: bond pdb=" CA ALA U 452 " pdb=" CB ALA U 452 " ideal model delta sigma weight residual 1.534 1.491 0.043 1.60e-02 3.91e+03 7.26e+00 bond pdb=" CA ALA 2 452 " pdb=" CB ALA 2 452 " ideal model delta sigma weight residual 1.534 1.491 0.043 1.60e-02 3.91e+03 7.24e+00 bond pdb=" CA ALA E 452 " pdb=" CB ALA E 452 " ideal model delta sigma weight residual 1.534 1.491 0.043 1.60e-02 3.91e+03 7.23e+00 bond pdb=" CA ALA I 452 " pdb=" CB ALA I 452 " ideal model delta sigma weight residual 1.534 1.492 0.043 1.60e-02 3.91e+03 7.11e+00 bond pdb=" CA ALA 9 452 " pdb=" CB ALA 9 452 " ideal model delta sigma weight residual 1.534 1.492 0.043 1.60e-02 3.91e+03 7.10e+00 ... (remaining 40945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 51210 0.93 - 1.87: 2773 1.87 - 2.80: 613 2.80 - 3.74: 288 3.74 - 4.67: 171 Bond angle restraints: 55055 Sorted by residual: angle pdb=" CA GLN B 263 " pdb=" C GLN B 263 " pdb=" O GLN B 263 " ideal model delta sigma weight residual 120.82 117.01 3.81 1.05e+00 9.07e-01 1.32e+01 angle pdb=" CA GLN Z 263 " pdb=" C GLN Z 263 " pdb=" O GLN Z 263 " ideal model delta sigma weight residual 120.82 117.01 3.81 1.05e+00 9.07e-01 1.31e+01 angle pdb=" CA GLN 6 263 " pdb=" C GLN 6 263 " pdb=" O GLN 6 263 " ideal model delta sigma weight residual 120.82 117.02 3.80 1.05e+00 9.07e-01 1.31e+01 angle pdb=" CA GLN X 263 " pdb=" C GLN X 263 " pdb=" O GLN X 263 " ideal model delta sigma weight residual 120.82 117.02 3.80 1.05e+00 9.07e-01 1.31e+01 angle pdb=" CA GLN H 263 " pdb=" C GLN H 263 " pdb=" O GLN H 263 " ideal model delta sigma weight residual 120.82 117.03 3.79 1.05e+00 9.07e-01 1.30e+01 ... (remaining 55050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.79: 19436 10.79 - 21.58: 2824 21.58 - 32.37: 1750 32.37 - 43.16: 1015 43.16 - 53.95: 490 Dihedral angle restraints: 25515 sinusoidal: 10640 harmonic: 14875 Sorted by residual: dihedral pdb=" CD ARG M 393 " pdb=" NE ARG M 393 " pdb=" CZ ARG M 393 " pdb=" NH1 ARG M 393 " ideal model delta sinusoidal sigma weight residual 0.00 35.02 -35.02 1 1.00e+01 1.00e-02 1.74e+01 dihedral pdb=" CD ARG Z 393 " pdb=" NE ARG Z 393 " pdb=" CZ ARG Z 393 " pdb=" NH1 ARG Z 393 " ideal model delta sinusoidal sigma weight residual 0.00 35.00 -35.00 1 1.00e+01 1.00e-02 1.74e+01 dihedral pdb=" CD ARG T 393 " pdb=" NE ARG T 393 " pdb=" CZ ARG T 393 " pdb=" NH1 ARG T 393 " ideal model delta sinusoidal sigma weight residual 0.00 35.00 -35.00 1 1.00e+01 1.00e-02 1.74e+01 ... (remaining 25512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 4063 0.028 - 0.055: 1384 0.055 - 0.083: 364 0.083 - 0.111: 419 0.111 - 0.138: 70 Chirality restraints: 6300 Sorted by residual: chirality pdb=" CA GLU 3 453 " pdb=" N GLU 3 453 " pdb=" C GLU 3 453 " pdb=" CB GLU 3 453 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA GLU X 453 " pdb=" N GLU X 453 " pdb=" C GLU X 453 " pdb=" CB GLU X 453 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA GLU T 453 " pdb=" N GLU T 453 " pdb=" C GLU T 453 " pdb=" CB GLU T 453 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 6297 not shown) Planarity restraints: 7280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 393 " -0.627 9.50e-02 1.11e+02 2.81e-01 4.82e+01 pdb=" NE ARG G 393 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG G 393 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG G 393 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 393 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG O 393 " -0.626 9.50e-02 1.11e+02 2.81e-01 4.81e+01 pdb=" NE ARG O 393 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG O 393 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG O 393 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG O 393 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG T 393 " -0.626 9.50e-02 1.11e+02 2.81e-01 4.81e+01 pdb=" NE ARG T 393 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG T 393 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG T 393 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG T 393 " -0.020 2.00e-02 2.50e+03 ... (remaining 7277 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 9373 2.80 - 3.33: 33639 3.33 - 3.85: 59994 3.85 - 4.38: 64674 4.38 - 4.90: 125744 Nonbonded interactions: 293424 Sorted by model distance: nonbonded pdb=" OG1 THR 1 395 " pdb=" O GLY Z 432 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASP Z 437 " pdb=" N GLY Z 439 " model vdw 2.281 3.120 nonbonded pdb=" OD1 ASP T 437 " pdb=" N GLY T 439 " model vdw 2.281 3.120 nonbonded pdb=" OD1 ASP 9 437 " pdb=" N GLY 9 439 " model vdw 2.282 3.120 nonbonded pdb=" OD1 ASP 3 437 " pdb=" N GLY 3 439 " model vdw 2.282 3.120 ... (remaining 293419 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: 0.15 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 33.450 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.200 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: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 0.003 0.043 40950 Z= 0.189 Angle : 0.588 4.673 55055 Z= 0.361 Chirality : 0.039 0.138 6300 Planarity : 0.020 0.281 7280 Dihedral : 17.214 53.946 15785 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.79 % Allowed : 31.50 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.12), residues: 4900 helix: 2.50 (0.13), residues: 1505 sheet: 2.15 (0.13), residues: 1855 loop : -2.13 (0.12), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 373 TYR 0.004 0.001 TYR 9 290 PHE 0.007 0.001 PHE 7 436 HIS 0.001 0.000 HIS O 383 Details of bonding type rmsd covalent geometry : bond 0.00329 (40950) covalent geometry : angle 0.58833 (55055) hydrogen bonds : bond 0.22305 ( 2074) hydrogen bonds : angle 5.94226 ( 5910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 1063 time to evaluate : 1.690 Fit side-chains REVERT: 2 369 LYS cc_start: 0.8050 (mmmm) cc_final: 0.7716 (mttp) REVERT: 2 450 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7947 (tttp) REVERT: 3 298 MET cc_start: 0.8794 (ptp) cc_final: 0.8584 (ptm) REVERT: 3 369 LYS cc_start: 0.8022 (mmmm) cc_final: 0.7690 (mttp) REVERT: 5 278 ASP cc_start: 0.8020 (m-30) cc_final: 0.7764 (m-30) REVERT: 5 311 ASP cc_start: 0.8870 (t0) cc_final: 0.8575 (t70) REVERT: 7 311 ASP cc_start: 0.8746 (t0) cc_final: 0.8533 (t0) REVERT: 7 450 LYS cc_start: 0.7805 (ttmt) cc_final: 0.7099 (tppt) REVERT: 8 373 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7596 (mtm-85) REVERT: 8 450 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7733 (tppt) REVERT: 9 287 TYR cc_start: 0.7916 (t80) cc_final: 0.7603 (t80) REVERT: 9 297 GLN cc_start: 0.9006 (tt0) cc_final: 0.8785 (tt0) REVERT: 9 373 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7745 (mtm-85) REVERT: 9 450 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7782 (tppt) REVERT: A 443 LEU cc_start: 0.9103 (tp) cc_final: 0.8863 (mt) REVERT: A 450 LYS cc_start: 0.8312 (ttmt) cc_final: 0.7867 (tttp) REVERT: B 450 LYS cc_start: 0.8450 (ttmt) cc_final: 0.7905 (tppt) REVERT: C 298 MET cc_start: 0.7985 (ptp) cc_final: 0.7762 (ptp) REVERT: E 299 ASP cc_start: 0.8726 (p0) cc_final: 0.8498 (p0) REVERT: G 269 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8264 (mm-40) REVERT: H 281 LEU cc_start: 0.8862 (mt) cc_final: 0.8607 (mt) REVERT: H 393 ARG cc_start: 0.9387 (OUTLIER) cc_final: 0.9003 (ttp-170) REVERT: J 297 GLN cc_start: 0.7960 (tt0) cc_final: 0.7631 (tt0) REVERT: J 309 ARG cc_start: 0.7973 (ttp-110) cc_final: 0.7587 (mtm180) REVERT: J 369 LYS cc_start: 0.8157 (mmmm) cc_final: 0.7928 (mtpp) REVERT: J 393 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8764 (ttp-170) REVERT: K 297 GLN cc_start: 0.7960 (tt0) cc_final: 0.7643 (tt0) REVERT: K 309 ARG cc_start: 0.7965 (ttp-110) cc_final: 0.7622 (mtt90) REVERT: K 326 TYR cc_start: 0.7818 (m-80) cc_final: 0.7390 (m-10) REVERT: L 326 TYR cc_start: 0.7838 (m-80) cc_final: 0.7600 (m-80) REVERT: M 326 TYR cc_start: 0.7909 (m-80) cc_final: 0.7649 (m-80) REVERT: M 443 LEU cc_start: 0.8981 (tp) cc_final: 0.8745 (mt) REVERT: N 278 ASP cc_start: 0.8129 (m-30) cc_final: 0.7815 (m-30) REVERT: N 290 TYR cc_start: 0.8543 (p90) cc_final: 0.8325 (p90) REVERT: N 311 ASP cc_start: 0.8841 (t0) cc_final: 0.8566 (t0) REVERT: N 326 TYR cc_start: 0.7829 (m-80) cc_final: 0.7612 (m-80) REVERT: O 450 LYS cc_start: 0.7691 (ttmt) cc_final: 0.7360 (tppt) REVERT: P 450 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7592 (tppt) REVERT: Q 450 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7581 (tppt) REVERT: R 450 LYS cc_start: 0.8353 (ttmt) cc_final: 0.7732 (tppt) REVERT: S 450 LYS cc_start: 0.8415 (ttmt) cc_final: 0.7831 (tppt) REVERT: T 278 ASP cc_start: 0.7912 (m-30) cc_final: 0.7654 (m-30) REVERT: T 299 ASP cc_start: 0.8523 (p0) cc_final: 0.8221 (p0) REVERT: T 418 MET cc_start: 0.7195 (mtt) cc_final: 0.6895 (ttm) REVERT: T 424 ASN cc_start: 0.8918 (t0) cc_final: 0.8694 (t0) REVERT: U 299 ASP cc_start: 0.8461 (p0) cc_final: 0.8094 (p0) REVERT: U 418 MET cc_start: 0.6868 (mtt) cc_final: 0.6652 (ttm) REVERT: V 295 ASP cc_start: 0.7517 (p0) cc_final: 0.6996 (p0) REVERT: V 395 THR cc_start: 0.7774 (p) cc_final: 0.7555 (p) REVERT: W 269 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8145 (mm-40) REVERT: W 281 LEU cc_start: 0.8701 (mt) cc_final: 0.8378 (mt) REVERT: W 299 ASP cc_start: 0.8579 (p0) cc_final: 0.8261 (p0) REVERT: Y 290 TYR cc_start: 0.8006 (p90) cc_final: 0.7575 (p90) REVERT: Y 393 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.9088 (ttt180) REVERT: Z 290 TYR cc_start: 0.7782 (p90) cc_final: 0.7488 (p90) REVERT: Z 299 ASP cc_start: 0.8702 (p0) cc_final: 0.8396 (p0) REVERT: Z 309 ARG cc_start: 0.7760 (ttp-110) cc_final: 0.7317 (mtm110) REVERT: Z 369 LYS cc_start: 0.8262 (mmmm) cc_final: 0.7957 (mttp) REVERT: Z 393 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8785 (ttt180) outliers start: 35 outliers final: 2 residues processed: 1098 average time/residue: 0.2615 time to fit residues: 463.3479 Evaluate side-chains 838 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 832 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain H residue 393 ARG Chi-restraints excluded: chain J residue 393 ARG Chi-restraints excluded: chain Y residue 393 ARG Chi-restraints excluded: chain Z residue 393 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 0.6980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 470 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 263 GLN 2 263 GLN 2 271 GLN 3 263 GLN 4 263 GLN 5 263 GLN 5 445 ASN 6 263 GLN 6 445 ASN 7 263 GLN 7 445 ASN 8 263 GLN 9 263 GLN A 263 GLN B 263 GLN C 263 GLN D 263 GLN D 445 ASN E 271 GLN E 445 ASN F 263 GLN F 445 ASN G 263 GLN H 263 GLN H 271 GLN H 313 ASN J 263 GLN K 263 GLN K 445 ASN L 263 GLN L 445 ASN M 263 GLN M 445 ASN N 263 GLN N 445 ASN O 263 GLN P 263 GLN P 445 ASN Q 263 GLN R 263 GLN S 263 GLN S 445 ASN T 263 GLN U 263 GLN V 263 GLN V 445 ASN W 263 GLN X 263 GLN X 313 ASN Y 263 GLN Y 313 ASN Y 445 ASN Z 263 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104126 restraints weight = 57889.428| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.97 r_work: 0.3252 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 40950 Z= 0.131 Angle : 0.501 6.156 55055 Z= 0.269 Chirality : 0.040 0.129 6300 Planarity : 0.003 0.022 7280 Dihedral : 3.877 27.573 5624 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.31 % Allowed : 26.77 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.12), residues: 4900 helix: 3.13 (0.13), residues: 1435 sheet: 1.30 (0.10), residues: 2345 loop : -2.56 (0.13), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 385 TYR 0.016 0.001 TYR Z 321 PHE 0.008 0.001 PHE D 375 HIS 0.001 0.000 HIS 3 383 Details of bonding type rmsd covalent geometry : bond 0.00293 (40950) covalent geometry : angle 0.50113 (55055) hydrogen bonds : bond 0.06178 ( 2074) hydrogen bonds : angle 4.50899 ( 5910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 859 time to evaluate : 2.174 Fit side-chains revert: symmetry clash REVERT: 2 371 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8262 (m) REVERT: 2 450 LYS cc_start: 0.8500 (ttmt) cc_final: 0.8037 (tttp) REVERT: 3 311 ASP cc_start: 0.9036 (t0) cc_final: 0.8824 (t0) REVERT: 3 373 ARG cc_start: 0.8447 (mtm-85) cc_final: 0.8135 (mtm-85) REVERT: 3 438 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8414 (mm-40) REVERT: 5 278 ASP cc_start: 0.7898 (m-30) cc_final: 0.7651 (m-30) REVERT: 7 324 GLU cc_start: 0.7939 (tt0) cc_final: 0.7402 (tm-30) REVERT: 9 450 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8025 (tttp) REVERT: A 373 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.8048 (mtm180) REVERT: A 421 SER cc_start: 0.7935 (m) cc_final: 0.7714 (p) REVERT: A 450 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8012 (tttp) REVERT: C 450 LYS cc_start: 0.8494 (ttmt) cc_final: 0.7956 (tppt) REVERT: D 386 LYS cc_start: 0.9071 (mmmm) cc_final: 0.8827 (mmmm) REVERT: E 371 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8277 (m) REVERT: F 278 ASP cc_start: 0.7514 (m-30) cc_final: 0.7269 (m-30) REVERT: F 371 SER cc_start: 0.8379 (OUTLIER) cc_final: 0.8159 (m) REVERT: G 269 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8441 (mm-40) REVERT: J 297 GLN cc_start: 0.8001 (tt0) cc_final: 0.7711 (tt0) REVERT: J 299 ASP cc_start: 0.8439 (p0) cc_final: 0.8136 (p0) REVERT: K 297 GLN cc_start: 0.7928 (tt0) cc_final: 0.7638 (tt0) REVERT: K 326 TYR cc_start: 0.8229 (m-80) cc_final: 0.7883 (m-80) REVERT: K 450 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8038 (tttp) REVERT: L 326 TYR cc_start: 0.8171 (m-80) cc_final: 0.7962 (m-80) REVERT: M 450 LYS cc_start: 0.8531 (ttmt) cc_final: 0.7862 (tttp) REVERT: N 311 ASP cc_start: 0.9206 (t0) cc_final: 0.8912 (t0) REVERT: O 450 LYS cc_start: 0.8468 (ttmt) cc_final: 0.7909 (tttp) REVERT: P 324 GLU cc_start: 0.8070 (tt0) cc_final: 0.7702 (tm-30) REVERT: Q 450 LYS cc_start: 0.8569 (ttmt) cc_final: 0.7982 (tttp) REVERT: U 299 ASP cc_start: 0.8404 (p0) cc_final: 0.8140 (p0) REVERT: W 299 ASP cc_start: 0.8620 (p0) cc_final: 0.8404 (p0) REVERT: X 285 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8429 (mt) REVERT: Z 299 ASP cc_start: 0.8383 (p0) cc_final: 0.8139 (p0) outliers start: 147 outliers final: 84 residues processed: 988 average time/residue: 0.2379 time to fit residues: 393.5966 Evaluate side-chains 837 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 749 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 279 SER Chi-restraints excluded: chain 1 residue 390 THR Chi-restraints excluded: chain 2 residue 279 SER Chi-restraints excluded: chain 2 residue 371 SER Chi-restraints excluded: chain 3 residue 279 SER Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 4 residue 390 THR Chi-restraints excluded: chain 5 residue 279 SER Chi-restraints excluded: chain 5 residue 431 ILE Chi-restraints excluded: chain 6 residue 279 SER Chi-restraints excluded: chain 6 residue 390 THR Chi-restraints excluded: chain 6 residue 429 VAL Chi-restraints excluded: chain 6 residue 431 ILE Chi-restraints excluded: chain 7 residue 279 SER Chi-restraints excluded: chain 7 residue 377 LEU Chi-restraints excluded: chain 7 residue 447 LEU Chi-restraints excluded: chain 8 residue 279 SER Chi-restraints excluded: chain 8 residue 281 LEU Chi-restraints excluded: chain 8 residue 447 LEU Chi-restraints excluded: chain 9 residue 279 SER Chi-restraints excluded: chain 9 residue 390 THR Chi-restraints excluded: chain 9 residue 447 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 371 SER Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 371 SER Chi-restraints excluded: chain H residue 446 VAL Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 284 ILE Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain L residue 279 SER Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 390 THR Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 431 ILE Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain O residue 429 VAL Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 431 ILE Chi-restraints excluded: chain P residue 447 LEU Chi-restraints excluded: chain Q residue 279 SER Chi-restraints excluded: chain Q residue 447 LEU Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 418 MET Chi-restraints excluded: chain R residue 423 ILE Chi-restraints excluded: chain R residue 447 LEU Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 281 LEU Chi-restraints excluded: chain S residue 443 LEU Chi-restraints excluded: chain T residue 279 SER Chi-restraints excluded: chain U residue 279 SER Chi-restraints excluded: chain U residue 371 SER Chi-restraints excluded: chain U residue 390 THR Chi-restraints excluded: chain U residue 397 SER Chi-restraints excluded: chain V residue 279 SER Chi-restraints excluded: chain V residue 281 LEU Chi-restraints excluded: chain W residue 279 SER Chi-restraints excluded: chain X residue 279 SER Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 285 LEU Chi-restraints excluded: chain X residue 390 THR Chi-restraints excluded: chain X residue 397 SER Chi-restraints excluded: chain Y residue 279 SER Chi-restraints excluded: chain Y residue 371 SER Chi-restraints excluded: chain Z residue 279 SER Chi-restraints excluded: chain Z residue 390 THR Chi-restraints excluded: chain Z residue 446 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 392 optimal weight: 0.0970 chunk 414 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 453 optimal weight: 2.9990 chunk 358 optimal weight: 1.9990 chunk 356 optimal weight: 0.9980 chunk 288 optimal weight: 0.8980 chunk 272 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 445 ASN 2 271 GLN 2 445 ASN E 263 GLN F 445 ASN H 445 ASN I 445 ASN J 271 GLN N 445 ASN V 445 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.100932 restraints weight = 57902.686| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.98 r_work: 0.3202 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 40950 Z= 0.122 Angle : 0.459 4.800 55055 Z= 0.248 Chirality : 0.039 0.124 6300 Planarity : 0.002 0.018 7280 Dihedral : 3.701 12.683 5600 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.95 % Allowed : 26.82 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.12), residues: 4900 helix: 3.19 (0.13), residues: 1435 sheet: 1.28 (0.10), residues: 2345 loop : -2.44 (0.14), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 385 TYR 0.011 0.001 TYR Y 290 PHE 0.006 0.001 PHE M 310 HIS 0.001 0.000 HIS U 383 Details of bonding type rmsd covalent geometry : bond 0.00272 (40950) covalent geometry : angle 0.45923 (55055) hydrogen bonds : bond 0.06123 ( 2074) hydrogen bonds : angle 4.11954 ( 5910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 826 time to evaluate : 1.552 Fit side-chains REVERT: 1 311 ASP cc_start: 0.8920 (t0) cc_final: 0.8462 (t0) REVERT: 2 299 ASP cc_start: 0.8561 (p0) cc_final: 0.8344 (p0) REVERT: 2 450 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8139 (tttp) REVERT: 3 281 LEU cc_start: 0.8323 (mt) cc_final: 0.8110 (mt) REVERT: 3 437 ASP cc_start: 0.8460 (t0) cc_final: 0.8257 (t0) REVERT: 4 281 LEU cc_start: 0.8368 (mt) cc_final: 0.8044 (mt) REVERT: 5 278 ASP cc_start: 0.7880 (m-30) cc_final: 0.7636 (m-30) REVERT: 5 421 SER cc_start: 0.8048 (m) cc_final: 0.7832 (p) REVERT: 6 450 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8017 (tttp) REVERT: 7 295 ASP cc_start: 0.8132 (p0) cc_final: 0.7875 (p0) REVERT: 9 311 ASP cc_start: 0.9072 (t0) cc_final: 0.8838 (t0) REVERT: 9 324 GLU cc_start: 0.8202 (tt0) cc_final: 0.7906 (tm-30) REVERT: A 326 TYR cc_start: 0.8203 (m-80) cc_final: 0.7987 (m-80) REVERT: A 450 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8049 (tttp) REVERT: D 437 ASP cc_start: 0.8541 (t0) cc_final: 0.8318 (t0) REVERT: E 371 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8281 (m) REVERT: F 278 ASP cc_start: 0.7682 (m-30) cc_final: 0.7333 (m-30) REVERT: F 371 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8165 (m) REVERT: G 269 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8524 (mm-40) REVERT: I 326 TYR cc_start: 0.8220 (m-80) cc_final: 0.7964 (m-80) REVERT: J 297 GLN cc_start: 0.8106 (tt0) cc_final: 0.7808 (tt0) REVERT: J 299 ASP cc_start: 0.8745 (p0) cc_final: 0.8306 (p0) REVERT: K 450 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8172 (tttp) REVERT: L 278 ASP cc_start: 0.7982 (m-30) cc_final: 0.7769 (m-30) REVERT: M 450 LYS cc_start: 0.8595 (ttmt) cc_final: 0.8005 (tttp) REVERT: O 450 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8169 (ttmt) REVERT: P 324 GLU cc_start: 0.8174 (tt0) cc_final: 0.7934 (tm-30) REVERT: Q 450 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8075 (tttp) REVERT: R 324 GLU cc_start: 0.8169 (tt0) cc_final: 0.7699 (tm-30) REVERT: S 324 GLU cc_start: 0.8259 (tt0) cc_final: 0.7958 (tm-30) REVERT: T 324 GLU cc_start: 0.8280 (tt0) cc_final: 0.7869 (tm-30) REVERT: T 438 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8596 (mm-40) REVERT: U 299 ASP cc_start: 0.8335 (p0) cc_final: 0.8058 (p0) REVERT: V 437 ASP cc_start: 0.8389 (t0) cc_final: 0.8090 (t0) REVERT: V 438 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8582 (mm-40) REVERT: W 285 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8377 (mt) REVERT: W 299 ASP cc_start: 0.8579 (p0) cc_final: 0.8308 (p0) REVERT: Y 269 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8521 (mm-40) REVERT: Z 445 ASN cc_start: 0.8375 (m110) cc_final: 0.8016 (m110) outliers start: 131 outliers final: 91 residues processed: 942 average time/residue: 0.2324 time to fit residues: 368.3789 Evaluate side-chains 839 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 745 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 279 SER Chi-restraints excluded: chain 1 residue 284 ILE Chi-restraints excluded: chain 1 residue 390 THR Chi-restraints excluded: chain 2 residue 279 SER Chi-restraints excluded: chain 2 residue 284 ILE Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 279 SER Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 4 residue 390 THR Chi-restraints excluded: chain 4 residue 423 ILE Chi-restraints excluded: chain 5 residue 279 SER Chi-restraints excluded: chain 5 residue 433 THR Chi-restraints excluded: chain 6 residue 279 SER Chi-restraints excluded: chain 6 residue 390 THR Chi-restraints excluded: chain 6 residue 423 ILE Chi-restraints excluded: chain 6 residue 433 THR Chi-restraints excluded: chain 7 residue 279 SER Chi-restraints excluded: chain 7 residue 447 LEU Chi-restraints excluded: chain 8 residue 279 SER Chi-restraints excluded: chain 8 residue 281 LEU Chi-restraints excluded: chain 8 residue 423 ILE Chi-restraints excluded: chain 9 residue 279 SER Chi-restraints excluded: chain 9 residue 390 THR Chi-restraints excluded: chain 9 residue 447 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 371 SER Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 371 SER Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 284 ILE Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 423 ILE Chi-restraints excluded: chain L residue 279 SER Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 390 THR Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 423 ILE Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 447 LEU Chi-restraints excluded: chain Q residue 279 SER Chi-restraints excluded: chain Q residue 296 ILE Chi-restraints excluded: chain Q residue 446 VAL Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 281 LEU Chi-restraints excluded: chain S residue 296 ILE Chi-restraints excluded: chain S residue 423 ILE Chi-restraints excluded: chain S residue 443 LEU Chi-restraints excluded: chain T residue 279 SER Chi-restraints excluded: chain U residue 279 SER Chi-restraints excluded: chain U residue 281 LEU Chi-restraints excluded: chain U residue 371 SER Chi-restraints excluded: chain U residue 423 ILE Chi-restraints excluded: chain V residue 279 SER Chi-restraints excluded: chain V residue 281 LEU Chi-restraints excluded: chain W residue 268 SER Chi-restraints excluded: chain W residue 279 SER Chi-restraints excluded: chain W residue 285 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 390 THR Chi-restraints excluded: chain X residue 397 SER Chi-restraints excluded: chain Y residue 279 SER Chi-restraints excluded: chain Y residue 371 SER Chi-restraints excluded: chain Z residue 279 SER Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 284 ILE Chi-restraints excluded: chain Z residue 390 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 320 optimal weight: 0.8980 chunk 216 optimal weight: 0.9990 chunk 471 optimal weight: 0.3980 chunk 468 optimal weight: 0.9980 chunk 305 optimal weight: 1.9990 chunk 457 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 224 optimal weight: 0.6980 chunk 334 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 291 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 271 GLN L 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100897 restraints weight = 57706.953| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.97 r_work: 0.3182 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 40950 Z= 0.122 Angle : 0.462 6.785 55055 Z= 0.248 Chirality : 0.039 0.125 6300 Planarity : 0.002 0.034 7280 Dihedral : 3.756 13.279 5600 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.62 % Allowed : 26.73 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.12), residues: 4900 helix: 3.22 (0.13), residues: 1435 sheet: 1.30 (0.10), residues: 2240 loop : -2.29 (0.13), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 8 373 TYR 0.012 0.001 TYR F 321 PHE 0.008 0.001 PHE S 436 HIS 0.001 0.000 HIS M 383 Details of bonding type rmsd covalent geometry : bond 0.00282 (40950) covalent geometry : angle 0.46246 (55055) hydrogen bonds : bond 0.05964 ( 2074) hydrogen bonds : angle 4.07245 ( 5910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 814 time to evaluate : 1.609 Fit side-chains REVERT: 1 311 ASP cc_start: 0.8992 (t0) cc_final: 0.8613 (t0) REVERT: 1 400 ILE cc_start: 0.8736 (mt) cc_final: 0.8525 (mp) REVERT: 2 299 ASP cc_start: 0.8576 (p0) cc_final: 0.8326 (p0) REVERT: 2 450 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8198 (tttp) REVERT: 3 385 ARG cc_start: 0.8336 (ttp-110) cc_final: 0.8051 (ttm110) REVERT: 3 386 LYS cc_start: 0.8987 (mmtp) cc_final: 0.8750 (mttm) REVERT: 3 437 ASP cc_start: 0.8550 (t0) cc_final: 0.8301 (t0) REVERT: 5 269 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8349 (mm-40) REVERT: 5 278 ASP cc_start: 0.7895 (m-30) cc_final: 0.7579 (m-30) REVERT: 5 438 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8595 (mm-40) REVERT: 6 297 GLN cc_start: 0.8269 (tt0) cc_final: 0.8060 (tt0) REVERT: 6 447 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8648 (pp) REVERT: 6 450 LYS cc_start: 0.8503 (ttmt) cc_final: 0.7949 (tttp) REVERT: 9 311 ASP cc_start: 0.9079 (t0) cc_final: 0.8845 (t0) REVERT: A 450 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8004 (tttp) REVERT: D 437 ASP cc_start: 0.8544 (t0) cc_final: 0.8272 (t0) REVERT: E 371 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8259 (m) REVERT: E 386 LYS cc_start: 0.8976 (mmtp) cc_final: 0.8667 (mttm) REVERT: F 278 ASP cc_start: 0.7717 (m-30) cc_final: 0.7317 (m-30) REVERT: F 371 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.8141 (m) REVERT: F 447 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8773 (pp) REVERT: G 269 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8571 (mm-40) REVERT: G 447 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8661 (pp) REVERT: I 326 TYR cc_start: 0.8320 (m-80) cc_final: 0.8110 (m-80) REVERT: J 269 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8479 (mm-40) REVERT: J 297 GLN cc_start: 0.8172 (tt0) cc_final: 0.7891 (tt0) REVERT: J 299 ASP cc_start: 0.8758 (p0) cc_final: 0.8355 (p0) REVERT: K 385 ARG cc_start: 0.8311 (ttp-110) cc_final: 0.8052 (ttp-110) REVERT: K 450 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8218 (tttp) REVERT: M 447 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8745 (pp) REVERT: M 450 LYS cc_start: 0.8590 (ttmt) cc_final: 0.7912 (tttp) REVERT: O 298 MET cc_start: 0.8880 (ptp) cc_final: 0.8667 (ptm) REVERT: O 447 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8819 (pp) REVERT: Q 326 TYR cc_start: 0.8132 (m-10) cc_final: 0.7795 (m-10) REVERT: Q 450 LYS cc_start: 0.8707 (ttmt) cc_final: 0.8090 (tttp) REVERT: R 326 TYR cc_start: 0.8082 (m-10) cc_final: 0.7508 (m-10) REVERT: S 324 GLU cc_start: 0.8200 (tt0) cc_final: 0.7973 (tm-30) REVERT: T 324 GLU cc_start: 0.8197 (tt0) cc_final: 0.7834 (tm-30) REVERT: T 438 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8520 (mm-40) REVERT: T 447 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8924 (pp) REVERT: U 377 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8665 (mp) REVERT: U 450 LYS cc_start: 0.8683 (ttpt) cc_final: 0.7993 (tttt) REVERT: V 437 ASP cc_start: 0.8372 (t0) cc_final: 0.8124 (t0) REVERT: W 299 ASP cc_start: 0.8512 (p0) cc_final: 0.8257 (p0) REVERT: X 269 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8109 (mm-40) REVERT: Y 402 ASP cc_start: 0.7830 (p0) cc_final: 0.7330 (t0) REVERT: Z 324 GLU cc_start: 0.8305 (tt0) cc_final: 0.7829 (tm-30) REVERT: Z 445 ASN cc_start: 0.8485 (m110) cc_final: 0.8169 (m110) outliers start: 161 outliers final: 102 residues processed: 957 average time/residue: 0.2327 time to fit residues: 374.0082 Evaluate side-chains 877 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 766 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 279 SER Chi-restraints excluded: chain 1 residue 284 ILE Chi-restraints excluded: chain 1 residue 419 SER Chi-restraints excluded: chain 1 residue 423 ILE Chi-restraints excluded: chain 1 residue 447 LEU Chi-restraints excluded: chain 2 residue 279 SER Chi-restraints excluded: chain 2 residue 284 ILE Chi-restraints excluded: chain 2 residue 397 SER Chi-restraints excluded: chain 2 residue 419 SER Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 4 residue 418 MET Chi-restraints excluded: chain 4 residue 423 ILE Chi-restraints excluded: chain 5 residue 266 GLU Chi-restraints excluded: chain 5 residue 279 SER Chi-restraints excluded: chain 5 residue 433 THR Chi-restraints excluded: chain 6 residue 279 SER Chi-restraints excluded: chain 6 residue 447 LEU Chi-restraints excluded: chain 7 residue 279 SER Chi-restraints excluded: chain 7 residue 296 ILE Chi-restraints excluded: chain 7 residue 377 LEU Chi-restraints excluded: chain 7 residue 447 LEU Chi-restraints excluded: chain 8 residue 279 SER Chi-restraints excluded: chain 8 residue 281 LEU Chi-restraints excluded: chain 8 residue 377 LEU Chi-restraints excluded: chain 8 residue 423 ILE Chi-restraints excluded: chain 8 residue 447 LEU Chi-restraints excluded: chain 9 residue 279 SER Chi-restraints excluded: chain 9 residue 447 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 371 SER Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 371 SER Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 284 ILE Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain L residue 279 SER Chi-restraints excluded: chain L residue 284 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 390 THR Chi-restraints excluded: chain L residue 418 MET Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 296 ILE Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain O residue 296 ILE Chi-restraints excluded: chain O residue 447 LEU Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 447 LEU Chi-restraints excluded: chain Q residue 279 SER Chi-restraints excluded: chain Q residue 296 ILE Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 281 LEU Chi-restraints excluded: chain S residue 296 ILE Chi-restraints excluded: chain S residue 443 LEU Chi-restraints excluded: chain T residue 279 SER Chi-restraints excluded: chain T residue 423 ILE Chi-restraints excluded: chain T residue 447 LEU Chi-restraints excluded: chain U residue 279 SER Chi-restraints excluded: chain U residue 281 LEU Chi-restraints excluded: chain U residue 371 SER Chi-restraints excluded: chain U residue 377 LEU Chi-restraints excluded: chain U residue 397 SER Chi-restraints excluded: chain V residue 279 SER Chi-restraints excluded: chain V residue 281 LEU Chi-restraints excluded: chain V residue 423 ILE Chi-restraints excluded: chain W residue 268 SER Chi-restraints excluded: chain W residue 279 SER Chi-restraints excluded: chain W residue 397 SER Chi-restraints excluded: chain X residue 279 SER Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 390 THR Chi-restraints excluded: chain X residue 397 SER Chi-restraints excluded: chain Y residue 371 SER Chi-restraints excluded: chain Y residue 423 ILE Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 284 ILE Chi-restraints excluded: chain Z residue 390 THR Chi-restraints excluded: chain Z residue 419 SER Chi-restraints excluded: chain Z residue 423 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 13 optimal weight: 4.9990 chunk 133 optimal weight: 0.0070 chunk 466 optimal weight: 1.9990 chunk 412 optimal weight: 0.9980 chunk 326 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 42 optimal weight: 0.0060 chunk 290 optimal weight: 3.9990 chunk 231 optimal weight: 0.2980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102156 restraints weight = 57447.561| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.97 r_work: 0.3213 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 40950 Z= 0.105 Angle : 0.452 7.392 55055 Z= 0.243 Chirality : 0.039 0.124 6300 Planarity : 0.002 0.027 7280 Dihedral : 3.607 11.787 5600 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.35 % Allowed : 27.87 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.12), residues: 4900 helix: 3.26 (0.13), residues: 1435 sheet: 1.43 (0.11), residues: 2240 loop : -2.20 (0.13), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 309 TYR 0.013 0.001 TYR H 321 PHE 0.008 0.001 PHE 1 436 HIS 0.001 0.000 HIS U 383 Details of bonding type rmsd covalent geometry : bond 0.00228 (40950) covalent geometry : angle 0.45172 (55055) hydrogen bonds : bond 0.05134 ( 2074) hydrogen bonds : angle 3.95689 ( 5910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 803 time to evaluate : 1.743 Fit side-chains REVERT: 1 311 ASP cc_start: 0.8935 (t0) cc_final: 0.8482 (t0) REVERT: 2 450 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8161 (tttp) REVERT: 3 386 LYS cc_start: 0.8992 (mmtp) cc_final: 0.8737 (mttm) REVERT: 3 437 ASP cc_start: 0.8491 (t0) cc_final: 0.8252 (t0) REVERT: 4 447 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8635 (pp) REVERT: 5 278 ASP cc_start: 0.7790 (m-30) cc_final: 0.7470 (m-30) REVERT: 6 297 GLN cc_start: 0.8161 (tt0) cc_final: 0.7920 (tt0) REVERT: 6 447 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8697 (pp) REVERT: 6 450 LYS cc_start: 0.8515 (ttmt) cc_final: 0.7963 (tttp) REVERT: 9 311 ASP cc_start: 0.9023 (t0) cc_final: 0.8774 (t0) REVERT: C 278 ASP cc_start: 0.7889 (m-30) cc_final: 0.7557 (t0) REVERT: C 326 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7428 (t80) REVERT: D 437 ASP cc_start: 0.8525 (t0) cc_final: 0.8289 (t0) REVERT: E 371 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.8233 (m) REVERT: E 386 LYS cc_start: 0.8974 (mmtp) cc_final: 0.8662 (mttm) REVERT: F 278 ASP cc_start: 0.7643 (m-30) cc_final: 0.7233 (m-30) REVERT: H 311 ASP cc_start: 0.8996 (t0) cc_final: 0.8695 (t0) REVERT: J 269 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8361 (mm-40) REVERT: J 297 GLN cc_start: 0.8108 (tt0) cc_final: 0.7820 (tt0) REVERT: J 299 ASP cc_start: 0.8692 (p0) cc_final: 0.8320 (p0) REVERT: K 450 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8239 (tttp) REVERT: L 278 ASP cc_start: 0.7981 (m-30) cc_final: 0.7681 (t0) REVERT: L 290 TYR cc_start: 0.8859 (p90) cc_final: 0.8581 (p90) REVERT: L 447 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8918 (pp) REVERT: M 269 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8283 (mm-40) REVERT: M 450 LYS cc_start: 0.8575 (ttmt) cc_final: 0.7939 (tttp) REVERT: N 447 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8844 (pp) REVERT: O 447 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8819 (pp) REVERT: Q 326 TYR cc_start: 0.7980 (m-10) cc_final: 0.7557 (m-10) REVERT: Q 450 LYS cc_start: 0.8742 (ttmt) cc_final: 0.8140 (tttp) REVERT: T 311 ASP cc_start: 0.8960 (t0) cc_final: 0.8577 (t0) REVERT: T 324 GLU cc_start: 0.8189 (tt0) cc_final: 0.7907 (tm-30) REVERT: T 438 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8489 (mm-40) REVERT: U 377 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8617 (mp) REVERT: U 447 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8833 (pp) REVERT: U 450 LYS cc_start: 0.8672 (ttpt) cc_final: 0.7993 (tttt) REVERT: V 377 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8423 (mp) REVERT: V 437 ASP cc_start: 0.8444 (t0) cc_final: 0.8177 (t0) REVERT: W 299 ASP cc_start: 0.8432 (p0) cc_final: 0.8179 (p0) REVERT: X 269 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8135 (mm-40) REVERT: Y 269 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8577 (mm-40) REVERT: Y 402 ASP cc_start: 0.7422 (p0) cc_final: 0.7066 (t0) REVERT: Z 324 GLU cc_start: 0.8288 (tt0) cc_final: 0.7805 (tm-30) REVERT: Z 445 ASN cc_start: 0.8544 (m110) cc_final: 0.8145 (m110) outliers start: 149 outliers final: 100 residues processed: 925 average time/residue: 0.2306 time to fit residues: 361.6985 Evaluate side-chains 879 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 769 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 277 ILE Chi-restraints excluded: chain 1 residue 279 SER Chi-restraints excluded: chain 1 residue 280 VAL Chi-restraints excluded: chain 1 residue 284 ILE Chi-restraints excluded: chain 1 residue 296 ILE Chi-restraints excluded: chain 1 residue 419 SER Chi-restraints excluded: chain 1 residue 447 LEU Chi-restraints excluded: chain 2 residue 279 SER Chi-restraints excluded: chain 2 residue 284 ILE Chi-restraints excluded: chain 2 residue 397 SER Chi-restraints excluded: chain 2 residue 419 SER Chi-restraints excluded: chain 3 residue 279 SER Chi-restraints excluded: chain 3 residue 280 VAL Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 4 residue 418 MET Chi-restraints excluded: chain 4 residue 423 ILE Chi-restraints excluded: chain 4 residue 447 LEU Chi-restraints excluded: chain 5 residue 266 GLU Chi-restraints excluded: chain 5 residue 279 SER Chi-restraints excluded: chain 6 residue 279 SER Chi-restraints excluded: chain 6 residue 377 LEU Chi-restraints excluded: chain 6 residue 418 MET Chi-restraints excluded: chain 6 residue 429 VAL Chi-restraints excluded: chain 6 residue 447 LEU Chi-restraints excluded: chain 7 residue 280 VAL Chi-restraints excluded: chain 7 residue 296 ILE Chi-restraints excluded: chain 7 residue 377 LEU Chi-restraints excluded: chain 7 residue 447 LEU Chi-restraints excluded: chain 8 residue 279 SER Chi-restraints excluded: chain 8 residue 281 LEU Chi-restraints excluded: chain 8 residue 447 LEU Chi-restraints excluded: chain 9 residue 279 SER Chi-restraints excluded: chain 9 residue 447 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 326 TYR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 296 ILE Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 418 MET Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain J residue 419 SER Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 423 ILE Chi-restraints excluded: chain L residue 279 SER Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 296 ILE Chi-restraints excluded: chain M residue 418 MET Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 423 ILE Chi-restraints excluded: chain N residue 447 LEU Chi-restraints excluded: chain O residue 296 ILE Chi-restraints excluded: chain O residue 447 LEU Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 447 LEU Chi-restraints excluded: chain Q residue 279 SER Chi-restraints excluded: chain Q residue 284 ILE Chi-restraints excluded: chain Q residue 296 ILE Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 281 LEU Chi-restraints excluded: chain S residue 296 ILE Chi-restraints excluded: chain S residue 423 ILE Chi-restraints excluded: chain S residue 443 LEU Chi-restraints excluded: chain T residue 279 SER Chi-restraints excluded: chain T residue 296 ILE Chi-restraints excluded: chain U residue 279 SER Chi-restraints excluded: chain U residue 281 LEU Chi-restraints excluded: chain U residue 377 LEU Chi-restraints excluded: chain U residue 397 SER Chi-restraints excluded: chain U residue 443 LEU Chi-restraints excluded: chain U residue 447 LEU Chi-restraints excluded: chain V residue 279 SER Chi-restraints excluded: chain V residue 281 LEU Chi-restraints excluded: chain V residue 377 LEU Chi-restraints excluded: chain V residue 423 ILE Chi-restraints excluded: chain W residue 268 SER Chi-restraints excluded: chain W residue 397 SER Chi-restraints excluded: chain W residue 423 ILE Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 397 SER Chi-restraints excluded: chain Y residue 279 SER Chi-restraints excluded: chain Y residue 423 ILE Chi-restraints excluded: chain Z residue 279 SER Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 284 ILE Chi-restraints excluded: chain Z residue 296 ILE Chi-restraints excluded: chain Z residue 419 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 481 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 374 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 263 GLN H 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.096648 restraints weight = 58384.875| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.04 r_work: 0.3124 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 40950 Z= 0.163 Angle : 0.504 6.534 55055 Z= 0.271 Chirality : 0.041 0.127 6300 Planarity : 0.003 0.023 7280 Dihedral : 3.988 15.350 5600 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 4.48 % Allowed : 26.77 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.12), residues: 4900 helix: 3.12 (0.13), residues: 1435 sheet: 1.22 (0.11), residues: 2240 loop : -2.45 (0.13), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 8 373 TYR 0.010 0.001 TYR O 290 PHE 0.010 0.001 PHE J 436 HIS 0.001 0.000 HIS U 383 Details of bonding type rmsd covalent geometry : bond 0.00398 (40950) covalent geometry : angle 0.50367 (55055) hydrogen bonds : bond 0.06918 ( 2074) hydrogen bonds : angle 4.13774 ( 5910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 793 time to evaluate : 1.798 Fit side-chains REVERT: 1 311 ASP cc_start: 0.9066 (t0) cc_final: 0.8692 (t0) REVERT: 2 450 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8171 (tttp) REVERT: 3 385 ARG cc_start: 0.8283 (ttp-110) cc_final: 0.7912 (ttm110) REVERT: 3 437 ASP cc_start: 0.8535 (t0) cc_final: 0.8172 (t0) REVERT: 4 447 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8630 (pp) REVERT: 5 278 ASP cc_start: 0.7941 (m-30) cc_final: 0.7620 (m-30) REVERT: 5 438 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8643 (mm-40) REVERT: 6 297 GLN cc_start: 0.8271 (tt0) cc_final: 0.8058 (tt0) REVERT: 6 419 SER cc_start: 0.7788 (p) cc_final: 0.7568 (t) REVERT: 6 447 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8643 (pp) REVERT: 6 450 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8123 (tttp) REVERT: 9 311 ASP cc_start: 0.9106 (t0) cc_final: 0.8724 (t0) REVERT: B 324 GLU cc_start: 0.8193 (tt0) cc_final: 0.7785 (tm-30) REVERT: D 437 ASP cc_start: 0.8586 (t0) cc_final: 0.8348 (t0) REVERT: E 386 LYS cc_start: 0.8977 (mmtp) cc_final: 0.8689 (mttm) REVERT: F 278 ASP cc_start: 0.7809 (m-30) cc_final: 0.7418 (m-30) REVERT: F 447 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8693 (pp) REVERT: G 447 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8650 (pp) REVERT: I 326 TYR cc_start: 0.8398 (m-80) cc_final: 0.8131 (m-80) REVERT: J 297 GLN cc_start: 0.8247 (tt0) cc_final: 0.7934 (tt0) REVERT: J 299 ASP cc_start: 0.8823 (p0) cc_final: 0.8407 (p0) REVERT: K 450 LYS cc_start: 0.8646 (ttmt) cc_final: 0.8188 (tttp) REVERT: L 324 GLU cc_start: 0.8283 (tt0) cc_final: 0.7954 (tm-30) REVERT: L 386 LYS cc_start: 0.9005 (mmtp) cc_final: 0.8770 (mttm) REVERT: L 447 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8882 (pp) REVERT: M 269 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8384 (mm-40) REVERT: M 447 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8760 (pp) REVERT: M 450 LYS cc_start: 0.8637 (ttmt) cc_final: 0.7999 (tttp) REVERT: N 324 GLU cc_start: 0.8190 (tt0) cc_final: 0.7865 (tm-30) REVERT: N 447 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8824 (pp) REVERT: O 269 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8433 (mm-40) REVERT: O 298 MET cc_start: 0.8877 (ptp) cc_final: 0.8648 (ptm) REVERT: O 447 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8837 (pp) REVERT: P 430 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8409 (mp) REVERT: Q 450 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8104 (tttp) REVERT: S 266 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: T 324 GLU cc_start: 0.8260 (tt0) cc_final: 0.7805 (tm-30) REVERT: T 438 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8562 (mm-40) REVERT: T 447 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8915 (pp) REVERT: U 377 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8651 (mp) REVERT: U 450 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8099 (tttt) REVERT: V 377 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8427 (mp) REVERT: V 437 ASP cc_start: 0.8584 (t0) cc_final: 0.8301 (t0) REVERT: W 299 ASP cc_start: 0.8497 (p0) cc_final: 0.8256 (p0) REVERT: X 447 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8572 (pp) REVERT: Y 269 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8485 (mm-40) REVERT: Z 324 GLU cc_start: 0.8328 (tt0) cc_final: 0.7792 (tm-30) outliers start: 199 outliers final: 149 residues processed: 962 average time/residue: 0.2354 time to fit residues: 379.5022 Evaluate side-chains 923 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 760 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 279 SER Chi-restraints excluded: chain 1 residue 280 VAL Chi-restraints excluded: chain 1 residue 284 ILE Chi-restraints excluded: chain 1 residue 296 ILE Chi-restraints excluded: chain 1 residue 419 SER Chi-restraints excluded: chain 1 residue 447 LEU Chi-restraints excluded: chain 2 residue 279 SER Chi-restraints excluded: chain 2 residue 284 ILE Chi-restraints excluded: chain 2 residue 377 LEU Chi-restraints excluded: chain 2 residue 397 SER Chi-restraints excluded: chain 2 residue 419 SER Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 279 SER Chi-restraints excluded: chain 3 residue 280 VAL Chi-restraints excluded: chain 4 residue 278 ASP Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 4 residue 280 VAL Chi-restraints excluded: chain 4 residue 418 MET Chi-restraints excluded: chain 4 residue 419 SER Chi-restraints excluded: chain 4 residue 423 ILE Chi-restraints excluded: chain 4 residue 447 LEU Chi-restraints excluded: chain 5 residue 279 SER Chi-restraints excluded: chain 5 residue 280 VAL Chi-restraints excluded: chain 5 residue 433 THR Chi-restraints excluded: chain 5 residue 447 LEU Chi-restraints excluded: chain 6 residue 279 SER Chi-restraints excluded: chain 6 residue 377 LEU Chi-restraints excluded: chain 6 residue 390 THR Chi-restraints excluded: chain 6 residue 418 MET Chi-restraints excluded: chain 6 residue 423 ILE Chi-restraints excluded: chain 6 residue 429 VAL Chi-restraints excluded: chain 6 residue 433 THR Chi-restraints excluded: chain 6 residue 447 LEU Chi-restraints excluded: chain 7 residue 279 SER Chi-restraints excluded: chain 7 residue 280 VAL Chi-restraints excluded: chain 7 residue 284 ILE Chi-restraints excluded: chain 7 residue 296 ILE Chi-restraints excluded: chain 7 residue 377 LEU Chi-restraints excluded: chain 7 residue 418 MET Chi-restraints excluded: chain 7 residue 447 LEU Chi-restraints excluded: chain 8 residue 279 SER Chi-restraints excluded: chain 8 residue 281 LEU Chi-restraints excluded: chain 8 residue 423 ILE Chi-restraints excluded: chain 8 residue 447 LEU Chi-restraints excluded: chain 9 residue 279 SER Chi-restraints excluded: chain 9 residue 284 ILE Chi-restraints excluded: chain 9 residue 447 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 296 ILE Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 418 MET Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 284 ILE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 419 SER Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 377 LEU Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 423 ILE Chi-restraints excluded: chain L residue 279 SER Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 418 MET Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 280 VAL Chi-restraints excluded: chain M residue 418 MET Chi-restraints excluded: chain M residue 423 ILE Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 423 ILE Chi-restraints excluded: chain N residue 447 LEU Chi-restraints excluded: chain O residue 284 ILE Chi-restraints excluded: chain O residue 296 ILE Chi-restraints excluded: chain O residue 447 LEU Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 397 SER Chi-restraints excluded: chain P residue 430 LEU Chi-restraints excluded: chain Q residue 279 SER Chi-restraints excluded: chain Q residue 284 ILE Chi-restraints excluded: chain Q residue 296 ILE Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 281 LEU Chi-restraints excluded: chain S residue 284 ILE Chi-restraints excluded: chain S residue 296 ILE Chi-restraints excluded: chain S residue 418 MET Chi-restraints excluded: chain S residue 423 ILE Chi-restraints excluded: chain S residue 443 LEU Chi-restraints excluded: chain T residue 268 SER Chi-restraints excluded: chain T residue 279 SER Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 296 ILE Chi-restraints excluded: chain T residue 371 SER Chi-restraints excluded: chain T residue 377 LEU Chi-restraints excluded: chain T residue 423 ILE Chi-restraints excluded: chain T residue 447 LEU Chi-restraints excluded: chain U residue 279 SER Chi-restraints excluded: chain U residue 377 LEU Chi-restraints excluded: chain U residue 397 SER Chi-restraints excluded: chain U residue 423 ILE Chi-restraints excluded: chain V residue 279 SER Chi-restraints excluded: chain V residue 281 LEU Chi-restraints excluded: chain V residue 377 LEU Chi-restraints excluded: chain V residue 423 ILE Chi-restraints excluded: chain W residue 266 GLU Chi-restraints excluded: chain W residue 268 SER Chi-restraints excluded: chain W residue 279 SER Chi-restraints excluded: chain W residue 397 SER Chi-restraints excluded: chain W residue 423 ILE Chi-restraints excluded: chain X residue 279 SER Chi-restraints excluded: chain X residue 295 ASP Chi-restraints excluded: chain X residue 390 THR Chi-restraints excluded: chain X residue 397 SER Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain Y residue 279 SER Chi-restraints excluded: chain Y residue 284 ILE Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Y residue 447 LEU Chi-restraints excluded: chain Z residue 279 SER Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 284 ILE Chi-restraints excluded: chain Z residue 296 ILE Chi-restraints excluded: chain Z residue 419 SER Chi-restraints excluded: chain Z residue 423 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 32 optimal weight: 2.9990 chunk 469 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 426 optimal weight: 0.9990 chunk 289 optimal weight: 2.9990 chunk 325 optimal weight: 1.9990 chunk 250 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 163 optimal weight: 0.0980 chunk 68 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.113520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.098552 restraints weight = 57722.131| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.97 r_work: 0.3167 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40950 Z= 0.115 Angle : 0.474 7.886 55055 Z= 0.254 Chirality : 0.039 0.125 6300 Planarity : 0.002 0.033 7280 Dihedral : 3.747 13.307 5600 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 4.03 % Allowed : 27.38 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.12), residues: 4900 helix: 3.25 (0.13), residues: 1435 sheet: 1.33 (0.11), residues: 2240 loop : -2.38 (0.13), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 385 TYR 0.011 0.001 TYR H 321 PHE 0.009 0.001 PHE Y 436 HIS 0.001 0.000 HIS U 383 Details of bonding type rmsd covalent geometry : bond 0.00261 (40950) covalent geometry : angle 0.47419 (55055) hydrogen bonds : bond 0.05485 ( 2074) hydrogen bonds : angle 3.99782 ( 5910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 803 time to evaluate : 1.761 Fit side-chains REVERT: 1 311 ASP cc_start: 0.9049 (t0) cc_final: 0.8665 (t0) REVERT: 2 450 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8140 (tttp) REVERT: 3 385 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.8003 (ttm110) REVERT: 3 437 ASP cc_start: 0.8550 (t0) cc_final: 0.8197 (t0) REVERT: 4 447 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8642 (pp) REVERT: 5 278 ASP cc_start: 0.7815 (m-30) cc_final: 0.7483 (m-30) REVERT: 5 438 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8619 (mm-40) REVERT: 6 297 GLN cc_start: 0.8158 (tt0) cc_final: 0.7916 (tt0) REVERT: 6 447 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8674 (pp) REVERT: 6 450 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8110 (tttp) REVERT: 9 311 ASP cc_start: 0.9054 (t0) cc_final: 0.8811 (t0) REVERT: B 324 GLU cc_start: 0.8062 (tt0) cc_final: 0.7679 (tm-30) REVERT: C 278 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7629 (t0) REVERT: D 437 ASP cc_start: 0.8598 (t0) cc_final: 0.8372 (t0) REVERT: E 371 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8178 (m) REVERT: E 386 LYS cc_start: 0.8973 (mmtp) cc_final: 0.8717 (mttm) REVERT: F 278 ASP cc_start: 0.7716 (m-30) cc_final: 0.7328 (m-30) REVERT: F 447 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8760 (pp) REVERT: G 447 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8647 (pp) REVERT: I 326 TYR cc_start: 0.8297 (m-80) cc_final: 0.8054 (m-80) REVERT: J 269 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8397 (mm-40) REVERT: J 297 GLN cc_start: 0.8162 (tt0) cc_final: 0.7866 (tt0) REVERT: J 299 ASP cc_start: 0.8725 (p0) cc_final: 0.8346 (p0) REVERT: K 450 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8217 (tttp) REVERT: L 386 LYS cc_start: 0.8989 (mmtp) cc_final: 0.8758 (mttm) REVERT: L 447 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8908 (pp) REVERT: M 269 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8297 (mm-40) REVERT: M 447 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8704 (pp) REVERT: M 450 LYS cc_start: 0.8607 (ttmt) cc_final: 0.7981 (tttp) REVERT: N 324 GLU cc_start: 0.8185 (tt0) cc_final: 0.7873 (tm-30) REVERT: N 447 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8805 (pp) REVERT: O 269 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8213 (mm-40) REVERT: O 447 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8808 (pp) REVERT: P 430 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8339 (mp) REVERT: Q 450 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8133 (tttp) REVERT: T 324 GLU cc_start: 0.8181 (tt0) cc_final: 0.7831 (tm-30) REVERT: T 438 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8523 (mm-40) REVERT: T 447 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8883 (pp) REVERT: U 377 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8579 (mp) REVERT: U 450 LYS cc_start: 0.8717 (ttpt) cc_final: 0.8058 (tttt) REVERT: V 377 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8226 (mp) REVERT: V 437 ASP cc_start: 0.8594 (t0) cc_final: 0.8328 (t0) REVERT: X 269 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8156 (mm-40) REVERT: X 447 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8549 (pp) REVERT: Y 269 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8546 (mm-40) REVERT: Z 324 GLU cc_start: 0.8281 (tt0) cc_final: 0.7887 (tm-30) outliers start: 179 outliers final: 137 residues processed: 951 average time/residue: 0.2360 time to fit residues: 380.3492 Evaluate side-chains 922 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 770 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 279 SER Chi-restraints excluded: chain 1 residue 280 VAL Chi-restraints excluded: chain 1 residue 284 ILE Chi-restraints excluded: chain 1 residue 296 ILE Chi-restraints excluded: chain 1 residue 390 THR Chi-restraints excluded: chain 1 residue 419 SER Chi-restraints excluded: chain 1 residue 447 LEU Chi-restraints excluded: chain 2 residue 279 SER Chi-restraints excluded: chain 2 residue 284 ILE Chi-restraints excluded: chain 2 residue 397 SER Chi-restraints excluded: chain 2 residue 419 SER Chi-restraints excluded: chain 3 residue 279 SER Chi-restraints excluded: chain 3 residue 280 VAL Chi-restraints excluded: chain 4 residue 278 ASP Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 4 residue 280 VAL Chi-restraints excluded: chain 4 residue 418 MET Chi-restraints excluded: chain 4 residue 419 SER Chi-restraints excluded: chain 4 residue 423 ILE Chi-restraints excluded: chain 4 residue 447 LEU Chi-restraints excluded: chain 5 residue 266 GLU Chi-restraints excluded: chain 5 residue 279 SER Chi-restraints excluded: chain 5 residue 280 VAL Chi-restraints excluded: chain 5 residue 418 MET Chi-restraints excluded: chain 5 residue 447 LEU Chi-restraints excluded: chain 6 residue 279 SER Chi-restraints excluded: chain 6 residue 377 LEU Chi-restraints excluded: chain 6 residue 418 MET Chi-restraints excluded: chain 6 residue 423 ILE Chi-restraints excluded: chain 6 residue 429 VAL Chi-restraints excluded: chain 6 residue 447 LEU Chi-restraints excluded: chain 7 residue 279 SER Chi-restraints excluded: chain 7 residue 280 VAL Chi-restraints excluded: chain 7 residue 296 ILE Chi-restraints excluded: chain 7 residue 377 LEU Chi-restraints excluded: chain 7 residue 418 MET Chi-restraints excluded: chain 7 residue 447 LEU Chi-restraints excluded: chain 8 residue 279 SER Chi-restraints excluded: chain 8 residue 281 LEU Chi-restraints excluded: chain 8 residue 447 LEU Chi-restraints excluded: chain 9 residue 279 SER Chi-restraints excluded: chain 9 residue 284 ILE Chi-restraints excluded: chain 9 residue 447 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 296 ILE Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 418 MET Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 284 ILE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 419 SER Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 397 SER Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 423 ILE Chi-restraints excluded: chain L residue 279 SER Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 418 MET Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 418 MET Chi-restraints excluded: chain M residue 423 ILE Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 423 ILE Chi-restraints excluded: chain N residue 447 LEU Chi-restraints excluded: chain O residue 280 VAL Chi-restraints excluded: chain O residue 296 ILE Chi-restraints excluded: chain O residue 447 LEU Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 397 SER Chi-restraints excluded: chain P residue 430 LEU Chi-restraints excluded: chain Q residue 279 SER Chi-restraints excluded: chain Q residue 284 ILE Chi-restraints excluded: chain Q residue 296 ILE Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 281 LEU Chi-restraints excluded: chain S residue 284 ILE Chi-restraints excluded: chain S residue 296 ILE Chi-restraints excluded: chain S residue 418 MET Chi-restraints excluded: chain S residue 423 ILE Chi-restraints excluded: chain S residue 443 LEU Chi-restraints excluded: chain T residue 279 SER Chi-restraints excluded: chain T residue 296 ILE Chi-restraints excluded: chain T residue 377 LEU Chi-restraints excluded: chain T residue 447 LEU Chi-restraints excluded: chain U residue 279 SER Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 281 LEU Chi-restraints excluded: chain U residue 377 LEU Chi-restraints excluded: chain U residue 397 SER Chi-restraints excluded: chain V residue 279 SER Chi-restraints excluded: chain V residue 281 LEU Chi-restraints excluded: chain V residue 377 LEU Chi-restraints excluded: chain V residue 423 ILE Chi-restraints excluded: chain W residue 268 SER Chi-restraints excluded: chain W residue 279 SER Chi-restraints excluded: chain W residue 397 SER Chi-restraints excluded: chain W residue 423 ILE Chi-restraints excluded: chain X residue 279 SER Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 390 THR Chi-restraints excluded: chain X residue 397 SER Chi-restraints excluded: chain X residue 423 ILE Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain Y residue 279 SER Chi-restraints excluded: chain Y residue 419 SER Chi-restraints excluded: chain Y residue 447 LEU Chi-restraints excluded: chain Z residue 279 SER Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 284 ILE Chi-restraints excluded: chain Z residue 296 ILE Chi-restraints excluded: chain Z residue 419 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 20 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 321 optimal weight: 0.9980 chunk 281 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.098189 restraints weight = 57468.638| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.96 r_work: 0.3165 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 40950 Z= 0.119 Angle : 0.477 6.313 55055 Z= 0.256 Chirality : 0.039 0.125 6300 Planarity : 0.002 0.026 7280 Dihedral : 3.741 13.546 5600 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.94 % Allowed : 27.85 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.12), residues: 4900 helix: 3.27 (0.13), residues: 1435 sheet: 1.36 (0.11), residues: 2240 loop : -2.38 (0.13), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 8 373 TYR 0.009 0.001 TYR H 321 PHE 0.008 0.001 PHE Y 436 HIS 0.001 0.000 HIS U 383 Details of bonding type rmsd covalent geometry : bond 0.00275 (40950) covalent geometry : angle 0.47696 (55055) hydrogen bonds : bond 0.05586 ( 2074) hydrogen bonds : angle 3.98727 ( 5910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 782 time to evaluate : 1.757 Fit side-chains REVERT: 1 311 ASP cc_start: 0.9034 (t0) cc_final: 0.8648 (t0) REVERT: 2 450 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8174 (tttp) REVERT: 3 385 ARG cc_start: 0.8308 (ttp-110) cc_final: 0.8017 (ttm110) REVERT: 3 437 ASP cc_start: 0.8566 (t0) cc_final: 0.8218 (t0) REVERT: 4 447 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8627 (pp) REVERT: 5 278 ASP cc_start: 0.7824 (m-30) cc_final: 0.7516 (m-30) REVERT: 6 297 GLN cc_start: 0.8178 (tt0) cc_final: 0.7949 (tt0) REVERT: 6 447 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8677 (pp) REVERT: 6 450 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8141 (tttp) REVERT: 7 438 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8626 (mm-40) REVERT: 9 311 ASP cc_start: 0.9051 (t0) cc_final: 0.8787 (t0) REVERT: D 437 ASP cc_start: 0.8610 (t0) cc_final: 0.8385 (t0) REVERT: E 371 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.8196 (m) REVERT: E 386 LYS cc_start: 0.8982 (mmtp) cc_final: 0.8731 (mttm) REVERT: F 278 ASP cc_start: 0.7782 (m-30) cc_final: 0.7380 (m-30) REVERT: F 447 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8764 (pp) REVERT: G 447 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8666 (pp) REVERT: J 269 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8380 (mm-40) REVERT: J 297 GLN cc_start: 0.8182 (tt0) cc_final: 0.7887 (tt0) REVERT: J 299 ASP cc_start: 0.8760 (p0) cc_final: 0.8374 (p0) REVERT: K 450 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8217 (tttp) REVERT: L 386 LYS cc_start: 0.8995 (mmtp) cc_final: 0.8769 (mttm) REVERT: L 447 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8882 (pp) REVERT: M 447 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8745 (pp) REVERT: M 450 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8006 (tttp) REVERT: N 324 GLU cc_start: 0.8174 (tt0) cc_final: 0.7905 (tm-30) REVERT: N 447 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8829 (pp) REVERT: O 269 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8289 (mm-40) REVERT: O 447 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8832 (pp) REVERT: P 430 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8373 (mp) REVERT: Q 450 LYS cc_start: 0.8765 (ttmt) cc_final: 0.8200 (tttp) REVERT: T 324 GLU cc_start: 0.8194 (tt0) cc_final: 0.7869 (tm-30) REVERT: T 438 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8574 (mm-40) REVERT: T 447 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8887 (pp) REVERT: U 377 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8623 (mp) REVERT: U 450 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8078 (tttt) REVERT: V 377 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8241 (mp) REVERT: V 437 ASP cc_start: 0.8603 (t0) cc_final: 0.8356 (t0) REVERT: X 269 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8153 (mm-40) REVERT: X 447 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8557 (pp) REVERT: Y 269 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8542 (mm-40) REVERT: Z 324 GLU cc_start: 0.8302 (tt0) cc_final: 0.7894 (tm-30) outliers start: 175 outliers final: 153 residues processed: 923 average time/residue: 0.2346 time to fit residues: 367.4408 Evaluate side-chains 934 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 767 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 279 SER Chi-restraints excluded: chain 1 residue 280 VAL Chi-restraints excluded: chain 1 residue 284 ILE Chi-restraints excluded: chain 1 residue 296 ILE Chi-restraints excluded: chain 1 residue 419 SER Chi-restraints excluded: chain 1 residue 447 LEU Chi-restraints excluded: chain 2 residue 279 SER Chi-restraints excluded: chain 2 residue 284 ILE Chi-restraints excluded: chain 2 residue 397 SER Chi-restraints excluded: chain 2 residue 419 SER Chi-restraints excluded: chain 3 residue 279 SER Chi-restraints excluded: chain 3 residue 280 VAL Chi-restraints excluded: chain 4 residue 278 ASP Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 4 residue 280 VAL Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 418 MET Chi-restraints excluded: chain 4 residue 419 SER Chi-restraints excluded: chain 4 residue 423 ILE Chi-restraints excluded: chain 4 residue 447 LEU Chi-restraints excluded: chain 5 residue 266 GLU Chi-restraints excluded: chain 5 residue 279 SER Chi-restraints excluded: chain 5 residue 280 VAL Chi-restraints excluded: chain 5 residue 298 MET Chi-restraints excluded: chain 5 residue 418 MET Chi-restraints excluded: chain 5 residue 433 THR Chi-restraints excluded: chain 5 residue 447 LEU Chi-restraints excluded: chain 6 residue 279 SER Chi-restraints excluded: chain 6 residue 377 LEU Chi-restraints excluded: chain 6 residue 418 MET Chi-restraints excluded: chain 6 residue 423 ILE Chi-restraints excluded: chain 6 residue 429 VAL Chi-restraints excluded: chain 6 residue 447 LEU Chi-restraints excluded: chain 7 residue 279 SER Chi-restraints excluded: chain 7 residue 280 VAL Chi-restraints excluded: chain 7 residue 296 ILE Chi-restraints excluded: chain 7 residue 377 LEU Chi-restraints excluded: chain 7 residue 418 MET Chi-restraints excluded: chain 7 residue 447 LEU Chi-restraints excluded: chain 8 residue 279 SER Chi-restraints excluded: chain 8 residue 281 LEU Chi-restraints excluded: chain 8 residue 423 ILE Chi-restraints excluded: chain 8 residue 447 LEU Chi-restraints excluded: chain 9 residue 279 SER Chi-restraints excluded: chain 9 residue 284 ILE Chi-restraints excluded: chain 9 residue 447 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 296 ILE Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 418 MET Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 284 ILE Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 419 SER Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 423 ILE Chi-restraints excluded: chain L residue 279 SER Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 284 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 418 MET Chi-restraints excluded: chain L residue 443 LEU Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 280 VAL Chi-restraints excluded: chain M residue 296 ILE Chi-restraints excluded: chain M residue 418 MET Chi-restraints excluded: chain M residue 423 ILE Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 423 ILE Chi-restraints excluded: chain N residue 447 LEU Chi-restraints excluded: chain O residue 280 VAL Chi-restraints excluded: chain O residue 284 ILE Chi-restraints excluded: chain O residue 296 ILE Chi-restraints excluded: chain O residue 447 LEU Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 430 LEU Chi-restraints excluded: chain Q residue 279 SER Chi-restraints excluded: chain Q residue 284 ILE Chi-restraints excluded: chain Q residue 296 ILE Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 280 VAL Chi-restraints excluded: chain S residue 281 LEU Chi-restraints excluded: chain S residue 284 ILE Chi-restraints excluded: chain S residue 296 ILE Chi-restraints excluded: chain S residue 418 MET Chi-restraints excluded: chain S residue 423 ILE Chi-restraints excluded: chain S residue 443 LEU Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 447 LEU Chi-restraints excluded: chain T residue 279 SER Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 377 LEU Chi-restraints excluded: chain T residue 447 LEU Chi-restraints excluded: chain U residue 279 SER Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 281 LEU Chi-restraints excluded: chain U residue 377 LEU Chi-restraints excluded: chain U residue 397 SER Chi-restraints excluded: chain V residue 279 SER Chi-restraints excluded: chain V residue 280 VAL Chi-restraints excluded: chain V residue 281 LEU Chi-restraints excluded: chain V residue 377 LEU Chi-restraints excluded: chain V residue 423 ILE Chi-restraints excluded: chain W residue 268 SER Chi-restraints excluded: chain W residue 279 SER Chi-restraints excluded: chain W residue 397 SER Chi-restraints excluded: chain W residue 423 ILE Chi-restraints excluded: chain X residue 279 SER Chi-restraints excluded: chain X residue 390 THR Chi-restraints excluded: chain X residue 397 SER Chi-restraints excluded: chain X residue 423 ILE Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain Y residue 279 SER Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Y residue 419 SER Chi-restraints excluded: chain Y residue 447 LEU Chi-restraints excluded: chain Z residue 279 SER Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 284 ILE Chi-restraints excluded: chain Z residue 296 ILE Chi-restraints excluded: chain Z residue 419 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 478 optimal weight: 0.9980 chunk 340 optimal weight: 1.9990 chunk 316 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 441 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 379 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 362 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 322 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095968 restraints weight = 58179.821| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.03 r_work: 0.3126 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 40950 Z= 0.159 Angle : 0.517 8.624 55055 Z= 0.277 Chirality : 0.040 0.128 6300 Planarity : 0.003 0.028 7280 Dihedral : 3.986 15.620 5600 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 4.27 % Allowed : 27.58 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.12), residues: 4900 helix: 3.16 (0.13), residues: 1435 sheet: 1.22 (0.11), residues: 2240 loop : -2.53 (0.12), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 385 TYR 0.013 0.001 TYR O 290 PHE 0.009 0.001 PHE J 436 HIS 0.001 0.000 HIS M 383 Details of bonding type rmsd covalent geometry : bond 0.00389 (40950) covalent geometry : angle 0.51679 (55055) hydrogen bonds : bond 0.06716 ( 2074) hydrogen bonds : angle 4.10195 ( 5910) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 753 time to evaluate : 1.740 Fit side-chains REVERT: 1 311 ASP cc_start: 0.9092 (t0) cc_final: 0.8739 (t0) REVERT: 1 438 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8537 (mm-40) REVERT: 2 450 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8126 (tttp) REVERT: 3 385 ARG cc_start: 0.8275 (ttp-110) cc_final: 0.7915 (ttm110) REVERT: 3 437 ASP cc_start: 0.8569 (t0) cc_final: 0.8180 (t0) REVERT: 4 447 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8652 (pp) REVERT: 5 278 ASP cc_start: 0.7925 (m-30) cc_final: 0.7604 (m-30) REVERT: 5 326 TYR cc_start: 0.8180 (m-80) cc_final: 0.7939 (m-80) REVERT: 6 297 GLN cc_start: 0.8243 (tt0) cc_final: 0.8011 (tt0) REVERT: 6 447 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8659 (pp) REVERT: 6 450 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8134 (tttp) REVERT: 7 438 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8688 (mm-40) REVERT: 8 287 TYR cc_start: 0.8975 (t80) cc_final: 0.8759 (t80) REVERT: B 324 GLU cc_start: 0.8120 (tt0) cc_final: 0.7814 (tm-30) REVERT: D 437 ASP cc_start: 0.8648 (t0) cc_final: 0.8439 (t0) REVERT: E 386 LYS cc_start: 0.8989 (mmtp) cc_final: 0.8708 (mttm) REVERT: E 450 LYS cc_start: 0.8672 (ttmm) cc_final: 0.8034 (tttp) REVERT: F 278 ASP cc_start: 0.7858 (m-30) cc_final: 0.7462 (m-30) REVERT: F 447 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8716 (pp) REVERT: G 447 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8665 (pp) REVERT: I 326 TYR cc_start: 0.8431 (m-80) cc_final: 0.8154 (m-80) REVERT: J 297 GLN cc_start: 0.8248 (tt0) cc_final: 0.7943 (tt0) REVERT: J 299 ASP cc_start: 0.8836 (p0) cc_final: 0.8433 (p0) REVERT: K 450 LYS cc_start: 0.8664 (ttmt) cc_final: 0.8235 (tttp) REVERT: L 324 GLU cc_start: 0.8297 (tt0) cc_final: 0.8058 (tm-30) REVERT: L 386 LYS cc_start: 0.9006 (mmtp) cc_final: 0.8772 (mttm) REVERT: L 447 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8891 (pp) REVERT: M 447 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8775 (pp) REVERT: M 450 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8017 (tttp) REVERT: N 324 GLU cc_start: 0.8233 (tt0) cc_final: 0.7978 (tm-30) REVERT: N 447 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8807 (pp) REVERT: O 298 MET cc_start: 0.8892 (ptp) cc_final: 0.8648 (ptm) REVERT: O 324 GLU cc_start: 0.8205 (tt0) cc_final: 0.7909 (tm-30) REVERT: O 447 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8844 (pp) REVERT: P 430 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8413 (mp) REVERT: Q 450 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8183 (tttp) REVERT: T 324 GLU cc_start: 0.8224 (tt0) cc_final: 0.7778 (tm-30) REVERT: T 438 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8581 (mm-40) REVERT: T 447 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8898 (pp) REVERT: U 377 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8721 (mp) REVERT: U 450 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8059 (tttt) REVERT: V 377 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8301 (mp) REVERT: V 437 ASP cc_start: 0.8691 (t0) cc_final: 0.8428 (t0) REVERT: X 269 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8155 (mm-40) REVERT: X 309 ARG cc_start: 0.8162 (ttp-110) cc_final: 0.7870 (ttp-110) REVERT: X 447 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8546 (pp) REVERT: Y 269 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8529 (mm-40) REVERT: Z 324 GLU cc_start: 0.8341 (tt0) cc_final: 0.7883 (tm-30) outliers start: 190 outliers final: 171 residues processed: 910 average time/residue: 0.2366 time to fit residues: 363.3948 Evaluate side-chains 922 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 738 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 279 SER Chi-restraints excluded: chain 1 residue 280 VAL Chi-restraints excluded: chain 1 residue 284 ILE Chi-restraints excluded: chain 1 residue 296 ILE Chi-restraints excluded: chain 1 residue 317 THR Chi-restraints excluded: chain 1 residue 419 SER Chi-restraints excluded: chain 1 residue 447 LEU Chi-restraints excluded: chain 2 residue 279 SER Chi-restraints excluded: chain 2 residue 284 ILE Chi-restraints excluded: chain 2 residue 377 LEU Chi-restraints excluded: chain 2 residue 397 SER Chi-restraints excluded: chain 2 residue 419 SER Chi-restraints excluded: chain 3 residue 279 SER Chi-restraints excluded: chain 3 residue 280 VAL Chi-restraints excluded: chain 3 residue 419 SER Chi-restraints excluded: chain 4 residue 278 ASP Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 4 residue 280 VAL Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 418 MET Chi-restraints excluded: chain 4 residue 419 SER Chi-restraints excluded: chain 4 residue 423 ILE Chi-restraints excluded: chain 4 residue 447 LEU Chi-restraints excluded: chain 5 residue 266 GLU Chi-restraints excluded: chain 5 residue 279 SER Chi-restraints excluded: chain 5 residue 280 VAL Chi-restraints excluded: chain 5 residue 298 MET Chi-restraints excluded: chain 5 residue 418 MET Chi-restraints excluded: chain 5 residue 433 THR Chi-restraints excluded: chain 5 residue 447 LEU Chi-restraints excluded: chain 6 residue 279 SER Chi-restraints excluded: chain 6 residue 377 LEU Chi-restraints excluded: chain 6 residue 390 THR Chi-restraints excluded: chain 6 residue 418 MET Chi-restraints excluded: chain 6 residue 423 ILE Chi-restraints excluded: chain 6 residue 429 VAL Chi-restraints excluded: chain 6 residue 447 LEU Chi-restraints excluded: chain 7 residue 279 SER Chi-restraints excluded: chain 7 residue 280 VAL Chi-restraints excluded: chain 7 residue 284 ILE Chi-restraints excluded: chain 7 residue 296 ILE Chi-restraints excluded: chain 7 residue 377 LEU Chi-restraints excluded: chain 7 residue 418 MET Chi-restraints excluded: chain 7 residue 447 LEU Chi-restraints excluded: chain 8 residue 279 SER Chi-restraints excluded: chain 8 residue 281 LEU Chi-restraints excluded: chain 8 residue 423 ILE Chi-restraints excluded: chain 8 residue 447 LEU Chi-restraints excluded: chain 9 residue 279 SER Chi-restraints excluded: chain 9 residue 284 ILE Chi-restraints excluded: chain 9 residue 447 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 418 MET Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 296 ILE Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 418 MET Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 284 ILE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain J residue 419 SER Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 423 ILE Chi-restraints excluded: chain L residue 279 SER Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 284 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 418 MET Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 280 VAL Chi-restraints excluded: chain M residue 296 ILE Chi-restraints excluded: chain M residue 418 MET Chi-restraints excluded: chain M residue 423 ILE Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 419 SER Chi-restraints excluded: chain N residue 423 ILE Chi-restraints excluded: chain N residue 447 LEU Chi-restraints excluded: chain O residue 280 VAL Chi-restraints excluded: chain O residue 284 ILE Chi-restraints excluded: chain O residue 296 ILE Chi-restraints excluded: chain O residue 447 LEU Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 397 SER Chi-restraints excluded: chain P residue 430 LEU Chi-restraints excluded: chain Q residue 279 SER Chi-restraints excluded: chain Q residue 284 ILE Chi-restraints excluded: chain Q residue 296 ILE Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 281 LEU Chi-restraints excluded: chain S residue 284 ILE Chi-restraints excluded: chain S residue 296 ILE Chi-restraints excluded: chain S residue 418 MET Chi-restraints excluded: chain S residue 423 ILE Chi-restraints excluded: chain S residue 443 LEU Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain T residue 279 SER Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 377 LEU Chi-restraints excluded: chain T residue 447 LEU Chi-restraints excluded: chain U residue 279 SER Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 281 LEU Chi-restraints excluded: chain U residue 377 LEU Chi-restraints excluded: chain U residue 397 SER Chi-restraints excluded: chain V residue 279 SER Chi-restraints excluded: chain V residue 280 VAL Chi-restraints excluded: chain V residue 281 LEU Chi-restraints excluded: chain V residue 284 ILE Chi-restraints excluded: chain V residue 377 LEU Chi-restraints excluded: chain V residue 423 ILE Chi-restraints excluded: chain W residue 266 GLU Chi-restraints excluded: chain W residue 268 SER Chi-restraints excluded: chain W residue 279 SER Chi-restraints excluded: chain W residue 397 SER Chi-restraints excluded: chain W residue 423 ILE Chi-restraints excluded: chain X residue 279 SER Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 295 ASP Chi-restraints excluded: chain X residue 390 THR Chi-restraints excluded: chain X residue 397 SER Chi-restraints excluded: chain X residue 423 ILE Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain Y residue 279 SER Chi-restraints excluded: chain Y residue 298 MET Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Y residue 419 SER Chi-restraints excluded: chain Y residue 447 LEU Chi-restraints excluded: chain Z residue 279 SER Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 284 ILE Chi-restraints excluded: chain Z residue 296 ILE Chi-restraints excluded: chain Z residue 418 MET Chi-restraints excluded: chain Z residue 419 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 439 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 372 optimal weight: 1.9990 chunk 280 optimal weight: 0.0970 chunk 454 optimal weight: 0.6980 chunk 326 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 430 optimal weight: 2.9990 chunk 179 optimal weight: 0.2980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.099685 restraints weight = 57176.437| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.95 r_work: 0.3174 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 40950 Z= 0.111 Angle : 0.483 7.898 55055 Z= 0.259 Chirality : 0.039 0.125 6300 Planarity : 0.002 0.031 7280 Dihedral : 3.705 13.738 5600 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 3.53 % Allowed : 28.14 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.12), residues: 4900 helix: 3.29 (0.13), residues: 1435 sheet: 1.35 (0.11), residues: 2240 loop : -2.40 (0.13), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 7 385 TYR 0.011 0.001 TYR O 290 PHE 0.009 0.001 PHE G 436 HIS 0.001 0.000 HIS M 383 Details of bonding type rmsd covalent geometry : bond 0.00249 (40950) covalent geometry : angle 0.48252 (55055) hydrogen bonds : bond 0.05174 ( 2074) hydrogen bonds : angle 3.95940 ( 5910) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9800 Ramachandran restraints generated. 4900 Oldfield, 0 Emsley, 4900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 785 time to evaluate : 1.770 Fit side-chains REVERT: 1 438 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8507 (mm-40) REVERT: 2 377 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8609 (mp) REVERT: 2 450 LYS cc_start: 0.8576 (ttmt) cc_final: 0.8146 (tttp) REVERT: 3 385 ARG cc_start: 0.8333 (ttp-110) cc_final: 0.8043 (ttm110) REVERT: 3 437 ASP cc_start: 0.8601 (t0) cc_final: 0.8270 (t0) REVERT: 4 447 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8623 (pp) REVERT: 5 278 ASP cc_start: 0.7791 (m-30) cc_final: 0.7465 (m-30) REVERT: 5 326 TYR cc_start: 0.8037 (m-80) cc_final: 0.7698 (m-80) REVERT: 6 297 GLN cc_start: 0.8157 (tt0) cc_final: 0.7927 (tt0) REVERT: 6 447 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8683 (pp) REVERT: 6 450 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8102 (tttp) REVERT: 7 438 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8651 (mm-40) REVERT: 8 287 TYR cc_start: 0.8952 (t80) cc_final: 0.8729 (t80) REVERT: 8 326 TYR cc_start: 0.8266 (m-80) cc_final: 0.8018 (m-80) REVERT: B 324 GLU cc_start: 0.8039 (tt0) cc_final: 0.7764 (tm-30) REVERT: D 437 ASP cc_start: 0.8577 (t0) cc_final: 0.8373 (t0) REVERT: E 371 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8180 (m) REVERT: E 386 LYS cc_start: 0.8971 (mmtp) cc_final: 0.8725 (mttm) REVERT: E 450 LYS cc_start: 0.8658 (ttmm) cc_final: 0.8029 (tttp) REVERT: F 278 ASP cc_start: 0.7703 (m-30) cc_final: 0.7311 (m-30) REVERT: F 447 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8778 (pp) REVERT: G 447 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8675 (pp) REVERT: I 326 TYR cc_start: 0.8464 (m-80) cc_final: 0.8222 (m-80) REVERT: J 269 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8365 (mm-40) REVERT: J 297 GLN cc_start: 0.8164 (tt0) cc_final: 0.7876 (tt0) REVERT: J 299 ASP cc_start: 0.8711 (p0) cc_final: 0.8347 (p0) REVERT: K 450 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8220 (tttp) REVERT: L 386 LYS cc_start: 0.8992 (mmtp) cc_final: 0.8766 (mttm) REVERT: L 447 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8889 (pp) REVERT: M 447 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8679 (pp) REVERT: M 450 LYS cc_start: 0.8613 (ttmt) cc_final: 0.8002 (tttp) REVERT: N 324 GLU cc_start: 0.8182 (tt0) cc_final: 0.7925 (tm-30) REVERT: N 447 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8838 (pp) REVERT: O 269 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8380 (mm-40) REVERT: O 447 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8819 (pp) REVERT: Q 450 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8184 (tttp) REVERT: T 324 GLU cc_start: 0.8152 (tt0) cc_final: 0.7896 (tm-30) REVERT: T 438 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8610 (mm-40) REVERT: T 447 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8866 (pp) REVERT: U 377 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8607 (mp) REVERT: U 450 LYS cc_start: 0.8696 (ttpt) cc_final: 0.8022 (tttt) REVERT: V 437 ASP cc_start: 0.8596 (t0) cc_final: 0.8364 (t0) REVERT: X 269 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8209 (mm-40) REVERT: X 447 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8517 (pp) REVERT: Y 269 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8504 (mm-40) REVERT: Z 324 GLU cc_start: 0.8271 (tt0) cc_final: 0.7894 (tm-30) outliers start: 157 outliers final: 135 residues processed: 906 average time/residue: 0.2369 time to fit residues: 363.8718 Evaluate side-chains 907 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 759 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 279 SER Chi-restraints excluded: chain 1 residue 280 VAL Chi-restraints excluded: chain 1 residue 284 ILE Chi-restraints excluded: chain 1 residue 296 ILE Chi-restraints excluded: chain 1 residue 317 THR Chi-restraints excluded: chain 1 residue 419 SER Chi-restraints excluded: chain 1 residue 447 LEU Chi-restraints excluded: chain 2 residue 279 SER Chi-restraints excluded: chain 2 residue 284 ILE Chi-restraints excluded: chain 2 residue 377 LEU Chi-restraints excluded: chain 2 residue 397 SER Chi-restraints excluded: chain 3 residue 279 SER Chi-restraints excluded: chain 3 residue 280 VAL Chi-restraints excluded: chain 3 residue 419 SER Chi-restraints excluded: chain 3 residue 447 LEU Chi-restraints excluded: chain 4 residue 278 ASP Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 4 residue 280 VAL Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 418 MET Chi-restraints excluded: chain 4 residue 419 SER Chi-restraints excluded: chain 4 residue 423 ILE Chi-restraints excluded: chain 4 residue 447 LEU Chi-restraints excluded: chain 5 residue 280 VAL Chi-restraints excluded: chain 5 residue 298 MET Chi-restraints excluded: chain 5 residue 418 MET Chi-restraints excluded: chain 5 residue 447 LEU Chi-restraints excluded: chain 6 residue 279 SER Chi-restraints excluded: chain 6 residue 377 LEU Chi-restraints excluded: chain 6 residue 418 MET Chi-restraints excluded: chain 6 residue 423 ILE Chi-restraints excluded: chain 6 residue 429 VAL Chi-restraints excluded: chain 6 residue 447 LEU Chi-restraints excluded: chain 7 residue 279 SER Chi-restraints excluded: chain 7 residue 280 VAL Chi-restraints excluded: chain 7 residue 296 ILE Chi-restraints excluded: chain 7 residue 377 LEU Chi-restraints excluded: chain 7 residue 418 MET Chi-restraints excluded: chain 7 residue 447 LEU Chi-restraints excluded: chain 8 residue 279 SER Chi-restraints excluded: chain 8 residue 281 LEU Chi-restraints excluded: chain 8 residue 423 ILE Chi-restraints excluded: chain 8 residue 447 LEU Chi-restraints excluded: chain 9 residue 284 ILE Chi-restraints excluded: chain 9 residue 447 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 296 ILE Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 418 MET Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 284 ILE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 423 ILE Chi-restraints excluded: chain L residue 279 SER Chi-restraints excluded: chain L residue 284 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 419 SER Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain M residue 280 VAL Chi-restraints excluded: chain M residue 296 ILE Chi-restraints excluded: chain M residue 418 MET Chi-restraints excluded: chain M residue 423 ILE Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 419 SER Chi-restraints excluded: chain N residue 423 ILE Chi-restraints excluded: chain N residue 447 LEU Chi-restraints excluded: chain O residue 280 VAL Chi-restraints excluded: chain O residue 296 ILE Chi-restraints excluded: chain O residue 447 LEU Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 397 SER Chi-restraints excluded: chain Q residue 284 ILE Chi-restraints excluded: chain Q residue 296 ILE Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 281 LEU Chi-restraints excluded: chain S residue 284 ILE Chi-restraints excluded: chain S residue 296 ILE Chi-restraints excluded: chain S residue 418 MET Chi-restraints excluded: chain S residue 423 ILE Chi-restraints excluded: chain S residue 443 LEU Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain T residue 279 SER Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 377 LEU Chi-restraints excluded: chain T residue 447 LEU Chi-restraints excluded: chain U residue 279 SER Chi-restraints excluded: chain U residue 281 LEU Chi-restraints excluded: chain U residue 377 LEU Chi-restraints excluded: chain U residue 397 SER Chi-restraints excluded: chain V residue 279 SER Chi-restraints excluded: chain V residue 280 VAL Chi-restraints excluded: chain V residue 281 LEU Chi-restraints excluded: chain V residue 423 ILE Chi-restraints excluded: chain W residue 268 SER Chi-restraints excluded: chain W residue 423 ILE Chi-restraints excluded: chain X residue 279 SER Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 390 THR Chi-restraints excluded: chain X residue 397 SER Chi-restraints excluded: chain X residue 423 ILE Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain Y residue 279 SER Chi-restraints excluded: chain Y residue 419 SER Chi-restraints excluded: chain Y residue 447 LEU Chi-restraints excluded: chain Z residue 279 SER Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 284 ILE Chi-restraints excluded: chain Z residue 296 ILE Chi-restraints excluded: chain Z residue 418 MET Chi-restraints excluded: chain Z residue 419 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 391 optimal weight: 0.1980 chunk 231 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 383 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 314 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.098747 restraints weight = 57770.048| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.97 r_work: 0.3162 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40950 Z= 0.120 Angle : 0.492 11.202 55055 Z= 0.264 Chirality : 0.039 0.124 6300 Planarity : 0.003 0.040 7280 Dihedral : 3.742 13.795 5600 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 3.73 % Allowed : 27.99 % Favored : 68.28 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.12), residues: 4900 helix: 3.29 (0.13), residues: 1435 sheet: 1.36 (0.11), residues: 2240 loop : -2.38 (0.13), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 7 385 TYR 0.011 0.001 TYR O 290 PHE 0.008 0.001 PHE G 436 HIS 0.001 0.000 HIS Z 383 Details of bonding type rmsd covalent geometry : bond 0.00277 (40950) covalent geometry : angle 0.49209 (55055) hydrogen bonds : bond 0.05497 ( 2074) hydrogen bonds : angle 3.97347 ( 5910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11805.63 seconds wall clock time: 202 minutes 37.93 seconds (12157.93 seconds total)